Effects of dietary poly-β-hydroxybutyrate (PHB) on microbiota composition and the mTOR signaling pathway in the intestines of <Emphasis Type="Italic">litopenaeus vannamei</Emphasis>

Poly-β-hydroxybutyrate (PHB) is a natural polymer of the short chain fatty acid β-hydroxybutyrate, which acts as a microbial control agent. The mammalian target of the rapamycin (mTOR) signaling pathway plays a crucial role in intestine inflammation and epithelial morphogenesis. In this study, we examined the composition of intestine microbiota, and mTOR signaling-related gene expression in Pacific white shrimp Litopenaeus vannamei fed diets containing different levels of PHB: 0% (Control), 1% (PHB1), 3% (PHB3), and 5% (PHB5) (w/w) for 35 days. High-throughput sequencing analysis revealed that dietary PHB altered the composition and diversity of intestine microbiota, and that the microbiota diversity decreased with the increasing doses of PHB. Specifically, dietary PHB increased the relative abundance of Proteobacteria and Tenericutes in the PHB1 and PHB5 groups, respectively, and increased that of Gammaproteobacteria in the three PHB groups. Alternatively, PHB decreased Alphaproteobacteria in the PHB3 and PHB5 groups. At the genus level, dietary PHB increased the abundance of beneficial bacteria, such as Bacillus, Lactobacillus, Lactococcus, Clostridium, and Bdellovibrio. The relative mRNA expression levels of the mTOR signaling-related genes TOR, 4E-BP, eIF4E1α, and eIF4E2 all increased in the three PHB treatment groups. These results revealed that dietary PHB supplementation had a beneficial effect on intestine health of L. vannamei by modulating the composition of intestine microbiota and activating mTOR signaling.     

Effects of neutrophils peptide-1 transgenic <Emphasis Type="Italic">Chlorella ellipsoidea</Emphasis> on the gut microbiota of male Sprague–Dawley rats,as revealed by high-throughput 16S rRNA sequencing

Rabbit neutrophils peptide-1 (NP-1) is a type of defensin that possesses a broad spectrum of antimicrobial activity. Chlorella ellipsoidea is a new eukaryotic expression system for exogenously producing NP-1. The NP-1 transgenic C. ellipsoidea can be directly added into feed as antimicrobial agent without any purification procedure for the NP-1 peptide. However, the effects of C. ellipsoidea and NP-1 on the host gut microbiota should be explored before application. In this study, diets containing different concentrations (1.25, 2.5, and 5 %) of C. ellipsoidea and NP-1 transgenic C. ellipsoidea were administered to male Sprague–Dawley rats. Compared with the chow diet control group, none of the experimental groups showed any significant differences in their growth indices, and no histopathological damage was observed. The phylotypes of gut microbiota in the control group, the 5 % C. ellipsoidea diet group and the 5 % NP-1 transgenic C. ellipsoidea diet group were determined by 16S rRNA sequencing. The results showed that both 5 % experimental groups had shifted community memberships of gut microbiota. In particular, the 5 % NP-1 transgenic C. ellipsoidea diet exhibited an increased abundance of most Gram-positive bacterial taxa and a reduced abundance of most Gram-negative bacterial taxa, and it promoted the growth of some lactic acid bacterial genera. Lactic acid bacteria, especially the Bifidobacterium and Lactobacillus, have been widely reported to be benefic effects on the host. Thus NP-1 transgenic C. ellipsoidea is promising feed additive and gut regulator, as it have the potential to increase the abundance of Bifidobacterium and Lactobacillus in gut microbiota of animal.     

