Search results for: firmicutes

Authors: Da Yoon Yu, Jeong A. Kim, In Sung Kim, Yeon Hee Hong, Jae Young Kim, Sang Suk Lee, Sung Chan Kim, So Hui Choe, In Soon Choi, Kwang Keun Cho

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The present study was conducted to identify the effects of synbiotics composed of lactic acid (LA) bacteria (LAB) and sea tangle on rat’s intestinal microorganisms and anti-obesity effects. The experiment was conducted for six weeks using an 8-week old male rat as experiment animals and the experimental design was to use six treatments groups of 4 repetitions using three mice per repetition. The treatment groups were organized into a normal fat diet control (NFC), a high fat (HF) diet control (HFC), a prebiotic 0% treatment (HF+LA+sea tangle 0%, ST0), a prebiotic 5% treatment (HF+LA+sea tangle 5%, ST5), a prebiotic 10% treatment (HF+LA+sea tangle 10%, ST10), and a prebiotic 15% treatment group (HF+LA+sea tangle 15%, ST15) to conduct experiments with various levels of prebiotics. According to the results of the experiment, the NFC group showed the highest daily weight gain (22.34g) and the ST0 group showed the lowest daily weight gain (19.41g). However, weight gains during the entire experimental period were the highest in the HFC group (475.73g) and the lowest in the ST0 group (454.23g). Feed efficiency was the highest in the HFC group (0.20). Treatment with synbiotics composed of LAB and sea tangle suppressed weight increases due to HF diet and reduced feed efficiency. Intestinal microorganisms were identified through pyrosequncing and according to the results, Firmicutes phylum (approximately 60%) and Bacteroidetes phylum (approximately 30%) accounted for approximately 90% or more of intestinal microorganisms in all of the treatment groups indicating these bacteria are dominating in the intestines. Firmicutes that is related to weight increases accounted for 64.96% of microorganisms in the NFC group, 75.32% in the HFC group, 59.51% in the ST0 group, 61.29% in the ST5 group, 49.91% in the ST10 group, and 39.65% in the ST15 group. Therefore, Firmicutes showed the highest share the HFC group that showed high weight gains and the lowest share in the group treated with mixed synbiotics composed of LAB and sea tangle. Bacteroidetes that is related to weight gain inhibition accounted for 32.12% of microorganisms in the NFC group, and HFC group 21.57%, ST0 group 37.66%, ST5 group 34.92%, ST10 group 44.46%, and ST15 group 53.22%. Therefore, the share of Bacteroidetes was the lowest in the HFC group with no addition of synbiotics and increased along with the level of treatment with synbiotics. Changes in blood components were not significantly different among the groups and SCFA yields were shown to be higher in groups treated with synbiotics than in groups not added with synbiotics. Through the present study, it was shown that the supply of synbiotics composed of LAB and sea tangle increased feed intake but led to weight losses and that the intake of synbiotics composed of LAB and sea tangle had anti-obesity effects due to decreases in Firmicutes which are microorganisms related to weight gains and increases in Bacteroidetes which are microorganisms related to weight losses. Therefore, synbiotics composed of LAB and sea tangle are considered to have the effect to prevent metabolic disorders in the rat.

Keywords: bacteroidetes, firmicutes, intestinal microbiota, lactic acid, sea tangle, synbiotics

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Authors: Yan Li, Qingxiang Meng, Bo Zhou, Zhenming Zhou

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The objective of this study was to compare the effects of ensiled mulberry leaves (EML), and sun-dried mulberry fruit pomace (SMFP) on fecal bacterial communities in Simmental crossbred finishing steers fed the following 3 diets: a standard TMR diet, standard diet containing EML and standard diet containing SMFP, and the diets had similar protein and energy levels. Bacterial communities in the fecal content were analyzed using Illumina Miseq sequencing of the V4 region of the 16S rRNA gene amplification. Quantitative real-time PCR was used to detect the selected bacterial species in the feces. Most of the sequences were assigned to phyla Firmicutes (56.67%) and Bacteroidetes(35.90%), followed by Proteobacteria(1.86%), Verrucomicrobia(1.80%) and Tenericutes(1.37%). And the predominant genera included the 5-7N15 (5.91%), CF231 (2.49%), Oscillospira (2.33%), Paludibacter (1.23%) and Akkermansia(1.11%). As for the treatments, no significant differences were observed in Firmicutes (p = 0.28), Bacteroidetes (p = 0.63), Proteobacteria (p = 0.46), Verrucomicrobia (p = 0.17) and Tenericutes (p = 0.75). On the genus level, classified genera with high abundance (more than 0.1%) mainly came from two phyla: Bacteroidetes and Firmicutes. Also no differences were observed in most genera level, 5-7N15 (p = 0.21), CF231 (p = 0.62), Oscillospira (p = 0.9), Paludibacter (p = 0.33) and Akkermansia (p = 0.37), except that rc4-4 were lower in the CON and SMFP groups compared to the EML animals (p = 0.02). Additionally, there were no differences in richness estimate and diversity indices (p > 0.16), and treatments had no significant effect on most selected bacterial species in the fecal (p > 0.06), except that Ruminococcus albus were higher in the EML group (p < 0.01) and Streptococcus bovis were lower in the CON group (p < 0.01). In conclusion, diets supplemented with EML and SMFP have little influence on fecal bacterial community composition in finishing steers.

Keywords: fecal bacteria community composition, sequencing, ensiled mulberry leaves (EML), sun-dried mulberry fruit pomace (SMFP)

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Authors: Luz Hurtado, Rodrigo Rojas, Jaime Romero, Christopher Concha

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The culture of the marine fish red cusk eel Genypterus chilensis is currently considered a priority for Chilean aquaculture which is a Chilean native species of high gastronomic demand and market value. The microbiota was analyzed in terms of diversity and structure using massive Illumina sequencing. The analysis of alpha diversity was performed in samples of G. chilensis larvae of 6, 18 and 32 dph (days post-hatching) and it was observed that there were significant differences (P = 0.05) between the days of culture for the Chao1 index, being the larvae of 18 dph the one with the highest index followed by the larvae of 6 dph, The lowest value for this index was presented in larvae of 32 dph. There were no significant differences in larvae between the days of culture for the Shannon (P=0.0857) and Simpson (P=0.0714) indices. In general, the larvae of G. chilensis have high rates of diversity. When analyzing the beta diversity, a differentiation between the bacterial communities is observed depending on the day of the culture of the larvae. Considering the PCoA elaborated from the unweighted UniFrac statistic, the explained variance was 46.2% (PC1 29.2% and PC2 17.0%) and in the case of the PCoA elaborated with the weighted UniFrac statistic; the explained variance was 65.5% (PC1 41.8% and PC2 23.7%) these differences were significant based on the Permanova statistical analysis (P= 0.002 and 0.037 respectively). When analyzing the taxonomic composition of the microbiota of the larvae in the different days of culture it was observed that at the phyla level the most abundant in the larvae of 6 dph were Proteobacteria (57%) Verrucomicrobia (24%) and Firmicutes (14%), for the larvae of 18 dph the predominant phyla were Proteobacteria (90%), Dependientiae (5%), Actinobacteria (2%) and Plactomyces (2%), for the larvae of 32 dph the phyla that presented the highest relative abundance were Proteobacteria (57%), Firmicutes (29%), Verrucomicrobia (5%) and Actinobacteria (5%), when comparing the larvae between the days it was observed that the phylum Proteobacteria was the most abundant in the samples of larvae of 6, 18 and 32 dph being the larvae of 18 dph those that present the highest relative abundance, the larvae of 6 dph were those that presented the highest relative abundance for the phylum Verrucomicrobia and in the larvae of 32 dph was observed greater abundance of the phylum Firmicutes compared to the other days of larval culture. At the level of genera, those with the highest relative abundance in larvae of 6 dph were Rubritalea (30%), Psychrobacter (28%), staphylococcus (17%) and Ralstonia (10%), for the larvae of 18 dph the genera with the highest abundance were Psychrobacter (47%), Litoreibacter (13%), Nautella (9%) and Cohesibacter (8%), for the larvae of 32 dph the most abundant genera were Alloiococcus (25%), Dialister (14%), Neptunomonas (13%) and Piscirickettsia (11%). When observing the taxonomic composition of the larvae between the days of larval culture, it is observed that there are differences between them.

