Relationship of Metabolic Dysfunction-Associated Steatohepatitis-Related Hepatocellular Carcinoma with Oral and Intestinal Microbiota: A Cross-Sectional Pilot Study.

Background and Objectives: The incidence of metabolic dysfunction-associated steatohepatitis (MASH)-related hepatocellular carcinoma (HCC) is increasing worldwide, alongside the epidemic of obesity and metabolic syndrome. Based on preliminary reports regarding the potential association of HCC and periodontitis, this study aimed to analyze the involvement of periodontal bacteria as well as the oral and intestinal bacterial flora in MASH-related HCC (MASH-HCC). Materials and Methods: Forty-one patients with MASH and nineteen with MASH-HCC participated in the study, completing survey questionnaires, undergoing periodontal examinations, and providing samples of saliva, mouth-rinsed water, feces, and peripheral blood. The oral and fecal microbiome profiles were analyzed by 16S ribosomal RNA sequencing. Bayesian network analysis was used to analyze the causation between various factors, including MASH-HCC, examinations, and bacteria. Results: The genus Fusobacterium had a significantly higher occupancy rate (p = 0.002) in the intestinal microflora of the MASH-HCC group compared to the MASH group. However, Butyricicoccus (p = 0.022) and Roseburia (p < 0.05) had significantly lower occupancy rates. The Bayesian network analysis revealed the absence of periodontal pathogenic bacteria and enteric bacteria affecting HCC. However, HCC directly affected the periodontal bacterial species Porphyromonas gingivalis, Tannerella forsythia, Fusobacterium nucleatum, and Prevotella intermedia in the saliva, as well as the genera Lactobacillus, Roseburia, Fusobacterium, Prevotella, Clostridium, Ruminococcus, Trabulsiella, and SMB53 in the intestine. Furthermore, P. gingivalis in the oral cavity directly affected the genera Lactobacillus and Streptococcus in the intestine. Conclusions: MASH-HCC directly affects periodontal pathogenic and intestinal bacteria, and P. gingivalis may affect the intestinal bacteria associated with gastrointestinal cancer.

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.

Comparison of microbiomes in ulcerative and normal mucosa of recurrent aphthous stomatitis (RAS)-affected patients.

BACKGROUND: Recurrent aphthous stomatitis (RAS) is the most common form of oral ulcerative disease, whose cause is still unknown. Researchers have found the association of many factors with the occurrence of RAS, and proposed oral bacterial infection could be a cause for this disease. METHODS: To investigate whether the occurrence of RAS is associated with oral bacterial infection, we performed high throughput sequencing analysis of bacterial samples collected from the normal oral mucosa and aphthous ulcers of 24 patients. RESULTS: Firmicutes, Proteobacteria and Bacteriodetes were the most abundant phyla in the microbiomes analysed. The alpha diversities of the oral mucosa and aphthous ulcer microbiomes were similar, suggesting a similar richness and diversity. The NMDS analysis showed the oral mucosa and aphthous ulcer microbiomes are significantly different. This suggestion is further supported by Anosim, MRPP, and Adonis analyses. More detailed comparison of the two groups of microbiomes suggested that the occurrence of RAS is significantly associated with the increase of Escherichia coli and Alloprevotella, as well as the decrease of Streptococcus. CONCLUSIONS: Considering E. coli is a very common intestinal bacterium, we propose that E. coli colonization could be a cause for RAS, and controlling E. coli colonization could help curing RAS.

A Microbial Signature of Psychological Distress in Irritable Bowel Syndrome.

OBJECTIVE: Irritable bowel syndrome (IBS) is associated with alterations along the brain-gut-microbiota axis. Previous studies have suggested a parallel segregation of microbial features and psychological burden in IBS. This study aimed at exploring the microbial correlates of psychological distress in patients with IBS. METHODS: Forty-eight patients with IBS (Rome III criteria, M (SD) age = 42 (15) years, 35 female, 25 diarrhea-dominant, 5 constipation-dominant, and 18 alternating-type IBS) were assessed for psychological and clinical variables with validated questionnaires, fecal samples underwent microbial 16S rRNA analyses (regions V1-2). Microbial analyses comprised examination of alpha and beta diversity, correlational analyses of bacterial abundance and comparisons among subgroups defined by thresholds of psychological and IBS symptom variables, and machine learning to identify bacterial patterns corresponding with psychological distress. RESULTS: Thirty-one patients (65%) showed elevated psychological distress, 22 (31%) anxiety, and 10 depression (21%). Microbial beta diversity was significantly associated with distress and depression (q = .036 each, q values are p values false discovery rate-corrected for multiple testing). Depression was negatively associated with Lachnospiraceae abundance (Spearman's ρ = -0.58, q = .018). Patients exceeding thresholds of distress, anxiety, depression, and stress perception showed significantly higher abundances of Proteobacteria (q = .020-.036). Patients with anxiety were characterized by elevated Bacteroidaceae (q = .036). A signature of 148 unclassified species accounting for 3.9% of total bacterial abundance co-varied systematically with the presence of psychological distress. CONCLUSIONS: Psychological variables significantly segregated gut microbial features, underscoring the role of brain-gut-microbiota interaction in IBS. A microbial signature corresponding with psychological distress was identified. CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov identifier NCT02536131, retrospectively registered.