Comparative analysis of the gut microbiota in distinct statin response patients in East China

Statin response shows great interindividual variations. Recently, emerging studies have shown that gut microbiota is linked to therapeutic responses to drugs, including statins. However, the association between the gut bacteria composition and statin response is still unclear. In this study, gut microbiota of 202 hyperlipidemic patients with statin sensitive (SS) response and statin resistant (SR) response in East China were investigated by high throughput sequencing to compare the gut bacteria composition and biodiversity in distinct statin response patients. Higher biodiversity was detected in Group SS than Group SR. Specifically, group SS showed significantly increased proportion of genera Lactobacillus (P = 0.001), Eubacterium (P = 0.004), Faecalibacterium (P = 0.005), and Bifidobacterium (P = 0.002) and decreased proportion of genus Clostridium (P = 0.001) compared to Group SR. The results indicated that higher gut biodiversity was associated with statin sensitive response. The increased genera Lactobacillus, Eubacterium, Faecalibacterium, Bifidobacterium, and decreased genus Clostridium in patient gut microbiota may predict patient's statin response, and hence may guide statin dosage adjustments.     

Composition and abundance of microbiota in the pharynx in patients with laryngeal carcinoma and vocal cord polyps

The pharynx is an important site of microbiota colonization, but the bacterial populations at this site have been relatively unexplored by culture-independent approaches. The aim of this study was to characterize the microbiota structure of the pharynx. Pyrosequencing of 16S rRNA gene libraries was used to characterize the pharyngeal microbiota using swab samples from 68 subjects with laryngeal cancer and 28 subjects with vocal cord polyps. Overall, the major phylum was Firmicutes, with Streptococcus as the predominant genus in the pharyngeal communities. Nine core operational taxonomic units detected from Streptococcus, Fusobacterium, Prevotella, Granulicatella, and Veillonella accounted for 21.3% of the total sequences detected. However, there was no difference in bacterial communities in the pharynx from patients with laryngeal cancer and vocal cord polyps. The relative abundance of Firmicutes was inversely correlated with Fusobacteria, Proteobacteria, Actinobacteria, and Bacteroidetes. The correlation was evident at the genus level, and the relative abundance of Streptococcus was inversely associated with Fusobacterium, Leptotrichia, Neisseria, Actinomyces, and Prevotella. This study presented a profile for the overall structure of the microbiota in pharyngeal swab samples. Inverse correlations were found between Streptococcus and other bacterial communities, suggesting that potential antagonism may exist among pharyngeal microbiota.     

Changes in the diversity and composition of gut microbiota of weaned piglets after oral administration of <Emphasis Type="Italic">Lactobacillus</Emphasis> or an antibiotic

The gut microbiota plays important roles in the health and well-being of animals, and high-throughput sequencing facilitates exploration of microbial populations in the animal gut. However, previous studies have focused on fecal samples instead of the gastrointestinal tract. In this study, we compared the microbiota diversity and composition of intestinal contents of weaned piglets treated with Lactobacillus reuteri or chlortetracycline (aureomycin) using high-throughput sequencing. Nine weaned piglets were randomly divided into three groups and supplemented with L. reuteri, chlortetracycline, or saline for 10 days, and then the contents of three intestinal segments (jejunum, colon, and cecum) were obtained and used for sequencing of the V3–V4 hypervariable region of the 16S rRNA gene. The microbiota diversity and composition in the jejunum were different from those in the colon and cecum among the three treatments. In the jejunum, treatment with L. reuteri increased the species richness of the microbiota, as indicated by the ACE and Chao1 indexes, compared with the chlortetracycline group, in which several taxa were eliminated. In the colon and cecum, relative abundances of the phylum Firmicutes and the genus Prevotella were higher in the chlortetracycline group than in the other groups. Distances between clustered samples revealed that the L. reuteri group was closer to the chlortetracycline group than the control group for jejunum samples, while colon and cecum samples of the L. reuteri group were clustered with those of the control group. This study provides fundamental knowledge for future studies such as the development of alternatives to antibiotics.     

Aged mice display altered numbers and phenotype of basophils,and bone marrow-derived basophil activation,with a limited role for aging-associated microbiota

Background

The influence of age on basophils is poorly understood, as well as the effect of aging-associated microbiota on basophils. Therefore, we studied the influence of aging and aging-associated microbiota on basophil frequency and phenotype, and differentiation from basophil precursors.

