Association between Gut Microbiota and Breast Cancer: Diet as a Potential Modulating Factor.

Breast cancer (BCa) has many well-known risk factors, including age, genetics, lifestyle, and diet; however, the influence of the gut microbiome on BCa remains an emerging area of investigation. This study explores the connection between the gut microbiome, dietary habits, and BCa risk. We enrolled newly diagnosed BCa patients and age-matched cancer-free controls in a case-control study. Comprehensive patient data was collected, including dietary habits assessed through the National Cancer Institute Diet History Questionnaire (DHQ). 16S rRNA amplicon sequencing was used to analyze gut microbiome composition and assess alpha and beta diversity. Microbiome analysis revealed differences in the gut microbiome composition between cases and controls, with reduced microbial diversity in BCa patients. The abundance of three specific microbial genera-Acidaminococus, Tyzzerella, and Hungatella-was enriched in the fecal samples taken from BCa patients. These genera were associated with distinct dietary patterns, revealing significant associations between the presence of these genera in the microbiome and specific HEI2015 components, such as vegetables and dairy for Hungatella, and whole fruits for Acidaminococus. Demographic characteristics were well-balanced between groups, with a significantly higher body mass index and lower physical activity observed in cases, underscoring the role of weight management in BCa risk. Associations between significant microbial genera identified from BCa cases and dietary intakes were identified, which highlights the potential of the gut microbiome as a source of biomarkers for BCa risk assessment. This study calls attention to the complex interplay between the gut microbiome, lifestyle factors including diet, and BCa risk.

Allocoprobacillus halotolerans gen. nov., sp. nov and Coprobacter tertius sp. nov., isolated from human gut microbiota.

Two novel bacterial isolates were cultured from faecal samples of patients attending the Breast Care clinic at the Norwich and Norfolk University Hospital. Strain LH1062T was isolated from a 58-year-old female diagnosed with invasive adenocarcinoma with ductal carcinoma in situ. Strain LH1063T was isolated from a healthy 51-year-old female. Isolate LH1062T was predicted to be a potential novel genus most closely related to Coprobacillus, whilst LH1063T was predicted to be a novel species belonging to Coprobacter. Both strains were characterized by polyphasic approaches including 16S rRNA gene analysis, core-genome analysis, average nucleotide identity (ANI) comparisons and phenotypic analysis. Initial screening of the 16S rRNA gene of LH1062T returned a nucleotide identity of 93.4 % to Longibaculum muris. For LH1063T, nucleotide identity was a 92.6 % to Coprobacter secundus. Further investigations showed that LH1062T had a genome size of 2.9 Mb and G+C content of 31.3 mol %. LH1063T had a genome size of 3.3Mb and G+C content of 39.2 mol %. Digital DNA-DNA hybridization (dDDH) and ANI values of LH1062T with its closest relative, Coprobacillus cateniformis JCM 10604T, were 20.9 and 79.54 %, respectively. For LH1063T, the dDDH and ANI values with its closest relative, Coprobacter secundus 177T, were 19.3 and 77.81 %, respectively. Phenotypic testing confirmed that LH1062T could not be matched to a known validly published isolate in any database; thereby indicating a novel genus for which the name Allocoprobacillus gen. nov. is now proposed with LH1062T (=DSM 114537T=NCTC 14686T) being the type strain of the proposed novel species Allocoprobacillus halotolerans sp. nov. Strain LH1063T (=DSM 114538T=NCTC 14698T) fits within the genus Coprobacter and, it being the third species within this genus, the name Coprobacter tertius sp. nov. is proposed.

Lutispora saccharofermentans sp. nov., a mesophilic, non-spore-forming bacterium isolated from a lab-scale methanogenic landfill bioreactor digesting anaerobic sludge, and emendation of the genus Lutispora to include species which are non-spore-forming and mesophilic.