Gut dysbiosis in acute-on-chronic liver failure and its predictive value for mortality.

BACKGROUND: Bacterial translocation from the gut plays an important role in the pathophysiology of acute-on-chronic liver failure (ACLF). However, gut dysbiosis in ACLF was not widely documented in previous studies. AIM: This research characterized the fecal microbiota in patients with ACLF and analyzed the temporal stability of gut microbiota during illness. METHODS: Fecal microbiota of 79 ACLF patients (42 patients were followed in the next 4 weeks after the first visit for longitudinal study) and 50 healthy controls was analyzed by 16S ribosomal DNA pyrosequencing. RESULTS: There was a marked difference between the ACLF group and the control group. The overall microbial diversity and richness were significantly lower in ACLF than in controls. ACLF patients had lower abundance of Bacteroidaceae, Ruminococcaceae, and Lanchnospiraceae, but higher abundance of Pasteurellaceae, Streptococcaceae, and Enterecoccaceae. The relative abundance of Lachnospiraceae was obviously decreased in ACLF patients with hepatic encephalopathy. The gut microbiota kept relatively stable in a short term after the onset of ACLF. The use of antibiotics only showed moderate impacts on the gut microbiota. The relative abundance of Pasteurellaceae and Model of End Stage Liver Disease score were independent factors predicting mortality rate. Network analysis comparison showed robust correlations between specific bacterial families (Ruminococcaceae and Lachnospiraceae) and inflammatory cytokines (interleukin [IL]-6, tumor necrosis factor alpha, IL-2) in ACLF patients. CONCLUSIONS: These data suggest gut dysbiosis in ACLF and its predictive value for mortality. The results thus open up the possibility of designing diagnostic biomarkers and targeted probiotics aimed at decreasing mortality in ACLF.

Falsiporphyromonas endometrii gen. nov., sp. nov., isolated from the post-partum bovine uterus, and emended description of the genus Porphyromonas Shah and Collins 1988.

Two black-pigmented, anaerobic bacterial strains, designated LMM 40(T) and LMM 41, were isolated from the bovine post-partum endometrium of two Holstein cows. The 16S rRNA gene sequences of the two strains were identical and showed the highest similarity to the 16S rRNA gene sequence of the type strain of Porphyromonas crevioricanis (90.2%) but only 85.1% 16S rRNA gene sequence similarity to the type strain of the type species of the genus Porphyromonas, Porphyromonas asaccharolytica. The major fatty acid profiles of the two strains were similar to those of species of the genus Porphyromonas, containing iso-C(15 : 0) as the major component and moderate amounts of anteiso-C(15 : 0), iso-C(13 : 0), C(15 : 0) and C(16 : 0). Hydroxylated fatty acids, such as iso-C(14 : 0) 3-OH, iso-C(16 : 0) 3-OH and iso-C(17 : 0) 3-OH, were also detected. The quinone profiles were dominated by the menaquinones MK-8 and MK-9, while spermidine was the major polyamine. The polar lipid profiles contained major amounts of phosphatidylethanolamine, an unidentified phospholipid, an unidentified aminophospholipid and two unidentified lipids and minor amounts of phosphatidylglycerol, an unidentified aminolipid, a second unidentified aminophospholipid and an unidentified glycolipid. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The genomic DNA G+C contents of LMM 40(T) and LMM 41 were 40.7 and 41.3 mol%, respectively. Based on a polyphasic approach, including phylogenetic analysis, physiological and biochemical tests as well as metabolic fingerprinting, it is proposed that the two strains are members of a novel genus and species, for which the name Falsiporphyromonas endometrii gen. nov., sp. nov. is proposed. The type strain of Falsiporphyromonas endometrii is LMM 40(T) ( = DSM 27210(T) = CCUG 64267(T)). An emended description of the genus Porphyromonas is also presented.