Keywords: microbiota, diversity, G. Chilensis, larvae

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Authors: Yaling Gou, Sucai Yang, Pengwei Qiao

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Integrated chemical-biological treatment is an attractive alternative to remove polycyclic aromatic hydrocarbons (PAHs) from contaminated soil; wherein indigenous bacteria is the key factor for the biodegradation of residual PAHs concentrations after the application of chemical oxidation. However, the systematical study on the impact of persulfate (PS) oxidation on indigenous bacteria as well as PAHs removal is still scarce. In this study, the influences of different PS dosages (1%, 3%, 6%, and 10% [w/w]), as well as various activation methods (native iron, H2O2, alkaline, ferrous iron, and heat) on PAHs removal and indigenous bacteria in highly contaminated aged soil were investigated. Apparent degradation of PAHs in the soil treated with PS oxidation was observed, and the removal efficiency of total PAHs in the soil ranged from 38.28% to 79.97%. The removal efficiency of total PAHs in the soil increased with increasing consumption of PS. However, the bacterial abundance in soil was negatively affected following oxidation for all of the treatments added with PS, with bacterial abundance in the soil decreased by 0.89~2.88 orders of magnitude compared to the untreated soil. Moreover, the number of total bacteria in the soil decreased as PS consumption increased. Different PS activation methods and PS dosages exhibited different influences on the bacterial community composition. Bacteria capable of degrading PAHs under anoxic conditions were composed predominantly by Proteobacteria and Firmicutes. The total amount of Proteobacteria and Firmicutes also decreased with increasing consumption of PS. The results of this study provide important insight into the design of PAHs contaminated soil remediation projects.

Keywords: activation method, chemical oxidation, indigenous bacteria, polycyclic aromatic hydrocarbon

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Authors: Awei Bainivalu, Joachim Larsen, Logesh Panneerselvan, Toby Mills, Brett Neilan, Megharaj Mallavarapu

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World War II (WWII) shipwrecks harbour up to 20 million tonnes of oil. More than 3000 wrecks are in the Pacific Ocean; 300 are oil tankers. Compared to other oil removal methods, bioremediation is environmentally friendly and cost-effective. Oil's microbial community and hydrocarbon properties from the Pacific WWII wrecks were identified. Dominant phyla are Proteobacteria, Actinobacteria, and Firmicutes. Native marine bacteria oil-degraders were isolated for bioremediation. Petroleum degradation data from the bacterial consortium will be analyzed over the next three months.

Keywords: oil bioremediation, marine bacteria, WWII shipwrecks, pacific

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Authors: Suganya Chandrababu, Dhundy Bastola

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Like in the gut, the subgingival microbiota plays a crucial role in oral hygiene, health, and cariogenic diseases. Human activities like diet, antibiotics, and periodontal treatments alter the bacterial communities, metabolism, and functions in the oral cavity, leading to a dysbiotic state and changes in the plaques of orthodontic patients. Fixed periodontal appliances hinder oral hygiene and cause changes in the dental plaques influencing the subgingival microbiota. However, the microbial species’ diversity and complexity pose a great challenge in understanding the taxa’s community distribution patterns and their role in oral health. In this research, we analyze the subgingival microbial samples from individuals with fixed dental appliances (metal/clear) using an in silico approach. We employ exploratory hypothesis-driven multivariate and regression analysis to shed light on the microbial community and its functional fluctuations due to dental appliances used and identify risks associated with complex disease phenotypes. Our findings confirm the changes in oral microbiota composition due to the presence and type of fixed orthodontal devices. We identified seven main periodontic pathogens, including Bacteroidetes, Actinobacteria, Proteobacteria, Fusobacteria, and Firmicutes, whose abundances were significantly altered due to the presence and type of fixed appliances used. In the case of metal braces, the abundances of Bacteroidetes, Proteobacteria, Fusobacteria, Candidatus saccharibacteria, and Spirochaetes significantly increased, while the abundance of Firmicutes and Actinobacteria decreased. However, in individuals With clear braces, the abundance of Bacteroidetes and Candidatus saccharibacteria increased. The highest abundance value (P-value=0.004 < 0.05) was observed with Bacteroidetes in individuals with the metal appliance, which is associated with gingivitis, periodontitis, endodontic infections, and odontogenic abscesses. Overall, the bacterial abundances decrease with clear type and increase with metal type of braces. Regression analysis further validated the multivariate analysis of variance (MANOVA) results, supporting the hypothesis that the presence and type of the fixed oral appliances significantly alter the bacterial abundance and composition.

Keywords: oral microbiota, statistical analysis, fixed or-thodontal appliances, bacterial abundance, multivariate analysis, regression analysis

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Authors: Ravi Prakash Maurya, Munaswamyreddygari Sreedhar

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The present studies on ecological engineering through soil amendments in cabbage crops for insect pests regulation were conducted at G. B. Pant University of Agriculture and Technology, Pantnagar, Udham Singh Nagar, Uttarakhand, India. Ten treatments viz., Farm Yard Manure (FYM), Neem cake (NC), Vermicompost (VC), Poultry manure (PM), PM+FYM, NC+VC, NC+PM, VC+FYM, Urea+ SSP+MOP (Standard Check) and Untreated Check were evaluated to study the effect of these amendments on the population of insect pests, natural enemies and the microbial community of the rhizosphere in the cabbage crop ecosystem. The results revealed that most of the cabbage pests, viz., aphids, head borer, gram pod borer, and armyworm, were more prevalent in FYM, followed by PM and NC-treated plots. The best cost-benefit ratio was found in PM + FYM treatment, which was 1: 3.62, while the lowest, 1: 0.97, was found in the VC plot. The population of natural enemies like spiders, coccinellids, syrphids, and other hymenopterans and dipterans was also found to be prominent in organic plots, namely FYM, followed by VC and PM plots. Diversity studies on organic manure-treated plots were also carried out, which revealed a total of nine insect orders (Hymenoptera, Hemiptera, Lepidoptera, Coleoptera, Neuroptera, Diptera, Orthoptera, Dermaptera, Thysanoptera, and one arthropodan class, Arachnida) in different treatments. The Simpson Diversity Index was also studied and found to be maximum in FYM plots. The metagenomic analysis of the rhizosphere microbial community revealed that the highest bacterial count was found in NC+PM plot as compared to standard check and untreated check. The diverse microbial population contributes to soil aggregation and stability. Healthier soil structures can improve water retention, aeration, and root penetration, which are all crucial for crop health. The further analysis also identified a total of 39 bacterial phyla, among which the most abundant were Actinobacteria, Firmicutes, and the SAR324 clade. Actinobacteria and Firmicutes are known for their roles in decomposing organic matter and mineralizing nutrients. Their highest abundance suggests improved nutrient cycling and availability, which can directly enhance plant growth. Hence, organic amendments in cabbage farming can transform the rhizosphere microbiome, reduce pest pressure, and foster populations of beneficial insects, leading to healthier crops and a more sustainable agricultural ecosystem.