Results

Basophils became more abundant in bone marrow (BM) and spleens of 19-month-old mice compared with 4-month-old mice. Aged basophils tended to express less CD200R3 and more CD123, both in BM and spleen. Differences in microbiota composition with aging were confirmed by 16S sequencing. Microbiota transfers from young and old mice to germ-free recipients revealed that CD11b tended to be lowered on splenic basophils by aging-associated microbiota. Furthermore, abundance of Alistipes, Oscillibacter, Bacteroidetes RC9 gut group, and S24–7 family positively correlated and CD123 expression, whereas Akkermansia abundance negatively correlated with basophils numbers.Subsequently, we purified FcεRIα⁺CD11c^?CD117^? BM-derived basophils and found that those from aged mice expressed lower levels of CD11b upon stimulation. Higher frequencies of IL-4⁺ basophils were generated from basophil precursors of aged mice, which could be reproduced in basophils derived from germ-free recipients of aging-associated microbiota.

Conclusions

Collectively, these results show the influence of aging on basophils. Furthermore, this study shows that aging-associated microbiota altered activation of BM-derived basophils in a similar fashion as observed in BM-derived basophils from aged mice.

     

Alterations in gut bacterial and fungal microbiomes are associated with bacterial Keratitis,an inflammatory disease of the human eye

Dysbiosis, or imbalance in the gut microbiome, has been implicated in auto-immune, inflammatory, neurological diseases as well as in cancers. More recently it has also been shown to be associated with ocular diseases. In the present study, the association of gut microbiome dysbiosis with bacterial Keratitis, an inflammatory eye disease which significantly contributes to corneal blindness, was investigated. Bacterial and fungal gut microbiomes were analysed using fecal samples of healthy controls (HC, n?=?21) and bacterial Keratitis patients (BK, n?=?19). An increase in abundance of several anti-inflammatory organisms including Dialister, Megasphaera, Faecalibacterium, Lachnospira, Ruminococcus and Mitsuokella and members of Firmicutes, Veillonellaceae, Ruminococcaceae and Lachnospiraceae was observed in HC compared to BK patients in the bacterial microbiome. In the fungal microbiome, a decrease in the abundance of Mortierella, Rhizopus, Kluyveromyces, Embellisia and Haematonectria and an increase in the abundance of pathogenic fungi Aspergillus and Malassezia were observed in BK patients compared to HC. In addition, heatmaps, PCoA plots and inferred functional profiles also indicated significant variations between the HC and BK microbiomes, which strongly suggest dysbiosis in the gut microbiome of BK patients. This is the first study demonstrating the association of gut microbiome with the pathophysiology of BK and thus supports the gut–eye axis hypothesis. Considering that Keratitis affects about 1 million people annually across the globe, the data could be the basis for developing alternate strategies for treatment like use of probiotics or fecal transplantation to restore the healthy microbiome as a treatment protocol for Keratitis.     

Altered gut microbiota associated with intestinal disease in grass carp (<Emphasis Type="Italic">Ctenopharyngodon idellus</Emphasis>)

Gut microbiota plays a crucial importance in their host. Disturbance of the microbial structure and function is known to be associated with inflammatory intestinal disorders. Enteritis is a significant cause of high mortality in fish species, including grass carp (Ctenopharyngodon idellus). Study regarding the association between microbial alternations and enteritis in grass carp is still absent. In this study, changes in the gut microbiota of grass carp suffering from enteritis were investigated using NGS-based 16S rRNA sequencing. Six healthy and ten abnormal fish (showing reddening anus, red odiferous fluid accumulating in the abdominal capacity, and flatulence and haemorrhage in the intestine) were collected from a fish farm in Huanggang Fisheries Institute (Hubei, China). Our results revealed that the diversity, structure, and function of gut microbiota were significantly different between diseased and healthy fish (P?<?0.05). Particularly, members of the genera Dechloromonas, Methylocaldum, Planctomyces, Rhodobacter, Caulobacter, Flavobacterium, and Pseudomonas were significantly increased in diseased fish compared with that in healthy fish (P?<?0.05). Predicted function indicated that microbiota significantly changed the specific metabolic pathways (related to amino acid metabolism, xenobiotics biodegradation and metabolism, and carbohydrate metabolism) in diseased fish (P?<?0.05). Taken together, our findings point out the association between changes of the gut microbiota and enteritis in grass carp, which provide basic information useful for diagnoses, prevention, and treatment of intestinal diseases occurring in cultured fish.     