First detection of endosymbiotic bacteria in biting midges Culicoides pulicaris and Culicoides punctatus, important Palaearctic vectors of bluetongue virus.

Heritable bacteria have been highlighted as important components of vector biology, acting as required symbionts with an anabolic role, altering competence for disease transmission, and affecting patterns of gene flow by altering cross compatibility. In this paper, we tested eight U.K. species of Culicoides (Diptera: Ceratopogonidae) midge for the presence of five genera of endosymbiotic bacteria: Cardinium (Bacteroidales: Bacteroidaceae); Wolbachia (Rickettsiales: Rickettsiaceae); Spiroplasma (Entomoplasmatales: Spiroplasmataceae); Arsenophonus (Enterobacteriales: Enterobacteriaceae), and Rickettsia (Rickettsiales: Rickettsiaceae). Cardinium spp. were detected in both sexes of Culicoides pulicaris and Culicoides punctatus, two known vectors of bluetongue virus. Cardinium spp. were not detected in any other species, including the Culicoides obsoletus group, the main vector of bluetongue and Schmallenberg viruses in northern Europe. The other endosymbionts were not detected in any Culicoides species. The Cardinium strain detected in U.K. Culicoides species is very closely related to the Candidatus Cardinium hertigii group C, previously identified in Culicoides species in Asia. Further, we infer that the symbiont is not a sex ratio distorter and shows geographic variation in prevalence within a species. Despite its detection in several species of Culicoides that vector arboviruses worldwide, the absence of Cardinium in the C. obsoletus group suggests that infections of these symbionts may not be necessary to the arboviral vector competence of biting midges.

Prevalence of Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis and Tannerella forsythia in Japanese patients with generalized chronic and aggressive periodontitis.

This study aimed to investigate the prevalence and levels of major periodontal pathogens, Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis and Tannerella forsythia in subgingival plaque samples of a group of Japanese patients with aggressive periodontitis (AgP) and chronic periodontitis (CP). A total of 40 patients with clinical diagnosis of AgP or CP and 10 periodontally healthy volunteers were subjected to clinical and microbiological analysis. Subgingival plaque samples were analyzed for A. actinomycetemcomitans, P. gingivalis and T. forsythia with a real-time polymerase chain reaction (PCR) technique. The prevalence of P. gingivalis and T. forsythia was relatively high in patients with periodontitis: over 60% of AgP or CP patients harbored these pathogens whereas they were not detected in the subgingival plaque samples from periodontally healthy individuals. P. gingivalis and T. forsythia were relatively frequently detected together in AgP and CP patients. No significant differences in the prevalence or level of the 3 pathogens were found between periodontitis groups. The proportion of T. forsythia was approximately 4-fold higher in CP group than in AgP group (P = 0.02). In periodontitis patients, a significant positive correlation was found between periodontal parameters (probing depth and clinical attachment level) and the numbers of total bacteria, P. gingivalis and T. forsythia. No distinct pattern of the subgingival profile of these pathogens was discerned between the two disease entities, except for the difference in the proportion of T. forsythia. The red complex bacteria, P. gingivalis and T. forsythia were highly prevalent in this population of Japanese AgP and CP patients, collaborating their roles in periodontitis.

Inulin and fructo-oligosaccharides have divergent effects on colitis and commensal microbiota in HLA-B27 transgenic rats.

Modulation of intestinal microbiota by non-digestible carbohydrates may reduce inflammation in inflammatory bowel disease (IBD). The aim of the present study was to assess the effects of inulin and fructo-oligosaccharides (FOS) on intestinal microbiota and colitis in HLA-B27 transgenic rats, a well-validated rodent model for IBD. In this study, 4-week-old rats were fed 8 g/kg body weight inulin or FOS for 12 weeks, or not. Faeces were collected at 4 and 16 weeks of age; and caecal samples were collected at necropsy. The effects of inulin and FOS on chronic intestinal inflammation were assessed using a gross gut score, histology score and levels of mucosal IL-1ß. Intestinal microbiota were characterised by quantitative PCR and denaturing gradient gel electrophoresis. Colitis was significantly reduced in all FOS-fed rats compared to the control diet, whereas inulin decreased chronic intestinal inflammation in only half the number of animals. Quantitative analysis of caecal microbiota demonstrated that inulin increased the numbers of total bacteria and the Bacteroides-Prevotella-Porphyromonas group, FOS increased bifidobacteria, and both fructans decreased Clostridium cluster XI. In the faecal samples, both inulin and FOS decreased total bacteria, Bacteroides-Prevotella-Porphyromonas group, and Clostridium clusters XI and XIVa. FOS increased Bifidobacterium spp., and mediated a decrease of gene copies of Enterobacteriaceae and Clostridium difficile toxin B in faeces. SCFA concentrations in the faecal and caecal samples were unaffected by the diets. In conclusion, FOS increased the abundance of Bifidobacterium spp., whereas both fructans reduced Clostridium cluster XI and C. difficile toxin gene expression, correlating with a reduction of chronic intestinal inflammation.