Keywords: cabbage ecosystem, organic amendments, rhizosphere microbiome, pest and natural enemy diversity

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Authors: Ilknur Tuncer, Nihayet Bizsel

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The studies in bacterial diversity and antimicrobial resistance in coastal areas are important to understand the variability in the community structures and metabolic activities. In the present study, antimicrobial susceptibility and phylogenetic analysis of bacteria isolated from stations with different depths and influenced by terrestrial and marine fluxes in eastern Aegean Sea were illustrated. 51% of the isolates were found as resistant and 14% showed high MAR index indicating the high-risk sources of contamination in the environment. The resistance and the intermediate levels and high MAR index of the study area were 38–60%, 11–38% and 0–40%, respectively. According to 16S rRNA gene analysis, it was found that the isolates belonged to two phyla Firmicutes and Gammaproteobacteria with the genera Bacillus, Halomonas, Oceanobacillus, Photobacterium, Pseudoalteromonas, Psychrobacter, and Vibrio. 47% of Bacillus strains which were dominant among all isolates were resistant. In addition to phylogenetically diverse bacteria, the variability in resistance, intermediate and high MAR index levels of the study area indicated the effect of geographical differences.

Keywords: bacterial diversity, multiple antibiotic resistance, 16S rRNA genes, Aegean Sea

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Authors: John N. Idenyi, Hadimundeen Abdallah, Abigeal D. Adeyemi, Jonathan C. Eya

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Gut microbiomes play a significant role in the growth, metabolism, and health of fish. However, we know very little about the interactive effects of variations in dietary composition and temperature on rainbow trout gut microbiota. Exactly 288 rainbow trout weighing 45.6g ± 0.05 (average ± SD) were fed four isocaloric, isolipidic, and isonitrogenous diets comprising 40% crude protein and 20% crude lipid and formulated as 100 % animal-based protein (AP) and a blend of 50 fish oil (FO)/50 camelina oil (CO), 100 % AP and100 % CO, 100 % plant-based protein (PP) and a blend of 50FO/50CO or 100 % PP and 100 % CO in 14 or 18°C for 150 days. Gut content was analyzed using 16S rRNA gene and shotgun sequencing. The most abundant phyla identified regardless of diet were Tenericutes, Firmicutes, Proteobacteria, Spirochaetes, Bacteroidetes, and Actinobacteria, while Aeromonadaceae and Enterobacteriaceae were dominant families in 18°C. Moreover, gut microbes were dominated by genes relating to an amino acid, carbohydrate, fat, and energy metabolisms and influenced by temperature. The shared functional profiles for all the diets suggest that plant protein sources in combination with CO could be as good as the fish meal with 50/50 FO & CO in rainbow trout farming.

Keywords: aquafeed, aquaculture, microbiome, rainbow trout

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Authors: Austin Belfiori, Kevin Rinek, Zach Barcroft, Jennifer Berglind

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Diet influences the composition of the gut microbiota and host's health. Disruption of the balance among the microbiota, epithelial cells, and resident immune cells in the intestine is involved in the pathogenesis of inflammatory bowel disease (IBD). To study the role of gut microbiota in intestinal inflammation, the microbiome of control mice (C57BL6) given a gluten-containing standard diet versus C57BL6 mice given the gluten-free (GF) feed (n=10 in each group) was examined. All mice received the 3% DSS for 5 days. Throughout the study, feces were collected and processed for DNA extraction and MiSeq Illumina sequencing of V4 region of bacterial 16S rRNA gene. Alpha and beta diversities and compositional differences at phylum and genus levels were determined in intestinal microbiota. The mice receiving the GF diet showed a significantly increased abundance of Firmicutes and a decrease of Bacteroides and Lactobacillus at phylum level. Therefore, the gluten free diet led to reductions in beneficial gut bacteria populations. These findings indicate a role of wheat gluten in dysbiosis of the intestinal microbiota.

Keywords: gluten, colitis, microbiota, DSS, dextran sulphate sodium

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Authors: Nourhan G. Sahly, Ahmed Moustafa, Mohamed S. Zaghloul, Tamer Z. Salem

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The gut microbiome plays important roles in the human body that includes but not limited to digestion, immunity, homeostasis and response to some drugs such as chemotherapy and immunotherapy. Its role has also been linked to radiotherapy and associated gastrointestinal injuries, where the microbial dysbiosis could be the driving force for dose determination or the complete suspension of the treatment protocol. Linking the gut microbiota alterations to different cancer treatment protocols is not easy especially in humans. However, enormous effort was exerted to understand this complex relationship. In the current study, we described the gut microbiota dysbiosis in pediatric sarcoma patients, in the pelvic region, with regards to radiotherapy and antibiotics. Fecal samples were collected as a source of microbial DNA for which the gene encoding for V3-V5 regions of 16S rRNA was sequenced. Two of the three patients understudy had experienced an increase in alpha diversity post exposure to 50.4 Gy. Although phylum Firmicutes overall relative abundance has generally decreased, six of its taxa increased in all patients. Our results may indicate the possibility of radiosensitivity or enrichment of the antibiotic resistance of the elevated taxa. Further studies are needed to describe the extent of radiosensitivity with regards to antibiotic resistance.

Keywords: combined radiotherapy and chemotherapy, gut microbiome, pediatric cancer, radiosensitivity

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Authors: Mabtho Moreroa-Monyelo, Grace Ijoma, Rosina Nkuna, Tonderayi Matambo

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A moving bed biofilm reactor (MBBR) was used for the bioremediation of high strength chemical oxygen demand (COD) Fisher-Tropsch (FT) wastewater. The aerobic MBBR system was operated over 60 days. For metagenomics profile assessment of the targeted 16S sequence of bacteria involved in the bioremediation of the chemical compounds, sludge samples were collected every second day of operation. Parameters such as pH and COD were measured daily to compare the system efficiency as the changedin microbial diversity progressed. The study revealed that pH was a contributing factor to microbial diversity, which further affected the efficiency of the MBBR system. The highest COD removal rate of 86.4% was achieved at pH 8.3. It was observed that when there was more, A higher bacterial diversity led to an improvement in the reduction of COD. Furthermore, an OTUof 4530 was obtained, which were divided into 12 phyla, 27 classes, 44 orders, 74 families, and 138 genera across all sludge samples from the MBBR. A determination of the relative abundance of microorganisms at phyla level indicates that the most abundant phylum on day it was Firmicutes (50%); thereafter, the most abundant phylum changed toProteobacteria.

Keywords: biodegradation, fischer-tropsch wastewater, metagenomics, moving bed biofilm reactor

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Authors: Xiaoxing Ye

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To investigate complex rumen microbial communities, 16S ribosomal RNA (rRNA) sequencing is widely used. Here, we evaluated the impact of bioinformatics pipelines on the observation of OTUs and taxonomic classification of 750 cattle rumen microbial samples by comparing three commonly used pipelines (LotuS, UPARSE, and QIIME) with Usearch. In LotuS-based analyses, 189 archaeal and 3894 bacterial OTUs were observed. The observed OTUs for the Usearch analysis were significantly larger than the LotuS results. We discovered 1495 OTUs for archaea and 92665 OTUs for bacteria using Usearch analysis. In addition, taxonomic assignments were made for the rumen microbial samples. All pipelines had consistent taxonomic annotations from the phylum to the genus level. A difference in relative abundance was calculated for all microbial levels, including Bacteroidetes (QIIME: 72.2%, Usearch: 74.09%), Firmicutes (QIIME: 18.3%, Usearch: 20.20%) for the bacterial phylum, Methanobacteriales (QIIME: 64.2%, Usearch: 45.7%) for the archaeal class, Methanobacteriaceae (QIIME: 35%, Usearch: 45.7%) and Methanomassiliicoccaceae (QIIME: 35%, Usearch: 31.13%) for archaeal family. However, the most prevalent archaeal class varied between these two annotation pipelines. The Thermoplasmata was the top class according to the QIIME annotation, whereas Methanobacteria was the top class according to Usearch.