Synbiotic effects of β-glucans from cauliflower mushroom and <Emphasis Type="Italic">Lactobacillus fermentum</Emphasis> on metabolic changes and gut microbiome in estrogen-deficient rats

Background

We investigated whether the long-term consumption of a symbiotic formulation with Lactobacillus fermentum (probiotic) and β-glucan from cauliflower mushroom (prebiotic) would delay the progression of post-menopausal symptoms in ovariectomized (OVX) rats and explored their mechanisms of action, including changes in gut microbiota.

Methods

OVX rats were fed with high-fat diets containing 1% dextrin (control), 1% lyophilized cauliflower mushroom extract (CFM), 0.1% L. fermentum JS (LFE), 1% CFM plus 0.1% LFE (CFLF), or 30 μg 17β-estradiol/kg body weight (positive-control) for 8 weeks.

Results

CFM contained 95.8% β-glucans. OVX increased the ratio of Firmicutes and Bacteroidetes in the large intestines. Only CFLF lowered tail skin temperature without increasing serum 17β-estradiol and uterine index. Visceral fat mass was lower in CFLF and positive-control groups by increasing daily energy expenditure and fat oxidation. Dyslipidemia induced by OVX was improved by CFM and CFLF as much as in the positive-control group. Homeostasis model assessment estimate of insulin resistance was lower in CFLF than in the positive-control. Hepatic insulin signaling (pAkt?GSK-3β) was potentiated in the ascending order of the control, LFE, CFM, CFLF, and positive-control. AMPK phosphorylation showed similar patterns of hepatic insulin signaling but LFE increased it more than CFM. The changes in gut microbiota were prevented by CFLF in OVX rats, and the ratio of Firmicutes and Bacteroidetes in the CFLF was similar to the positive-control group.

Conclusion

OVX changed gut microbiota and was associated with menopausal symptoms; however, the synbiotics, CFM and LFE, prevented menopausal symptoms and improved the gut microbiota in estrogen-deficient rats.

     

Ethnicity influences gut metabolites and microbiota of the tribes of Assam,India

Introduction

The human gut microbes and their metabolites are involved in multiple host metabolic pathways. Dysbiosis in the gut microbiota and altered metabolite profiles were reported in diseased state. In a region like Assam, where 12.4% of the populations are tribal population, evaluating the influence of ethnicity on gut microbiota and metabolites has become important to further differentiate it from the diseased state.

Objective

To study the influence of ethnicity on fecal metabolite profile and their association with the gut microbiota composition.

Methods

In this study, we determined the untargeted fecal metabolites from five ethnic groups of Assam (Tai-Aiton, Bodo, Karbi, Tea-tribe and Tai-Phake) using GC–MS and compared them among the tribes for common and unique metabolites. Metabolites of microbial origin were related with the available metagenomic data on gut bacterial profiles of the same ethnic groups and functional analysis were carried out based on HMDB.

Results

The core fecal metabolite profile of the Tea-tribe contained aniline, benzoate and acetaldehyde. PLS-DA based on the metabolites suggested that the individuals grouped based on their ethnicity. PCA plot of the data on bacterial abundance at the level of genus indicated clustering of individuals based on ethnicity. Positive correlations were observed between propionic acid and the genus Clostridium (R?=?0.43 and p?=?0.03), butyric acid and the genus Lactobacillus (R?=?0.45 and p?=?0.024), acetic acid and the genus Bacteroides (R?=?0.63 and p?=?0.001) and methane and the genus Escherichia (R?=?0.58 and p?=?0.002).

Conclusion

Results of this study indicated that ethnicity influences both gut bacterial profile and their metabolites.