A novel anaerobic, mesophilic, non-spore-forming bacterium (strain m25T) was isolated from methanogenic enrichment cultures obtained from a lab-scale methanogenic landfill bioreactor containing anaerobic digester sludge. Cells were Gram-stain-negative, catalase-positive, oxidase-negative, rod-shaped, and motile by means of a flagellum. The genomic DNA G+C content was 40.11 mol%. The optimal NaCl concentration, temperature and pH for growth were 2.5 g l-1, 35 °C and at pH 7.0, respectively. Strain m25T was able to grow in the absence of yeast extract on glycerol, pyruvate, arginine and cysteine. In the presence of 0.2 % yeast extract, strain m25T grew on carbohydrates and was able to use glucose, cellobiose, fructose, raffinose and galactose. The novel strain could utilize glycerol, urea, pyruvate, peptone and tryptone. The major fatty acids were iso-C15  :  0, C14  :  0, C16  :  0 DMA (dimethyl acetal) and iso-C15 : 0 DMA. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the new isolate was closely related to Lutispora thermophila EBR46T (95.02 % 16S rRNA gene sequence similarity). Genome relatedness was determined using both average nucleotide identity and amino acid identity analyses, the results of which both strongly supported that strain m25T belongs to the genus Lutispora. Based on its unique phylogenetic features, strain m25T is considered to represent a novel species within the genus Lutispora. Moreover, based on its unique physiologic features, mainly the lack of spore formation, a proposal to amend the genus Lutispora is also provided to include the non-spore-forming and mesophilic species. Lutispora saccharofermentans sp. nov. is proposed. The type strain of the species is m25T (=DSM 112749T=ATCC TSD-268T).

Characteristics of gut microbiota in patients with primary Sjögren's syndrome in Northern China.

This study analyzes and compares the structure and diversity of gut microbiota in patients with primary Sjögren's syndrome (pSS) in Northern China to healthy individuals to identify clinical features associated with dysbiosis. We included 60 Chinese pSS patients and 50 age- and gender-matched healthy controls. DNA was extracted from stool samples and subjected to 16S ribosomal RNA gene analysis (V3-V4) for intestinal dysbiosis. In addition, patients were examined for laboratory and serological pSS features. A Spearman's correlation analysis was performed to assess correlations between individual bacteria taxa and clinical characteristics. The alpha-diversity (Chao1 and Shannon Index) and beta-diversity (unweighted UniFrac distances) of the gut microbiota differed significantly between pSS patients and healthy controls. Further analysis showed that several gut opportunistic pathogens (Bacteroides, Megamonas, and Veillonella) were significantly more abundant in pSS patients and positively correlated with their clinical indicators. In contrast, some probiotic genera (Collinsella, unidentified_Ruminococcaceae, Romboutsia, and Dorea) were significantly decreased in pSS patients and negatively correlated with their clinical indicators. Therefore, pSS patients in Northern China showed a dysbiotic intestinal microbiome enriched for potentially pathogenic genera that might be associated with autoimmune disease.

Description of two novel anaerobic members in the family Clostridiaceae, Anaeromonas gelatinilytica gen.nov., sp. nov., and Anaeromonas frigoriresistens sp. nov., isolated from saline lake sediment.

Cells of members of the family Clostridiaceae, phylum Firmicutes, are generally obligate anaerobic rods. Strains D2Q-14T and D2Q-11T were isolated from sediment of the saline lake Manisi in the Xinjiang Uygur Autonomous Region, PR China. In this study, we employed a polyphasic approach and whole genome analysis of the two isolates. Cells of both isolates were Gram-stain-positive rods that were motile by means of flagella and could utilize sulphate, thiosulphate, elemental sulphur and nitrate as electron acceptors. Phylogenetic analyses based on 16S rRNA gene and whole genome sequences indicated that strains D2Q-14T and D2Q-11T constituted a coherent cluster affiliated to the family Clostridiaceae. In addition, genome analysis revealed that strain D2Q-14Tharboured one nonribosomal peptide synthetase gene cluster, making up 1.4 % of the entire genome. The genome-based analysis, including average nucleotide identity, average amino acid identity and in silico DNA-DNA hybridization, biochemical, phenotypic and chemotaxonomic characterization, indicated that strains D2Q-14T and D2Q-11T represented two novel species of a novel genus in the family Clostridiaceae, for which we propose the names Anaeromonas gelatinilytica gen. nov., sp. nov. and Anaeromonas frigoriresistens sp. nov., with the type strains D2Q-14T (=KCTC 15986T=MCCC 1K04634T) and D2Q-11T (=KCTC 15985T=MCCC 1K04391T), respectively.