Keywords: cattle rumen, rumen microbial, 16S rRNA gene sequencing, bioinformatics pipeline

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Authors: Hai Chi, Ibrahim Mehmeti, Kirill Ovchinnikov, Hegle Holo, Ingolf F. Nes, Dzung B. Diep

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By using a panel of multiple indicator strains of different bacterial species and genera, we screened a large collection of bacterial isolates (over 1800 isolates) derived from raw milk, for bacteriocin producers with broad inhibition spectra (BIS). Fourteen isolates with BIS were identified, and by 16S rDNA sequencing they were found to belong to Lactococcus garvieae (10 isolates) and Enterococcus feacalis (4 isolates). Further analysis of the ten L. garvieae isolates revealed that they were very similar, if not identical, to each other in metabolic and genetic terms: they had the same fermentation profile on different types of sugars, repetitive sequence-based PCR (rep-PCR) DNA pattern as well as they all had the same inhibition profile towards over 50 isolates of different species. The bacteriocin activity from one of the L. garvieae isolates was assessed further. The bacteriocin which was termed garvicin KS, was found to be heatstable and proteinase-labile and its inhibition spectrum contained many distantly related genera of Firmicutes, comprising most lactic acid bacteria (LAB) as well as problematic species of Bacillus, Listeria, Streptococcus and Staphylococcus and their antibiotic resistant derivatives (e.g. VRE, MRSA). Taken together, the results indicate that this is a potent bacteriocin from L. garvieae and that its very broad inhibition spectrum can be a very useful property for use in food preservation as well as in infection treatments caused by gram-positive pathogens and their antibiotic-derivatives.

Keywords: bacteriocin, lactic acid bacteria, Lactococcus garvieae, antibiotics resistance

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Authors: Abimbola M. Enitan, John O. Odiyo, Feroz M. Swalaha

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The study of microbial ecology and their function in anaerobic digestion processes are essential to control the biological processes. This is to know the symbiotic relationship between the microorganisms that are involved in the conversion of complex organic matter in the industrial wastewater to simple molecules. In this study, diversity and quantity of bacterial community in the granular sludge taken from the different compartments of a full-scale upflow anaerobic sludge blanket (UASB) reactor treating brewery wastewater was investigated using polymerase chain reaction (PCR) and real-time quantitative PCR (qPCR). The phylogenetic analysis showed three major eubacteria phyla that belong to Proteobacteria, Firmicutes and Chloroflexi in the full-scale UASB reactor, with different groups populating different compartment. The result of qPCR assay showed high amount of eubacteria with increase in concentration along the reactor’s compartment. This study extends our understanding on the diverse, topological distribution and shifts in concentration of microbial communities in the different compartments of a full-scale UASB reactor treating brewery wastewater. The colonization and the trophic interactions among these microbial populations in reducing and transforming complex organic matter within the UASB reactors were established.

Keywords: bacteria, brewery wastewater, real-time quantitative PCR, UASB reactor

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Authors: Yessentayeva K. Y., Berzhanova R. Z., Mukasheva T. D.

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The purpose of this study was to study the microbial diversity of soils with long-standing hydrocarbon pollution in the S. Balgimbayev field (Kazakhstan), where the transformation of meadow coastal soils technogenic solonchak soils, as well as the assessment of the degradation potential of microorganisms perspective for the use for bioremediation. In the present work autochthonous microorganisms of the surface horizon of soils were investigated. In samples with a low degree of pollution the number of microorganisms, was comparable to the number in the uncontaminated soil and was 103 - 104 CFU/g. and one and two orders of magnitude lower in samples with high oil content. A collection of microorganisms was created using different culture media, which made it possible to isolate isolates that play a key role in different successional stages of biodegradation of petroleum hydrocarbons. The collection included the main bacterial filiiments, Protobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Mycelial fungi andyeast-like fungwere assigned to the Ascomycota division. Studies showed that the percentage of isolates capable of growth in hydrocarbons varied. More than 50 % of the isolates grew on crude oil, a low percentage of less than 10 % of the isolates grew on an anthracene, phenanthrene and naphthalene, more than 20 % of the isolates belonging to different genera Pseudomonas, Bacillus, Rhodococcus, Achromobacter, Gordonia, Microbacterium, and Trichosporon, characterized the growth on two or three different hydrocarbons. The ability to grow using all hydrocarbons, associated with the synthesis of biosurfactants, was detected only in a few isolates.

Keywords: oil, soil, number of bioremediation, biodegradation, microorganisms, hydrocarbons – oxidizing microorganisms

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Authors: Mian Adnan Kakakhel, NIshita Narwal, Majid Rasta, Shi Xiaotao

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The widespread use of nanoparticles means that they are significantly increasing in the aquatic ecosystem, where they are likely to pose threat to aquatic organism. In particular, the influence of nanoparticles exposure combined with varying water velocities on fish behavior remain poorly understood. Emerging evidences suggested a probable correlation between fish swimming behavior and gut bacterial dysbiosis. Therefore, the current study aimed to investigate the effects of nanomaterials in different water velocities on fish gut bacterial composition, which in results change in fish swimming behavior. The obtained findings showed that the contamination of nanoparticles was reduced as the velocity increased. However, the synergetic effects of nanoparticles and water velocity significantly (p < 0.05) decreased the bacterial composition, which plays a critical role in fish development, metabolism, digestion, enzymes production, and energy production such as Bacteroidetes and Firmicutes. This group of bacterial also support fish in swimming behavior by providing them a significant energy during movement. The obtained findings of this study suggested that the presence of nanoparticles in different water velocities have had a significant correlation with fish gut bacterial dysbiosis, as results the gut dysbiosis had been linked to the change in fish behavior. The study provides an important insight into the mechanisms by which the nanoparticles possibly affect the fish behavior.

Keywords: water velocities, fish behavior, gut bacteria, secondary metabolites, regulation

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Authors: O. Ubani, H. I. Atagana, M. S. Thantsha, R. Adeleke

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The oil sludge components (polycyclic aromatic hydrocarbons, PAHs) have been found to be cytotoxic, mutagenic and potentially carcinogenic and microorganisms such as bacteria and fungi can degrade the oil sludge to less toxic compounds such as carbon dioxide, water and salts. In the present study, we isolated different bacteria with PAH-degrading potentials from the co-composting of oil sludge and different animal manure. These bacteria were isolated on the mineral base medium and mineral salt agar plates as a growth control. A total of 31 morphologically distinct isolates were carefully selected from 5 different compost treatments for identification using polymerase chain reaction (PCR) of the 16S rDNA gene with specific primers (16S-P1 PCR and 16S-P2 PCR). The amplicons were sequenced and sequences were compared with the known nucleotides from the gene bank database. The phylogenetical analyses of the isolates showed that they belong to 3 different clades namely Firmicutes, Proteobacteria and Actinobacteria. These bacteria identified were closely related to genera Bacillus, Arthrobacter, Staphylococcus, Brevibacterium, Variovorax, Paenibacillus, Ralstonia and Geobacillus species. The results showed that Bacillus species were more dominant in all treated compost piles. Based on their characteristics these bacterial isolates have high potential to utilise PAHs of different molecular weights as carbon and energy sources. These identified bacteria are of special significance in their capacity to emulsify the PAHs and their ability to utilize them. Thus, they could be potentially useful for bioremediation of oil sludge and composting processes.