     

Core gut microbiota in Jinhua pigs and its correlation with strain,farm and weaning age

Gut microbial diversity and the core microbiota of the Jinhua pig, which is a traditional, slow-growing Chinese breed with a high body-fat content, were examined from a total of 105 fecal samples collected from 6 groups of pigs at 3 weaning ages that originated from 2 strains and were raised on 3 different pig farms. The bacterial community was analyzed following high-throughput pyrosequencing of 16S rRNA genes, and the fecal concentrations of short-chain fatty acids (SCFAs) were measured by gas chromatograph. Our results showed that Firmicutes and Bacteroidetes were the dominant phyla, and Lactobacillus, Streptococcus, Clostridium, SMB53, and Bifidobacterium were the most abundant genera. Fifteen predominant genera present in every Jinhua pig sample constituted a phylogenetic core microbiota and included the probiotics Lactobacillus and Bifidobacterium, and the SCFA-producing bacteria Clostridium, Prevotella, Bacteroides, Coprococcus, Roseburia, Ruminococcus, Blautia, and Butyricicoccus. Comparisons of the microbiota compositions and SCFA concentrations across the 6 groups of pigs demonstrated that genetic background and weaning age affected the structure of the gut microbiota more significantly than the farm. The relative abundance of the core genera in the pigs, including Lactobacillus, Clostridium, Prevotella, Bacteroides, Roseburia, Ruminococcus, Blautia, and Butyricicoccus varied dramatically in pigs among the 2 origins and 3 weaning ages, while Oscillospira, Megasphaera, Parabacteroides, and Corynebacterium differed among pigs from different farms. Interestingly, there was a more significant influence of strain and weaning age than of rearing farm on the SCFA concentrations. Therefore, strain and weaning age appear to be the more important factors shaping the intestinal microbiome of pigs.     

Variability,stability, and resilience of fecal microbiota in dairy cows fed whole crop corn silage

The microbiota of whole crop corn silage and feces of silage-fed dairy cows were examined. A total of 18 dairy cow feces were collected from six farms in Japan and China, and high-throughput Illumina sequencing of the V4 hypervariable region of 16S rRNA genes was performed. Lactobacillaceae were dominant in all silages, followed by Acetobacteraceae, Bacillaceae, and Enterobacteriaceae. In feces, the predominant families were Ruminococcaceae, Bacteroidaceae, Clostridiaceae, Lachnospiraceae, Rikenellaceae, and Paraprevotellaceae. Therefore, Lactobacillaceae of corn silage appeared to be eliminated in the gastrointestinal tract. Although fecal microbiota composition was similar in most samples, relative abundances of several families, such as Ruminococcaceae, Christensenellaceae, Turicibacteraceae, and Succinivibrionaceae, varied between farms and countries. In addition to the geographical location, differences in feeding management between total mixed ration feeding and separate feeding appeared to be involved in the variations. Moreover, a cow-to-cow variation for concentrate-associated families was demonstrated at the same farm; two cows showed high abundance of Succinivibrionaceae and Prevotellaceae, whereas another had a high abundance of Porphyromonadaceae. There was a negative correlation between forage-associated Ruminococcaceae and concentrate-associated Succinivibrionaceae and Prevotellaceae in 18 feces samples. Succinivibrionaceae, Prevotellaceae, p-2534-18B5, and Spirochaetaceae were regarded as highly variable taxa in this study. These findings help to improve our understanding of variation and similarity of the fecal microbiota of dairy cows with regard to individuals, farms, and countries. Microbiota of naturally fermented corn silage had no influence on the fecal microbiota of dairy cows.     

Stability and resilience of the intestinal microbiota in children in daycare – a 12 month cohort study

Background

We performed a 12-month cohort study of the stability and resilience of the intestinal microbiota of healthy children in daycare in Denmark in relation to diarrheal events and exposure to known risk factors for gastrointestinal health such as travelling and antibiotic use. In addition, we analyzed how gut microbiota recover from such exposures.