Complete genome sequence of Crassaminicella sp. 143-21，isolated from a deep-sea hydrothermal vent.

Crassaminicella sp. 143-21, a putative new species isolated from deep-sea hydrothermal vent chimney on the Central Indian Ridge (CIR), is an anaerobic, thermophilic and rod-shaped bacterium belonging to the family Clostridiaceae. In this study, we present the complete genome sequence of strain 143-21, comprising 2,756,133 bp with a G + C content of 31.1%. In total, 2427 protein coding genes, 121 tRNA genes and 33 rRNA genes were obtained. Genomic analysis of strain 143-21 revealed that numerous genes related to organic matter transport and catabolism, including peptide transport, amino acid transport, saccharide transport, ethanolamine transport and corresponding metabolic pathways. Further, the genome contains a large proportion of genes involved in translation, ribosomal structure, and signal transduction. These genes might facilitate microbial survival in deep-sea hydrothermal vent environment. The genome of strain 143-21 will be helpful for further understanding its adaptive strategies in the deep-sea hydrothermal vent environment.

Analyses of publicly available Hungatella hathewayi genomes revealed genetic distances indicating they belong to more than one species.

Hungatella hathewayi has been observed to be a member of the gut microbiome. Unfortunately, little is known about this organism in spite of being associated with human fatalities; it is important to understand virulence mechanisms and epidemiological prospective to cause disease. In this study, a patient with chronic neurologic symptoms presented to the clinic with subsequent isolation of a strain with phenotypic characteristics suggestive of Clostridium difficile. However, whole-genome sequence found the organism to be H. hathewayi. Analysis including publicly available Hungatella genomes found substantial genomic differences as compared to the type strain, indicating this isolate was not C. difficile. We examined the whole-genome of Hungatella species and related genera, using comparative genomics to fully examine species identification and toxin production. Orthogonal phylogenetic using the 16S rRNA gene and entire genome analyses that included genome distance analyses using Genome-to-Genome Distance (GGDC), Average Nucleotide Identity (ANI), and a pan-genome analysis with inclusion of available public genomes determined the speciation to be Hungatella. Two clearly differentiated groups were identified, one including a reference H. hathewayi genome (strain DSM-13,479) and a second group that was determined to be H. effluvii, which included our clinical isolate. Also, some genomes reported as H. hathewayi were found to belong to other genera, including Clostridium and Faecalicatena. We show that the Hungatella species have an open pan-genome reflecting high genomic diversity. This study highlights the importance of correctly assigning taxonomic identification, particularly in disease-associated strains, to better understand virulence and therapeutic options.

A rare case of necrotizing fasciitis of the abdominal wall due to Hungatella effluvii and Streptococcus constellatus.

We report a rare case of necrotizing fasciitis of the abdominal wall caused by Hungatella effluvii and Streptococcus constellatus. Necrotizing fasciitis has high mortality, so early diagnosis and aggressive treatment are essential for good clinical outcome. Identification of the microbial contribution to these infections is crucial for targeted antibiotic treatment.

Network Analysis of Gut Microbiome and Metabolome to Discover Microbiota-Linked Biomarkers in Patients Affected by Non-Small Cell Lung Cancer.

Several studies in recent times have linked gut microbiome (GM) diversity to the pathogenesis of cancer and its role in disease progression through immune response, inflammation and metabolism modulation. This study focused on the use of network analysis and weighted gene co-expression network analysis (WGCNA) to identify the biological interaction between the gut ecosystem and its metabolites that could impact the immunotherapy response in non-small cell lung cancer (NSCLC) patients undergoing second-line treatment with anti-PD1. Metabolomic data were merged with operational taxonomic units (OTUs) from 16S RNA-targeted metagenomics and classified by chemometric models. The traits considered for the analyses were: (i) condition: disease or control (CTRLs), and (ii) treatment: responder (R) or non-responder (NR). Network analysis indicated that indole and its derivatives, aldehydes and alcohols could play a signaling role in GM functionality. WGCNA generated, instead, strong correlations between short-chain fatty acids (SCFAs) and a healthy GM. Furthermore, commensal bacteria such as Akkermansia muciniphila, Rikenellaceae, Bacteroides, Peptostreptococcaceae, Mogibacteriaceae and Clostridiaceae were found to be more abundant in CTRLs than in NSCLC patients. Our preliminary study demonstrates that the discovery of microbiota-linked biomarkers could provide an indication on the road towards personalized management of NSCLC patients.