Production of secoisolariciresinol from defatted flaxseed by bacterial biotransformation.

AIMS: Secoisolariciresinol (SECO) is increasingly recognized for potential clinical application because of its preventive effects against breast and colon cancers, atherosclerosis and diabetes, and its production through biotransformation has been attempted. However, previously reported bacteria all required stringent anaerobic culture conditions, precluding large-scale production. Here, we report the isolation and characterization of bacteria that produce SECO under less stringent anaerobic culture conditions. METHODS AND RESULTS: Using defatted flaxseed as raw material, we isolated a facultative anaerobic bacterium from human faeces that hydrolysed secoisolariciresinol diglucoside-3-hydroxy-3-methyl glutaric acid (SDG-HMGA) oligomers in flaxseed to produce SECO. Both conventional assays and 16S rRNA gene sequence analysis demonstrated its close relatedness with Bacteroides uniformis. The transformation efficiency of SDG in defatted flaxseed to SECO was more than 80% by this bacterial strain. We investigated factors that might influence fermentation, such as redox potential and pH, for large-scale fermentation of defatted flaxseed to produce SECO. CONCLUSIONS: The method to produce SECO through biotransformation of defatted flaxseed with this bacterial strain is highly efficient and economic. SIGNIFICANCE AND IMPACT OF THE STUDY: This bacterial strain can transform SDG to SECO under less stringent anaerobic culture conditions, which will greatly facilitate industry-scale production of SECO.

Paraphocaeicola brunensis gen. nov., sp. nov., Carrying Two Variants of nimB Resistance Gene from Bacteroides fragilis, and Caecibacteroides pullorum gen. nov., sp. nov., Two Novel Genera Isolated from Chicken Caeca.

Three difficult-to-cultivate, strictly anaerobic strains, AN20T, AN421T, and AN502, were analyzed within a project studying possible probiotics for newly hatched chickens. Phylogenetic analyses showed that strains AN20T, AN421T, and AN502 formed two well-separated phylogenetic lineages in all phylogenetic and phylogenomic trees comprising members of the family Bacteroidaceae. Comparison to reference genomes of type species Bacteroides fragilis NCTC 9343T, Phocaeicola abscessus CCUG 55929T, and Capsularis zoogleoformans ATCC 33285T showed low relatedness based on the calculated genome-to-genome distance and orthologous average nucleotide identity. Analysis of fatty acid profiles showed iso-C15:0, anteiso-C15:0, C16:0, C18:1ω9c, and iso-C17:0 3OH as the major fatty acids for all three strains and additionally C16:0 3OH for AN421T and AN502. A specific combination of respiratory quinones different from related taxa was found in analyzed strains, MK-5 plus MK-11 in strain AN20T and MK-5 plus MK-10 in strains AN421T and AN502. Strains AN421T and AN502 harbor complete CRISPR loci with CRISPR array, type II-C, accompanied by a set of cas genes (cas9, cas1, and cas2) in close proximity. Interestingly, strain AN20T was found to harbor two copies of nimB gene with >95% similarity to nimB of B. fragilis, suggesting a horizontal gene transfer between these taxa. In summary, three isolates characterized in this study represent two novel species, which we proposed to be classified in two novel genera of the family Bacteroidaceae, for which the names Paraphocaeicola brunensis sp. nov. (AN20T = CCM 9041T = DSM 111154T) and Caecibacteroides pullorum sp. nov. (AN421T= CCM 9040T = DSM 111155T) are proposed. IMPORTANCE This study represents follow-up research on three difficult-to-cultivate anaerobic isolates originally isolated within a project focused on strains that are able to stably colonize newly hatched chickens, thus representing possible probiotics. This project is exceptional in that it successfully isolates several miscellaneous strains that required modified and richly supplemented anaerobic media, as information on many gut-colonizing bacteria is based predominantly on metagenomic studies. Superior colonization of newly hatched chickens by Bacteroides spp., Phocaeicola spp., or related taxa can be considered of importance for development of future probiotics. Although different experiments can also be performed with provisionally characterized isolates, precise taxonomical definition is necessary for subsequent broad communication. The aim of this study is therefore to thoroughly characterize these isolates that represent novel genera and precisely determine their taxonomic position among related taxa to facilitate further research and communication involving these strains.