Results

We monitored 32 children in daycare aged 1–6?years. Fecal samples were submitted every second month during a one-year observational period. Information regarding exposures and diarrheal episodes was obtained through questionnaires. Bacterial communities were identified using 16S rRNA gene sequencing. The core microbiota (mean abundance >?95%) dominated the intestinal microbiota, and none of the tested exposures (diarrheal events, travel, antibiotic use) were associated with decreases in the relative abundance of the core microbiota. Samples exhibited lower intra-individual variation than inter-individual variation. Half of all the variation between samples was explained by which child a sample originated from. Age explained 7.6–9.6% of the variation, while traveling, diarrheal events, and antibiotic use explained minor parts of the beta diversity. We found an age-dependent increase of alpha diversity in children aged 1–3?years, and while diarrheal events caused a decrease in alpha diversity, a recovery time of 40–45?days was observed.Among children having had a diarrheal event, we observed a 10x higher relative abundance of Prevotella. After travelling, a higher abundance of two Bacteroides species and 40% less Lachnospiraceae were seen. Antibiotic use did not correlate with changes in the abundance of any bacteria.

Conclusion

We present data showing that Danish children in daycare have stable intestinal microbiota, resilient to the exposures investigated. An early age-dependent increase in the diversity was demonstrated. Diarrheal episodes decreased alpha diversity with an estimated recovery time of 40–45?days.

     

Understanding the mechanisms of zinc bacitracin and avilamycin on animal production: linking gut microbiota and growth performance in chickens

Unravelling the mechanisms of how antibiotics influence growth performance through changes in gut microbiota can lead to the identification of highly productive microbiota in animal production. Here we investigated the effect of zinc bacitracin and avilamycin on growth performance and caecal microbiota in chickens and analysed associations between individual bacteria and growth performance. Two trials were undertaken; each used 96 individually caged 15-day-old Cobb broilers. Trial 1 had a control group (n = 48) and a zinc bacitracin (50 ppm) treatment group (n = 48). Trial 2 had a control group (n = 48) and an avilamycin (15 ppm) treatment group (n = 48). Chicken growth performance was evaluated over a 10-day period, and caecal microbiota was characterised by sequencing of bacterial 16S rRNA gene amplicons. Avilamycin produced no effect on growth performance and exhibited little significant disturbance of the microbiota structure. However, zinc bacitracin reduced the feed conversion ratio (FCR) in treated birds, changed the composition and increased the diversity of their caecal microbiota by reducing dominant species. Avilamycin only produced minor reductions in the abundance of two microbial taxa, whereas zinc bacitracin produced relatively large shifts in a number of taxa, primarily Lactobacillus species. Also, a number of phylotypes closely related to lactobacilli species were positively or negatively correlated with FCR values, suggesting contrasting effects of Lactobacillus spp. on chicken growth performance. By harnessing such bacteria, it may be possible to develop high-productivity strategies in poultry that rely on the use of probiotics and less on in-feed antibiotics.     

Genetic diversity of <Emphasis Type="Italic">Escherichia coli</Emphasis> in gut microbiota of patients with Crohn’s disease discovered using metagenomic and genomic analyses

Background

Crohn’s disease is associated with gut dysbiosis. Independent studies have shown an increase in the abundance of certain bacterial species, particularly Escherichia coli with the adherent-invasive pathotype, in the gut. The role of these species in this disease needs to be elucidated.

Methods

We performed a metagenomic study investigating the gut microbiota of patients with Crohn’s disease. A metagenomic reconstruction of the consensus genome content of the species was used to assess the genetic variability.

Results

The abnormal shifts in the microbial community structures in Crohn’s disease were heterogeneous among the patients. The metagenomic data suggested the existence of multiple E. coli strains within individual patients. We discovered that the genetic diversity of the species was high and that only a few samples manifested similarity to the adherent-invasive varieties. The other species demonstrated genetic diversity comparable to that observed in the healthy subjects. Our results were supported by a comparison of the sequenced genomes of isolates from the same microbiota samples and a meta-analysis of published gut metagenomes.