Metagenomic insights into the diversity of carbohydrate-degrading enzymes in the yak fecal microbial community.

BACKGROUND: Yaks are able to utilize the gastrointestinal microbiota to digest plant materials. Although the cellulolytic bacteria in the yak rumen have been reported, there is still limited information on the diversity of the major microorganisms and putative carbohydrate-metabolizing enzymes for the degradation of complex lignocellulosic biomass in its gut ecosystem. RESULTS: Here, this study aimed to decode biomass-degrading genes and genomes in the yak fecal microbiota using deep metagenome sequencing. A comprehensive catalog comprising 4.5 million microbial genes from the yak feces were established based on metagenomic assemblies from 92 Gb sequencing data. We identified a full spectrum of genes encoding carbohydrate-active enzymes, three-quarters of which were assigned to highly diversified enzyme families involved in the breakdown of complex dietary carbohydrates, including 120 families of glycoside hydrolases, 25 families of polysaccharide lyases, and 15 families of carbohydrate esterases. Inference of taxonomic assignments to the carbohydrate-degrading genes revealed the major microbial contributors were Bacteroidaceae, Ruminococcaceae, Rikenellaceae, Clostridiaceae, and Prevotellaceae. Furthermore, 68 prokaryotic genomes were reconstructed and the genes encoding glycoside hydrolases involved in plant-derived polysaccharide degradation were identified in these uncultured genomes, many of which were novel species with lignocellulolytic capability. CONCLUSIONS: Our findings shed light on a great diversity of carbohydrate-degrading enzymes in the yak gut microbial community and uncultured species, which provides a useful genetic resource for future studies on the discovery of novel enzymes for industrial applications.

Interactions of Segmented Filamentous Bacteria (Candidatus Savagella) and bacterial drivers in colitis-associated colorectal cancer development.

Colorectal cancer (CRC) risk is influenced by host genetics, sex, and the gut microbiota. Using a genetically susceptible mouse model of CRC induced via inoculation with pathobiont Helicobacter spp. and demonstrating variable tumor incidence, we tested the ability of the Th17-enhancing commensal Candidatus Savagella, more commonly denoted as Segmented Filamentous Bacteria (SFB), to influence the incidence and severity of colitis-associated CRC in male and female mice. To document the composition of the gut microbiota during CRC development and identify taxa associated with disease, fecal samples were collected before and throughout disease development and characterized via 16S rRNA sequencing. While there were no significant SFB-dependent effects on disease incidence or severity, SFB was found to exert a sex-dependent protective effect in male mice. Furthermore, SFB stabilized the GM against Helicobacter-induced changes post-inoculation, resulting in a shift in disease association from Helicobacter spp. to Escherichia coli. These data support sex-dependent SFB-mediated effects on CRC risk, and highlight the complex community dynamics within the GM during exposure to inflammatory pathobionts.

Genome analysis of Crassaminicella sp. SY095, an anaerobic mesophilic marine bacterium isolated from a deep-sea hydrothermal vent on the Southwest Indian Ridge.

Crassaminicella sp. strain SY095 is an anaerobic mesophilic marine bacterium that was recently isolated from a deep-sea hydrothermal vent on the Southwest Indian Ridge. Here, we present the complete genome sequence of strain SY095. The genome consists of a chromosome of 3,046,753 bp (G + C content of 30.81%) and a plasmid of 36,627 bp (G + C content of 31.29%), encodes 2966 protein, 135 tRNA genes, and 34 rRNA genes. Numerous genes are related to peptide transport, amino acid metabolism, motility, and sporulation. This agrees with the observation that strain SY095 is a spore-forming, motile, and chemoheterotrophic bacterium. Further, the genome harbors multiple prophages that carry all the genes necessary for viral particle synthesis. Some prophages carry additional genes that may be involved in the regulation of sporulation. This is the first reported genome of a bacterium from the genus Crassaminicella, providing insights into the microbial adaptation strategies to the deep-sea hydrothermal vent environment.