Keywords: bioaugmentation, biodegradation, bioremediation, composting, oil sludge, PAHs, animal manures

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Authors: Futo Asano, Yusuke Yatsushiro, Hirokuni Miyamoto, Hiroaki Kodama

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A thermophile-fermented compost is produced using small fishes, crabs, and shrimps under a high temperature (approximately 75℃) by fermentation-associated self-heating. This compost has been used as a feed additive for pigs and hens in Japan, and the fecundity of this livestock is enhanced. Firmicutes is a dominant phylum in the microbial composition of the compost. We first reported that improvement of female larval fitness of Hercules beetle can be achieved by amendment of this compost to the humus. When the 90-d-old larvae were reared for subsequent 72 days in the humus with this compost, the growth of female larvae was significantly enhanced when compared with the growth of female larvae in the humus without the compost. In contrast, the growth of male larvae in the compost-free humus was the same as the larvae grow in the compost-amended humus. The bacterial composition of the feces of larvae was determined at 0 days and 46 days after transfer to the humus with or without the compost. The most dominant bacterium in the feces was Xylanimonas. Interestingly, the growth improvement of female larvae was associated with an increased abundance of Mollicutes in the fecal samples. These results indicate that the compost act as a probiotic material for enhancing the female larvae growth by supporting Mollicutes. Here, we tried to isolate Mollicutes from the contents of the midgut and hindgut of the 3rd instar female larvae of the Hercules beetle. These gut contents were spread onto a selective agar medium for Mollicutes (PPLO agar broth, BD Difco, NJ, USA). Although we isolated none of the Mollicutes until now, several bacteria that are closely related to Xylanimonas and Luteimicrobium were isolated. These isolates have xylanase and glucanase (CMCase) activities. We show the gut bacterial profiles of larvae and discuss how the fitness of female larvae of the Hercules beetle is improved by the compost.

Keywords: compost, beetle, mollicutes, woody biomass

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Authors: Asmuddin Natsir, A. Mujnisa, Syahriani Syahrir, Marhamah Nadir, Nurul Purnomo

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Bacteria, protozoa, Archaea, and fungi are the dominant microorganisms found in the rumen ecosystem that has an important role in converting feed ingredients into components that can be digested and utilized by the livestock host. This study was conducted to assess the diversity of rumen bacteria of bali cattle raised under traditional farming condition. Three adult bali cattle were used in this experiment. The rumen fluid samples from the three experimental animals were obtained by the Stomach Tube method before the morning feeding. The results of study indicated that the Illumina sequencing was successful in identifying 301,589 sequences, averaging 100,533 sequences, from three rumen fluid samples of three cattle. Furthermore, based on the SILVA taxonomic database, there were 19 kinds of phyla that had been successfully identified. Of the 19 phyla, there were only two dominant groups across the three samples, namely Bacteroidetes and Firmicutes, with an average percentage of 83.68% and 13.43%, respectively. Other groups such as Synergistetes, Spirochaetae, Planctomycetes can also be identified but in relatively small percentage. At the genus level, there were 157 sequences obtained from all three samples. Of this number, the most dominant group was Prevotella 1 with a percentage of 71.82% followed by 6.94% of Christencenellaceae R-7 group. Other groups such as Prevotellaceae UCG-001, Ruminococcaceae NK4A214 group, Sphaerochaeta, Ruminococcus 2, Rikenellaceae RC9 gut group, Quinella were also identified but with very low percentages. The sequencing results were able to detect the presence of 3.06% and 3.92% respectively for uncultured rumen bacterium and uncultured bacterium. In conclusion, the results of this experiment can provide an opportunity for a better understanding of the rumen bacterial diversity of the bali cattle raised under traditional farming condition and insight regarding the uncultured rumen bacterium and uncultured bacterium that need to be further explored.

Keywords: 16S rRNA sequencing, bali cattle, rumen microbial diversity, uncultured rumen bacterium

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Authors: Sarah Almuhayya, Andrew Mcbain, Gavin Humphreys

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Background. The microbiome of the upper respiratory tract (URT) has received less research attention than other body sites. This study aims to investigate the microbial ecology of the human URT with a focus on the antagonism between the corynebacteria and staphylococci. Methods. Mucosal swabs were collected from the anterior nares and nasal turbinates of 20 healthy adult subjects. Genomic DNA amplification targeting the (V4) of the 16Sr RNA gene was conducted and analyzed using QIIME. Nasal swab isolates were cultured and identified using near full-length sequencing of the 16S rRNA gene. Isolates identified as corynebacteria or staphylococci were typed using (rep-PCR). Antagonism was determined using an agar-based inhibition assay. Results. Four major bacterial phyla (Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria) were identified from all volunteers. The typing of cultured staphylococci and corynebacteria suggested that intra-individual strain diversity was limited. Analysis of generated nasal microbiota profiles suggested an inverse correlation in terms of relative abundance between staphylococci and corynebacteria. Despite the apparent antagonism between these genera, it was limited when investigated on agar. Of 1000 pairwise interactions, observable zones of inhibition were only reported between a single strain of C.pseudodiphtheriticum and S.aureus. Imaging under EM revealed this effect to be bactericidal with clear lytic effects on staphylococcal cell morphology. Conclusion. Nasal microbiota is complex, but culturable staphylococci and corynebacteria were limited in terms of clone type. Analysis of generated nasal microbiota profiles suggested an inverse correlation in terms of relative abundance between these genera suggesting an antagonism or competition between these taxonomic groups.

Keywords: nasal, microbiota, S.aureus, microbioal interaction

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Authors: Lohendy Munoz-Vargas, Stephen O. Opiyo, Rose Digianantonio, Michele L. Williams, Asela Wijeratne, Gregory Habing

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Non-typhoidal Salmonella enterica is a zoonotic pathogen with critical importance in animal and public health. The persistence of Salmonella on farms affects animal productivity and health, and represents a risk for food safety. The intestinal microbiota plays a fundamental role in the colonization and invasion of this ubiquitous microorganism. To overcome the colonization resistance imparted by the gut microbiome, Salmonella uses invasion strategies and the host inflammatory response to survive, proliferate, and establish infections with diverse clinical manifestations. Cattle serve as reservoirs of Salmonella, and periparturient cows have high prevalence of Salmonella shedding; however, to author`s best knowledge, little is known about the association between the gut microbiome and the onset of Salmonella shedding during the periparturient period. Thus, the objective of this study was to assess the association between changes in bacterial communities and the onset of Salmonella shedding in cattle approaching parturition. In a prospective cohort study, fecal samples from 98 dairy cows originating from four different farms were collected at four time points relative to calving (-3 wks, -1 wk, +1 wk, +3 wks). All 392 samples were cultured for Salmonella. Sequencing of the V4 region of the 16S rRNA gene using the Illumina platform was completed to evaluate the fecal microbiome in a selected sample subset. Analyses of microbial composition, diversity, and structure were performed according to time points, farm, and Salmonella onset status. Individual cow fecal microbiomes, predominated by Bacteroidetes, Firmicutes, Spirochaetes, and Proteobacteria phyla, significantly changed before and after parturition. Microbial communities from different farms were distinguishable based on multivariate analysis. Although there were significant differences in some bacterial taxa between Salmonella positive and negative samples, our results did not identify differences in the fecal microbial diversity or structure for cows with and without the onset of Salmonella shedding. These data suggest that determinants other than the significant changes in the fecal microbiome influence the periparturient onset of Salmonella shedding in dairy cattle.