Conclusions

The genomic diversity of Crohn’s disease-associated E. coli within and among the patients paves the way towards an understanding of the microbial mechanisms underlying the onset and progression of the Crohn’s disease and the development of new strategies for the prevention and treatment of this disease.

     

Bioinformatics Analysis of Antimicrobial Resistance Genes and Prophages Colocalized in Human Gut Metagenomes

The constant increase of bacterial antibiotic-resistant strains is directly linked to a common use of antibiotics in medicine and animal breeding. It is suggested that the gut microbiota serves as a reservoir for antibiotic resistance genes that can be transferred from symbiotic bacteria to pathogenic ones, particularly due to phage transduction. In this study, using the PHASTER prophage predicting tool and CARD antibiotics resistance database we have searched for antibiotic resistance genes that are located within prophages in human gut microbiota. After analysing metagenomic assemblies of eight samples of antibiotic treated patients, lsaE, mdfA, and cpxR/cpxA genes were identified inside prophages. These genes confer resistance to antimicrobial peptides, pleuromutilin, lincomycins, streptogramins and also multidrug resistance. Three (0.46%) of 659 putative prophages predicted in the metagenomic assemblies contained antibiotics resistance genes in their sequences.     

Bile salt hydrolase-mediated inhibitory effect of <Emphasis Type="Italic">Bacteroides ovatus</Emphasis> on growth of <Emphasis Type="Italic">Clostridium difficile</Emphasis>

Clostridium difficile infection (CDI) is one of the most common nosocomial infections. Dysbiosis of the gut microbiota due to consumption of antibiotics is a major contributor to CDI. Recently, fecal microbiota transplantation (FMT) has been applied to treat CDI. However, FMT has important limitations including uncontrolled exposure to pathogens and standardization issues. Therefore, it is necessary to evaluate alternative treatment methods, such as bacteriotherapy, as well as the mechanism through which beneficial bacteria inhibit the growth of C. difficile. Here, we report bile acid-mediated inhibition of C. difficile by Bacteroides strains which can produce bile salt hydrolase (BSH). Bacteroides strains are not commonly used to treat CDI; however, as they comprise a large proportion of the intestinal microbiota, they can contribute to bile acid-mediated inhibition of C. difficile. The inhibitory effect on C. difficile growth increased with increasing bile acid concentration in the presence of Bacteroides ovatus SNUG 40239. Furthermore, this inhibitory effect on C. difficile growth was significantly attenuated when bile acid availability was reduced by cholestyramine, a bile acid sequestrant. The findings of this study are important due to the discovery of a new bacterial strain that in the presence of available bile acids inhibits growth of C. difficile. These results will facilitate development of novel bacteriotherapy strategies to control CDI.     

Microbiota dysbiosis in inflammatory bowel diseases: <Emphasis Type="Italic">in silico</Emphasis> investigation of the oxygen hypothesis

Background

Inflammatory bowel diseases (IBD), which include ulcerative colitis and Crohn’s disease, cause chronic inflammation of the digestive tract in approximately 1.6 million Americans. A signature of IBD is dysbiosis of the gut microbiota marked by a significant reduction of obligate anaerobes and a sharp increase in facultative anaerobes. Numerous experimental studies have shown that IBD is strongly correlated with a decrease of Faecalibacterium prausnitzii and an increase of Escherichia coli. One hypothesis is that chronic inflammation induces increased oxygen levels in the gut, which in turn causes an imbalance between obligate and facultative anaerobes.

Results

To computationally investigate the oxygen hypothesis, we developed a multispecies biofilm model based on genome-scale metabolic reconstructions of F. prausnitzii, E. coli and the common gut anaerobe Bacteroides thetaiotaomicron. Application of low bulk oxygen concentrations at the biofilm boundary reproduced experimentally observed behavior characterized by a sharp decrease of F. prausnitzii and a large increase of E. coli, demonstrating that dysbiosis consistent with IBD disease progression could be qualitatively predicted solely based on metabolic differences between the species. A diet with balanced carbohydrate and protein content was predicted to represent a metabolic “sweet spot” that increased the oxygen range over which F. prausnitzii could remain competitive and IBD could be sublimated. Host-microbiota feedback incorporated via a simple linear feedback between the average F. prausnitzii concentration and the bulk oxygen concentration did not substantially change the range of oxygen concentrations where dysbiosis was predicted, but the transition from normal species abundances to severe dysbiosis was much more dramatic and occurred over a much longer timescale. Similar predictions were obtained with sustained antibiotic treatment replacing a sustained oxygen perturbation, demonstrating how IBD might progress over several years with few noticeable effects and then suddenly produce severe disease symptoms.