A Hungatella effluvii isolate in blood culture of a patient with hematochezia.

Hungatella spp. are anaerobic bacteria, are known members of the gut microbiome and very rarely cause human infection. Hungatella effluvii was isolated from an effluent treatment plant in 2014. We report a case of bacteremia due to H. effluvii that occurred after hematochezia in a patient with prostate cancer. It was misidentified by the VITEK 2 system (bioMérieux, France) and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) and was correctly identified by 16S rRNA gene sequencing.

Sediment cooling triggers germination and sulfate reduction by heat-resistant thermophilic spore-forming bacteria.

Thermophilic endospores are widespread in cold marine sediments where the temperature is too low to support growth and activity of thermophiles in situ. These endospores are likely expelled from warm subsurface environments and subsequently dispersed by ocean currents. The endospore upper temperature limit for survival is 140°C, which can be tolerated in repeated short exposures, potentially enabling transit through hot crustal fluids. Longer-term thermal tolerance of endospores, and how long they could persist in an environment hotter than their maximum growth temperature, is less understood. To test whether thermophilic endospores can survive prolonged exposure to high temperatures, sediments were incubated at 80-90°C for 6, 12 or 463 days. Sediments were then cooled by 10-40°C, mimicking the cooling in subsurface oil reservoirs subjected to seawater injection. Cooling the sediments induced sulfate reduction, coinciding with an enrichment of endospore-forming Clostridia. Different Desulfofundulus, Desulfohalotomaculum, Desulfallas, Desulfotomaculum and Desulfofarcimen demonstrated different thermal tolerances, with some Desulfofundulus strains surviving for >1 year at 80°C. In an oil reservoir context, heat-resistant endospore-forming sulfate-reducing bacteria have a survival advantage if they are introduced to, or are resident in, an oil reservoir normally too hot for germination and growth, explaining observations of reservoir souring following cold seawater injection.

Performance of a novel IAHD-DSR process with methane and sulfide as co-electron donors.

A novel integrated autotrophic and heterotrophic denitrification- denitrifying sulfide removal (IAHD-DSR) process was established in this study for biogas desulfurization to simultaneously remove nitrogen in wastewater. The study demonstrated that the system could utilize methane and sulfide as co-electron donors to replace organic carbon source in IAHD process. Three batch tests (B1, B2 and B3) were set up with IAHD sludge to explore how the novel process works. According to mass balance in B2, methane oxidation and sulfide oxidation contributed 18.75 % and 71.25 % to nitrate removal, respectively; however, the contribution of methane oxidation to total nitrogen (TN) removal reached 84.36 %. Sulfide was mainly responsible for the reduction of nitrate to nitrite, while the methane was for nitrite to nitrogen gas in the presence of insufficient sulfide as electron donors. The TN removal in B2 was almost the same as in normal IAHD-DSR process B3-C. The functional genes mcrA and pmoA responsible for methane oxidation were detected in all three batches, with the abundance of 2.23 ×106 copies/(g dry soil) for mcrA in B1 being the highest in three batches. The sulfide addition in B2 increased the abundance of gene pmoA, indicating the enhancement of nitrite reduction coupled with methane oxidation.

Alterations in intestinal microbiota of colorectal cancer patients receiving radical surgery combined with adjuvant CapeOx therapy.