Keywords: dairy cattle, microbiome, periparturient, Salmonella

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Authors: Manuela Amorim, Cláudia S. Marques, Maria Conceição Calhau, Hélder J. Pinheiro, Maria Manuela Pintado

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Recently it has been recognized peptides from different food sources with biological activities. However, no relevant study has proven the potential of brewer yeast peptides in the modulation of gut microbiota. The importance of human intestinal microbiota in maintaining host health is well known. Probiotics, prebiotics and the combination of these two components, can contribute to support an adequate balance of the bacterial population in the human large intestine. The survival of many bacterial species inhabiting the large bowel depends essentially on the substrates made available to them, most of which come directly from the diet. Some of these substrates can be selectively considered as prebiotics, which are food ingredients that can stimulate beneficial bacteria such as Lactobacilli or Bifidobacteria growth in the colon. Moreover, conventional food can be used as vehicle to intake bioactive compounds that provide those health benefits and increase people well-being. In this way, the main objective of this work was to study the potential prebiotic activity of brewer yeast peptide extract (BYP) obtained via hydrolysis of yeast proteins by cardosins present in Cynara cardunculus extract for possible use as a functional ingredient. To evaluate the effect of BYP on the modulation of gut microbiota in diet-induced obesity model, Wistar rats were fed either with a standard or a high-fat diet. Quantified via 16S ribosomal RNA (rRNA) expression by quantitative PCR (qPCR), genera of beneficial bacteria (Lactobacillus spp. and Bifidobacterium spp.) and three main phyla (Firmicutes, Bacteroidetes and Actinobacteria) were assessed. Results showed relative abundance of Lactobacillus spp., Bifidobacterium spp. and Bacteroidetes was significantly increased (P < 0.05) by BYP. Consequently, the potential health-promoting effects of WPE through modulation of gut microbiota were demonstrated in vivo. Altogether, these findings highlight the possible intervention of BYP as gut microbiota enhancer, promoting healthy life style, and the incorporation in new food products, leads them bringing associated benefits endorsing a new trend in the improvement of new value-added food products.

Keywords: functional ingredients, gut microbiota, prebiotics, brewer yeast peptide extract

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Authors: Yuping Zhang, Teng Ma, Nadia Everaert, Hongfu Zhang

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Supplying dietary fiber during gestation is known to improve the welfare of feed-restricted sows. However, whether high fiber supplementation during pregnancy can improve the performance of sows and their offspring depends on the type, amount, source, etc., in which the solubility plays a key important role. Insoluble fibers have been shown to increase feed intake of sows in lactation, meet the needs of sows for milk production, reduce sow’s weight and backfat loss, and thus improve the performance of sows and their offspring. In this study, we investigated the effect of the addition of fermented feed mulberry (FFM), rich in insoluble fiber, during the whole gestation on the performance of sows and their offspring and explored possible mechanisms by determining serum hormones and fecal microbiota. The FFM-diet contained 25.5% FFM (on dry matter basis) and was compared with the control–diet (CON, corn, and soybean meal diet). The insoluble fiber content of the FFM and CON diet are respectively 29.3% and 19.1%. both groups were allocated 20 multiparous sows, and they are fed different feed allowance to make sure all the sows get the same digestible energy for each day. After farrowing, all sows were fed the same lactation diet ad libitum. The serum estradiol, progesterone concentration, blood glucose, and insulin levels at gestation day 0, 20, and 60 were tested. And also, the composition and differences fecal microbiota at day 60 of gestation were analyzed. Fecal consistency was determined with Bristol stool scale method, those with a score below 3 were counted as constipation The results showed that there was no impact of the FFM treatment on sows’ backfat, bodyweight changes, blood glucose, serum estradiol, and progesterone concentration, litter size, and performance of the offspring(p > 0.05), Except significant decrease in the concentration of insulin in sows’ serum at 60 days of gestation were observed in the FFM group compare to the CON group (P < 0.01). FFM diet also significantly increased feed intake on the first, third, and 21st days of sow lactation. (p < 0.01); The α- and β- diversity and abundance of the microbiota were significant increased (p < 0.01) compared with the CON group, The abundance of Firmicutes and Bacteroidetes were significantly increased, meanwhile the abundances of Spirochetes, Proteobacteria, and Euryarchaeota, were significantly reduced in the feces of the FFM group. We also analyzed the fecal microbiota of constipated sows vs non-constipated sows and found that the diversity and abundance did also differ between these two groups. FFM and CON group < 0.01). The relationship between sow’s constipation and microbiota merits further investigation.

Keywords: fermented feed mulberry, reproductive performance, fecal flora, sow

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Authors: Irina M. Kolesnikova, Andrey M. Gaponov, Sergey A. Roumiantsev, Tatiana V. Grigoryeva, Dilyara R. Khusnutdinova, Dilyara R. Kamaldinova, Alexander V. Shestopalov

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Background. Obese patients have unequal risks of metabolic disorders. It is accepted to distinguish between metabolically healthy obesity (MHO) and metabolically unhealthy obesity (MUHO). MUHO patients have a high risk of metabolic disorders, insulin resistance, and diabetes mellitus. Among the other things, the gut microbiota also contributes to the development of metabolic disorders in obesity. Obesity is accompanied by significant changes in the gut microbial community. In turn, bacterial translocation from the intestine is the basis for the blood microbiome formation. The aim was to study the features of the blood microbiome in patients with various metabolic types of obesity. Patients, materials, methods. The study included 116 healthy donors and 101 obese patients. Depending on the metabolic type of obesity, the obese patients were divided into subgroups with MHO (n=36) and MUHO (n=53). Quantitative and qualitative assessment of the blood microbiome was based on metagenomic analysis. Blood samples were used to isolate DNA and perform sequencing of the variable v3-v4 region of the 16S rRNA gene. Alpha diversity indices (Simpson index, Shannon index, Chao1 index, phylogenetic diversity, the number of observed operational taxonomic units) were calculated. Moreover, we compared taxa (phyla, classes, orders, and families) in terms of isolation frequency and the taxon share in the total bacterial DNA pool between different patient groups. Results. In patients with MHO, the characteristics of the alpha-diversity of the blood microbiome were like those of healthy donors. However, MUHO was associated with an increase in all diversity indices. The main phyla of the blood microbiome were Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria. Cyanobacteria, TM7, Thermi, Verrucomicrobia, Chloroflexi, Acidobacteria, Planctomycetes, Gemmatimonadetes, and Tenericutes were found to be less significant phyla of the blood microbiome. Phyla Acidobacteria, TM7, and Verrucomicrobia were more often isolated in blood samples of patients with MUHO compared with healthy donors. Obese patients had a decrease in some taxonomic ranks (Bacilli, Caulobacteraceae, Barnesiellaceae, Rikenellaceae, Williamsiaceae). These changes appear to be related to the increased diversity of the blood microbiome observed in obesity. An increase of Lachnospiraceae, Succinivibrionaceae, Prevotellaceae, and S24-7 was noted for MUHO patients, which, apparently, is explained by a magnification in intestinal permeability. Conclusion. Blood microbiome differs in obese patients and healthy donors at class, order, and family levels. Moreover, the nature of the changes is determined by the metabolic type of obesity. MUHO linked to increased diversity of the blood microbiome. This appears to be due to increased microbial translocation from the intestine and non-intestinal sources.