Conclusions

The multispecies biofilm metabolic model predicted that oxygen concentrations of ～1 micromolar within the gut could cause microbiota dysbiosis consistent with those observed experimentally for inflammatory bowel diseases. Our model predictions could be tested directly through the development of an appropriate in vitro system of the three species community and testing of microbiota-host interactions in gnotobiotic mice.

     

A first insight into the intestinal microbiota of snow trout (<Emphasis Type="Italic">Schizothorax zarudnyi</Emphasis>)

This study addresses the biodiversity profile of bacterial community in the intestinal lumen and mucosa of snow trout fish by applying 16S rRNA gene 454-pyrosequencing. A total of 209,106 sequences with average length 689 (±53) were filtered, denoised, trimmed, and then sorted into OTUs based on 97 % sequence similarity using the USEARCH software pipeline. Bacteria representing 10 phyla were found in the samples investigated. Fimicutes ribotypes were present in intestinal-mucosa and lumen in all fish and often dominated the libraries (average 43 and 38 %, respectively). Proteobacteria were also prevalent, but at a lower relative abundance, at 22 and 29 % in mucosa and lumen, respectively. The autochthonous microbiota was dominated by sequences belonging to the Bacilli (mean sequence abundance 24 %), in particular the Lactobacillaceae, with Lactobacillus and Pediococcous being the most abundant genera. Fewer Bacilli (mean sequence abundance 22 %) and Actinobacteria (2 %) were present in the lumen, and allochthonous communities consisted of a more even split among the bacterial classes, with increases in sequences assigned to members of the γ-Proteobacteria (16 %) and Fusobacteriia (8 %). The principal bacterial genera recorded in the lumen belonged to the lactic acid bacteria group, Cetobacterium, Clostridium and Synechococcus. Results obtained suggest that the lumen and mucosal layer of the snow trout intestine may host different microbial communities. Moreover, both regions harbour a diverse microbiome with a greater microbial diversity in the intestinal mucus compared with the luminal communities of the fish. Many of these microbes might be of high physiological relevance for the fish and may play key roles in the functioning of its gut.     

A standardized approach for co-culturing dothidealean rock-inhabiting fungi and lichen photobionts in vitro

Owing to the effect of symbiotic gut bacteria on the proliferation of infectious disease-transferring insects and their potential as paratransgenic tools, their identification or securing their use in controlling insect vectors is urgently needed. Bradysia agrestis is one of the major plant epidemic vectors in East Asia; however, its normal microbiota remains unstudied. This research was primarily designed to secure promising candidates for use in a paratransgenic approach to phytopathogen control, as well as to provide a picture of the gut microbiota of wild-caught B. agrestis from a blight field. A total of 180 larvae from three different regions in South Korea were analyzed for their gut microfloral composition. Diverse bacterial strains were purely isolated based on morphological differences in microbiological media. We found a total of 64 bacterial strains in the B. agrestis midgut and analyzed their 16S rRNA gene sequences for molecular identification and phylogenetic characterization. Furthermore, the microbial diversity of each normal microbiota group was analyzed with various diversity indices. Bacterial biota including species diversity, richness or species distribution, species constituents, and dominance varied by each regional vector group. The most widely distributed species was Bacillus aryabhattai, and the most common genera were Bacillus and Microbacterium. These saprophytic bacteria were isolated from all regional groups and their potential as paratransgenic candidates for controlling B. agrestis-mediated plant disease is discussed.