An intricate relationship exists and interactions occur between gut microbiota and colorectal cancer (CRC). Radical surgery combined with adjuvant chemotherapy (AC) serves as the mainstream therapeutic scheme for most CRC patients. The current research was conducted to assess the effect of surgery or chemotherapy on gut microbiota. Forty-three CRC patients who received radical surgery and AC were enrolled. Fecal samples were collected preoperatively, postoperatively, and after the first to fifth cycles of postoperative chemotherapy. The microbial community of each sample was analyzed using high throughput 16S rRNA amplicon sequencing. Compared with preoperative samples, fecal samples collected postoperatively exhibited a significant decrease of obligate anaerobes, tumor-related bacteria, and butyric acid-producing bacteria. However, a significant increase of some conditional pathogens was observed. In addition, the AC regimen (CapeOx) was found to alter intestinal microbiota dramatically. In particular, several changes were observed after chemotherapy including an increase of pathogenic bacteria, the "rebound effect" of chemotherapy-adapted bacteria, the shift of lactate-utilizing microbiota from Veillonella to Butyricimonas and Butyricicoccus, as well as the decrease of probiotics. Both radical surgery and CapeOx chemotherapy exert a non-negligible effect on the gut microbiota of CRC patients. Microbiota-based intervention may be beneficial for patients during postoperative clinical management.

Changes in the Active, Dead, and Dormant Microbial Community Structure across a Pleistocene Permafrost Chronosequence.

Permafrost hosts a community of microorganisms that survive and reproduce for millennia despite extreme environmental conditions, such as water stress, subzero temperatures, high salinity, and low nutrient availability. Many studies focused on permafrost microbial community composition use DNA-based methods, such as metagenomics and 16S rRNA gene sequencing. However, these methods do not distinguish among active, dead, and dormant cells. This is of particular concern in ancient permafrost, where constant subzero temperatures preserve DNA from dead organisms and dormancy may be a common survival strategy. To circumvent this, we applied (i) LIVE/DEAD differential staining coupled with microscopy, (ii) endospore enrichment, and (iii) selective depletion of DNA from dead cells to permafrost microbial communities across a Pleistocene permafrost chronosequence (19,000, 27,000, and 33,000 years old). Cell counts and analysis of 16S rRNA gene amplicons from live, dead, and dormant cells revealed how communities differ between these pools, how they are influenced by soil physicochemical properties, and whether they change over geologic time. We found evidence that cells capable of forming endospores are not necessarily dormant and that members of the class Bacilli were more likely to form endospores in response to long-term stressors associated with permafrost environmental conditions than members of the Clostridia, which were more likely to persist as vegetative cells in our older samples. We also found that removing exogenous "relic" DNA preserved within permafrost did not significantly alter microbial community composition. These results link the live, dead, and dormant microbial communities to physicochemical characteristics and provide insights into the survival of microbial communities in ancient permafrost.IMPORTANCE Permafrost soils store more than half of Earth's soil carbon despite covering ∼15% of the land area (C. Tarnocai et al., Global Biogeochem Cycles 23:GB2023, 2009, https://doi.org/10.1029/2008GB003327). This permafrost carbon is rapidly degraded following a thaw (E. A. G. Schuur et al., Nature 520:171-179, 2015, https://doi.org/10.1038/nature14338). Understanding microbial communities in permafrost will contribute to the knowledge base necessary to understand the rates and forms of permafrost C and N cycling postthaw. Permafrost is also an analog for frozen extraterrestrial environments, and evidence of viable organisms in ancient permafrost is of interest to those searching for potential life on distant worlds. If we can identify strategies microbial communities utilize to survive in permafrost, it may yield insights into how life (if it exists) survives in frozen environments outside of Earth. Our work is significant because it contributes to an understanding of how microbial life adapts and survives in the extreme environmental conditions in permafrost terrains.

An Increased Abundance of Clostridiaceae Characterizes Arthritis in Inflammatory Bowel Disease and Rheumatoid Arthritis: A Cross-sectional Study.