Keywords: blood microbiome, blood bacterial DNA, obesity, metabolically healthy obesity, metabolically unhealthy obesity

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Authors: K. Petrosyan, R. Piwowarczyk, K. Ruraż, S. Thijs, J. Vangronsveld, W. Kaca

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Holoparasitic plants are flowering heterotrophic angiosperms which with the help of an absorbing organ - haustorium, attach to another plant, the so-called the host. Due to the different hosts, unusual lifestyle, lack of roots, chlorophylls and photosynthesis, these plants are interesting and unique study objects for global biodiversity. The seeds germination of the parasitic plants also is unique: they germinate only in response to germination stimulants, namely strigolactones produced by the root of an appropriate host. Resistance of the seeds on different environmental conditions allow them to stay viable in the soil for more than 20 years. Among the wide range of plant protection mechanisms the endophytic communities have a specific role. In this way, they have the potential to mitigate the impacts of adverse conditions such as soil salinization. The major objective of our study was to compare the bacterial endo-microbiomes from seeds of two holoparasitic plants from Orobanchaceae family, Cistanche – C. armena (Armenia) and C. phelypaea (Portugal) – from saline habitats different in soil water status. The research aimed to perform how environmental conditions influence on the diversity of the bacterial communities of C. armena and C. phelypaea seeds. This was achieved by comparison of the endophytic microbiomes of two species and isolation of culturable bacteria. A combination of culture-dependent and molecular techniques was employed for the identification of the seed endomicrobiome (culturable and unculturable). Using the V3-V4 hypervariable region of the 16S rRNA gene, four main taxa were identified: Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes, but the relative proportion of the taxa was different in each type of seed. Generally, sixteen phyla, 323 genera and 710 bacterial species were identified, mainly Gram negative, halotolerant bacteria with an environmental origin. However, also some unclassified and unexplored taxonomic groups were found in the seeds of both plants. 16S rRNA gene sequencing analysis from both species identified the gram positive, endospore forming, halotolerant and alkaliphile Bacillus spp. which suggests that the endophytic bacteria of examined seeds possess traits that are correlated with the natural habitat of their hosts. The cultivable seed endophytes from C. armena and C. phelypaea were rather similar, notwithstanding the big distances between their growth habitats - Armenia and Portugal. Although the seed endophytic microbiomes of C. armena and C. phelypaea contain a high number of common bacterial taxa, also remarkable differences exist. We demonstrated that the environmental conditions or abiotic stresses influence on diversity of the bacterial communities of holoparasiotic seeds. To the best of our knowledge the research is the first report of endophytes from seeds of holoparasitic Cistanche armena and C. phelypaea plants.

Keywords: microbiome, parasitic plant, salinity, seeds

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Authors: Thais O. de Paula, Marjorie R. A. Sarmiento, Francis M. Borges, Alessandra B. Ferreira-Machado, Juliana A. Resende, Dioneia E. Cesar, Vania L. Silva, Claudio G. Diniz

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Obesity is currently a worldwide public health threat, being considered a pandemic multifactorial disease related to the human gut microbiota (GM). Add to that GM is considered an important reservoir of antimicrobial resistance genes (ARG) and little is known on GM and ARG in obesity, considering the altered physiology and xenobiotics intake. As regional and social behavior may play important roles in GM modulation, and most of the studies are based on small sample size and various methodological approaches resulting in difficulties for data comparisons, this study was focused on the investigation of GM bacterial diversity in obese (OB), overweight (OW) and eutrophic individuals (ET) considering their nutritional, clinical and social characteristics; and comparative screening of AGR related to their physiology and xenobiotics intake. Microbial community was accessed by FISH considering phyla as a taxonomic level, and PCR-DGGE followed by dendrograms evaluation (UPGMA method) from fecal metagenome of 72 volunteers classified according to their body mass index (BMI). Nutritional, clinical, social parameters and xenobiotics intake were recorded for correlation analysis. The fecal metagenome was also used as template for PCR targeting 59 different ARG. Overall, 62% of OB were hypertensive, and 12% or 4% were, regarding the OW and ET individuals. Most of the OB were rated as low income (80%). Lower relative bacterial densities were observed in the OB compared to ET for almost all studied taxa (p < 0.05) with Firmicutes/Bacteroidetes ratio increased in the OB group. OW individuals showed a bacterial density representative of GM more likely to the OB. All the participants were clustered in 3 different groups based on the PCR-DGGE fingerprint patterns (C1, C2, C3), being OB mostly grouped in C1 (83.3%) and ET mostly grouped in C3 (50%). The cluster C2 showed to be transitional. Among 27 ARG detected, a cluster of 17 was observed in all groups suggesting a common core. In general, ARG were observed mostly within OB individuals followed by OW and ET. The ratio between ARG and bacterial groups may suggest that AGR were more related to enterobacteria. Positive correlations were observed between ARG and BMI, calories and xenobiotics intake (especially use of sweeteners). As with nutritional and clinical characteristics, our data may suggest that GM of OW individuals behave in a heterogeneous pattern, occasionally more likely to the OB or to the ET. Regardless the regional and social behaviors of our population, the methodological approaches in this study were complementary and confirmatory. The imbalance of GM over the health-disease interface in obesity is a matter of fact, but its influence in host's physiology is still to be clearly elucidated to help understanding the multifactorial etiology of obesity. Although the results are in agreement with observations that GM is altered in obesity, the altered physiology in OB individuals seems to be also associated to the increased xenobiotics intake and may interfere with GM towards antimicrobial resistance, as observed by the fecal metagenome and ARG screening. Support: FAPEMIG, CNPQ, CAPES, PPGCBIO/UFJF.

Keywords: antimicrobial resistance, bacterial diversity, gut microbiota, obesity

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Authors: Khethiwe Mtshali, Zamantungwa T. H. Khumalo, Stanford Kwenda, Ismail Arshad, Oriel M. M. Thekisoe

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Ecologically, the gut, mammary glands and bloodstream consist of distinct microbial communities of commensals, mutualists and pathogens, forming a complex ecosystem of niches. The by-products derived from these body sites i.e. faeces, milk and blood, respectively, have many uses in rural communities where they aid in the facilitation of day-to-day household activities and occasional rituals. Thus, although livestock rearing plays a vital role in the sustenance of the livelihoods of rural communities, it may serve as a potent reservoir of different pathogenic organisms that could have devastating health and economic implications. This study aimed to simultaneously explore the microbial profiles of corresponding faecal, milk and blood samples from lactating cows using 16S rRNA metagenomic sequencing. Bacterial communities were inferred through the Divisive Amplicon Denoising Algorithm 2 (DADA2) pipeline coupled with SILVA database v138. All downstream analyses were performed in R v3.6.1. Alpha-diversity metrics showed significant differences between faeces and blood, faeces and milk, but did not vary significantly between blood and milk (Kruskal-Wallis, P < 0.05). Beta-diversity metrics on Principal Coordinate Analysis (PCoA) and Non-Metric Dimensional Scaling (NMDS) clustered samples by type, suggesting that microbial communities of the studied niches are significantly different (PERMANOVA, P < 0.05). A number of taxa were significantly differentially abundant (DA) between groups based on the Wald test implemented in the DESeq2 package (Padj < 0.01). The majority of the DA taxa were significantly enriched in faeces than in milk and blood, except for the genus Anaplasma, which was significantly enriched in blood and was, in turn, the most abundant taxon overall. A total of 30 phyla, 74 classes, 156 orders, 243 families and 408 genera were obtained from the overall analysis. The most abundant phyla obtained between the three body sites were Firmicutes, Bacteroidota, and Proteobacteria. A total of 58 genus-level taxa were simultaneously detected between the sample groups, while bacterial signatures of at least 8 of these occurred concurrently in corresponding faeces, milk and blood samples from the same group of animals constituting a pool. The important taxa identified in this study could be categorized into four potentially pathogenic clusters: i) arthropod-borne; ii) food-borne and zoonotic; iii) mastitogenic and; iv) metritic and abortigenic. This study provides insight into the microbial composition of bovine faeces, milk, and blood and its extent of overlapping. It further highlights the potential risk of disease occurrence and transmission between the animals and the inhabitants of the sampled rural community, pertaining to their unsanitary practices associated with the use of cattle by-products.

Keywords: microbial profiling, 16S rRNA, NGS, feces, milk, blood, lactating cows, small-scale farmers

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Authors: Alvarez M., Chapela M. J., Balboa E., Rubianes D., Sinde E., Fernandez de Ana C., Rodríguez-Blanco A.

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The gut microbiota plays an important role as gut inflammation could contribute to colorectal cancer development; however, this role is still not fully understood, and tools able to prevent this progression are yet to be developed. The main objective of this study was to monitor the effects of a mushroom extracts formulation in gut microbial community composition of an Azoxymethane (AOM)/Dextran sodium sulfate (DSS) mice model of inflammation-linked carcinogenesis. For the in vivo study, 41 adult male mice of the C57BL / 6 strain were obtained. 36 of them have been induced in a state of colon carcinogenesis by a single intraperitoneal administration of AOM at a dose of 12.5 mg/kg; the control group animals received instead of the same volume of 0.9% saline. DSS is an extremely toxic polysaccharide sulfate that causes chronic inflammation of the colon mucosa, favoring the appearance of severe colitis and the production of tumors induced by AOM. Induction by AOM/DSS is an interesting platform for chemopreventive intervention studies. This time the model was used to monitor gut microbiota changes as a result of supplementation with a specific mushroom extracts formulation previously shown to have prebiotic activity. The animals have been divided into three groups: (i) Cancer + mushroom extracts formulation experimental group: to which the MicoDigest2.0 mushroom extracts formulation developed by Hifas da Terra S.L has been administered dissolved in drinking water at an estimated concentration of 100 mg / ml. (ii) Control group of animals with Cancer: to which normal water has been administered without any type of treatment. (iii) Control group of healthy animals: these are the animals that have not been induced cancer or have not received any treatment in drinking water. This treatment has been maintained for a period of 3 months, after which the animals were sacrificed to obtain tissues that were subsequently analyzed to verify the effects of the mushroom extract formulation. A microbiological analysis has been carried out to compare the microbial communities present in the intestines of the mice belonging to each of the study groups. For this, the methodology of massive sequencing by molecular analysis of the 16S gene has been used (Ion Torrent technology). Initially, DNA extraction and metagenomics libraries were prepared using the 16S Metagenomics kit, always following the manufacturer's instructions. This kit amplifies 7 of the 9 hypervariable regions of the 16S gene that will then be sequenced. Finally, the data obtained will be compared with a database that makes it possible to determine the degree of similarity of the sequences obtained with a wide range of bacterial genomes. Results obtained showed that, similarly to certain natural compounds preventing colorectal tumorigenesis, a mushroom formulation enriched the Firmicutes and Proteobacteria phyla and depleted Bacteroidetes. Therefore, it was demonstrated that the consumption of the mushroom extracts’ formulation developed could promote the recovery of the microbial balance that is disrupted in the mice model of carcinogenesis. More preclinical and clinical studies are needed to validate this promising approach.

Keywords: carcinogenesis, microbiota, mushroom extracts, inflammation

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Authors: Hyemi Kim, Jay Kim, Kyunghoon Han, Ra-Yeong Choi, In-Woo Kim, Hyung Joo Suh, Ki-Bae Hong, Sung Hee Han

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Chitosan is used in various industries such as food and medical care because it is known to have various functions such as anti-obesity, anti-inflammatory and anti-cancer benefits. Most of the commercial chitosan is extracted from crustaceans. As the harvest rate of snow crabs and red snow crabs decreases and safety issues arise due to environmental pollution, research is underway to extract chitosan from insects. In this study, we used Response Surface Methodology (RSM) to predict the optimal conditions to produce chitosan oligosaccharides from mealworms (MCOS), which can be absorbed through the intestine as low-molecular-weight chitosan. The experimentally confirmed optimal conditions for MCOS production using chitosanase were found to be a substrate concentration of 2.5%, enzyme addition of 30 mg/g and a reaction time of 6 hours. The chemical structure and physicochemical properties of the produced MCOS were measured using MALDI-TOF mass spectra and FTIR spectra. The MALDI-TOF mass spectra revealed peaks corresponding to the dimer (375.045), trimer (525.214), tetramer (693.243), pentamer (826.296), and hexamer (987.360). In the FTIR spectra, commercial chitosan oligosaccharides exhibited a weak peak pattern at 3500-2500 cm-1, unlike chitosan or chitosan oligosaccharides. There was a difference in the peak at 3200~3500 cm-1, where different vibrations corresponding to OH and amine groups overlapped. Chitosan, chitosan oligosaccharide, and commercial chitosan oligosaccharide showed peaks at 2849, 2884, and 2885 cm-1, respectively, attributed to the absorption of the C-H stretching vibration of methyl or methine. The amide I, amide II, and amide III bands of chitosan, chitosan oligosaccharide, and commercial chitosan oligosaccharide exhibited peaks at 1620/1620/1602, 1553/1555/1505, and 1310/1309/1317 cm-1, respectively. Furthermore, the solubility of MCOS was 45.15±3.43, water binding capacity (WBC) was 299.25±4.57, and fat binding capacity (FBC) was 325.61±2.28 and the solubility of commercial chitosan oligosaccharides was 49.04±9.52, WBC was 280.55±0.50, and FBC was 157.22±18.15. Thus, the characteristics of MCOS and commercial chitosan oligosaccharides are similar. The results of investigating the impact of chitosan oligosaccharide on the proliferation of probiotics revealed increased growth in L. casei, L. acidophilus, and Bif. Bifidum. Therefore, the major short-chain fatty acids produced by gut microorganisms, such as acetic acid, propionic acid, and butyric acid, increased within 24 hours of adding 1% (p<0.01) and 2% (p<0.001) MCOS. The impact of MCOS on the overall gut microbiota was assessed, revealing that the Chao1 index did not show significant differences, but the Simpson index decreased in a concentration-dependent manner, indicating a higher species diversity. The addition of MCOS resulted in changes in the overall microbial composition, with an increase in Firmicutes and Verrucomicrobia (p<0.05) compared to the control group, while Proteobacteria and Actinobacteria (p<0.05) decreased. At the genus level, changes in microbiota due to MCOS supplementation showed an increase in beneficial bacteria like lactobacillus, Romboutsia, Turicibacter, and Akkermansia (p<0.0001) while harmful bacteria like Enterococcus, Morganella, Proterus, and Bacteroides (p<0.0001) decreased. In this study, chitosan oligosaccharides were successfully produced under established conditions from mealworms, and these chitosan oligosaccharides are expected to have prebiotic effects, similar to those obtained from crabs.

Keywords: mealworms, chitosan, chitosan oligosaccharide, prebiotics

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