BACKGROUND: Inflammatory bowel diseases (IBDs) are a group of heterogeneous inflammatory conditions affecting the gastrointestinal tract. Although there is considerable evidence linking the gut microbiota to intestinal inflammation, there is limited knowledge on its potential role in the development of extraintestinal manifestations of IBD. METHODS: Four groups of patients were included: IBD-associated arthropathy (IBD-A); IBD without arthropathy (IBD-N); rheumatoid arthritis (RA); and non-IBD, nonarthritis controls. DNA from stool samples was isolated and sequenced using the Illumina platform. Paired-end reads were quality-controlled using SHI7 and processed with SHOGUN. Abundance and diversity analyses were performed using QIIME, and compositional biomarker identification was performed using LEfSe. RESULTS: One hundred eighty patients were included in the analysis. IBD-A was associated with an increased abundance of microbial tyrosine degradation pathways when compared with IBD-N (P = 0.02), whereas IBD-A and RA patients both shared an increased abundance of Clostridiaceae when compared with controls (P = 0.045). We found that history of bowel surgery was a significant source of variability (P = 0.001) among all IBD patients and was associated with decreased alpha diversity and increased abundance of Enterobacteriaceae (P = 0.004). CONCLUSIONS: An increased abundance of gut microbial tyrosine degradation pathways was associated with IBD-A. An increased abundance of Clostridiaceae was shared by both IBD-A and RA patients and suggests a potentially common microbial link for inflammatory arthritis. The increased abundance of Enterobacteriaceae, previously reported in IBD, may be due to the effects of previous bowel surgery and highlights the importance of controlling for this variable in future studies.

Various Phyllosphere and Soil Bacterial Communities of Natural Grasses and the Impact Factors in a Copper Tailings Dam.

Copper mining caused severe damage to the ecological environment of mining areas. The combination of microbe and plant remediation has an application potential in improving the absorption and transformation efficiency of heavy metals. The phyllosphere is the largest biointerface on the planet, and bacteria are the dominant microbial inhabitants of the phyllosphere, believed to be critical to plant growth and health. This study investigated the phyllospheric and soil bacteria communities using high-throughput sequencing, and endophyte infection statuses of four natural grasses by toluidine blue heparin assay. Results showed variation in phyllospheric bacterial community structure. Gammaproteobacteria were the most abundant bacterial population. Bacilli were found in the phyllosphere of Bothriochloa ischaemum and Imperata cylindrica, while Clostridia were only found in Calamagrostis epigejos. Alphaproteobacteria were the dominant bacteria in soil. In addition, bacterial communities were influenced by endophytic infection statuses. Oxalobacteraceae was associated with soil carbon and sulfur. Enterobacteriaceae had negative correlation with the ratio of soil carbon and nitrogen, and had positive correlation with Cd content. These results offer useful insights into phyllospheric bacterial community variance in four different natural grasses in a copper tailings dam.

Investigation of the viral and bacterial microbiota in intestinal samples from mink (Neovison vison) with pre-weaning diarrhea syndrome using next generation sequencing.

Pre-weaning diarrhea (PWD) in mink kits is a common multifactorial syndrome on commercial mink farms. Several potential pathogens such as astroviruses, caliciviruses, Escherichia coli and Staphylococcus delphini have been studied, but the etiology of the syndrome seems complex. In pooled samples from 38 diarrheic and 42 non-diarrheic litters, each comprising of intestinal contents from 2-3 mink kits from the same litter, the bacterial populations were studied using Illumina Next Generation Sequencing technology and targeted 16S amplicon sequencing. In addition, we used deep sequencing to determine and compare the viral intestinal content in 31 healthy non-diarrheic and 30 diarrheic pooled samples (2-3 mink kits from the same litter per pool). The results showed high variations in composition of the bacterial species between the pools. Enterococci, staphylococci and streptococci dominated in both diarrheic and non-diarrheic pools. However, enterococci accounted for 70% of the reads in the diarrheic group compared to 50% in the non-diarrheic group and this increase was at the expense of staphylococci and streptococci which together accounted for 45% and 17% of the reads in the non-diarrheic and diarrheic group, respectively. Moreover, in the diarrheic pools there were more reads assigned to Clostridia, Escherichia-Shigella and Enterobacter compared to the non-diarrheic pools. The taxonomically categorized sequences from the virome showed that the most prevalent viruses in all pools were caliciviruses and mamastroviruses (almost exclusively type 10). However, the numbers of reads assigned to caliciviruses were almost 3 times higher in the diarrheic pools compared the non-diarrheic pools and Sapporo-like caliciviruses were more abundant than the Norwalk-like caliciviruses. The results from this study have contributed to the insight into the changes in the intestinal microbiota associated with the PWD syndrome of mink.