Effects of oral administration of Lactobacillus acidophilus L-92 on the symptoms and serum markers of atopic dermatitis in children.

BACKGROUND: Few studies have investigated the complementary effects of long-term oral administration of Lactobacillus acidophilus on traditional medical therapy in the treatment of patients with atopic dermatitis (AD). METHODS: The Atopic Dermatitis Area and Severity Index was used to evaluate AD severity. Symptom severity was assessed using the symptom score. The effect of medical therapy was evaluated by adding the medication score, calculated as the sum of each product of the amount of steroid ointment used for therapy and its designated strength graded on a 4-point scale, to the symptom score. The complementary effect of long-term oral administration of L. acidophilus strain L-92 (L-92) as a probiotic or biogenic strain in patients with AD was evaluated using the symptom-medication score, which was calculated as the sum of the symptom score and medication score. Both a preliminary casuistic study and a double-blinded, placebo-controlled study were performed to evaluate the effects of L-92 on the symptoms of AD in children. RESULTS: Orally administered L-92 significantly ameliorated the symptoms of AD in Japanese children. L-92 also affected the serum concentrations of thymus and activation-regulated chemokine in a time-dependent manner. CONCLUSIONS: The results of the preliminary trial and the double-blinded, placebo-controlled study revealed a complementary effect of oral L-92 on the standard medical therapy (topical application of a steroid ointment) in patients with AD that was mediated, at least in part, by alterations in the Th1/Th2 balance.

The fecal microbiota of piglets during weaning transition and its association with piglet growth across various farm environments.

This study describes the fecal microbiota from piglets reared in different living environments during the weaning transition, and presents the characteristics of microbiota associated with good growth of piglets after weaning. Fecal samples were collected pre- (d26) and post-weaning (d35) from 288 male piglets in 16 conventional indoor commercial farms located in the West of France. The changes one week after weaning on the most abundant microbial families was roughly the same in all farms: alpha diversity increased, the relative abundance of Bacteroidaceae (-61%), Christensenellaceae (-35%), Enterobacteriaceae (-42%), and Clostridiaceae (-32%) decreased, while the relative abundance of Prevotellaceae (+143%) and Lachnospiraceae (+21%) increased. Among all the collected samples, four enterotypes that were ubiquitous in all farms were identified. They could be discriminated by their respective relative abundances of Prevotella, Faecalibacterium, Roseburia, and Lachnospira, and likely corresponded to a gradual maturational shift from pre- to post-weaning microbiota. The rearing environment influenced the frequency of enterotypes, as well as the relative abundance of 6 families at d26 (including Christensenellaceae and Lactobacillaceae), and of 21 families at d35. In all farms, piglets showing the highest relative growth rate during the first three weeks after weaning, which were characterized as more robust, had a higher relative abundance of Bacteroidetes, a lower relative abundance of Proteobacteria, and showed a greater increase in Prevotella, Coprococcus, and Lachnospira in the post-weaning period. This study revealed the presence of ubiquitous enterotypes among the farms of this study, reflecting maturational stages of microbiota from a young suckling to an older cereal-eating profile. Despite significant variation in the microbial profile between farms, piglets whose growth after weaning was less disrupted were, those who had reached the more mature phenotype characterized by Prevotella the fastest.

Longitudinal evaluation of fecal microbiota transplantation for ameliorating calf diarrhea and improving growth performance.

Calf diarrhea is associated with enteric infections, and also provokes the overuse of antibiotics. Therefore, proper treatment of diarrhea represents a therapeutic challenge in livestock production and public health concerns. Here, we describe the ability of a fecal microbiota transplantation (FMT), to ameliorate diarrhea and restore gut microbial composition in 57 growing calves. We conduct multi-omics analysis of 450 longitudinally collected fecal samples and find that FMT-induced alterations in the gut microbiota (an increase in the family Porphyromonadaceae) and metabolomic profile (a reduction in fecal amino acid concentration) strongly correlate with the remission of diarrhea. During the continuous follow-up study over 24 months, we find that FMT improves the growth performance of the cattle. This first FMT trial in ruminants suggest that FMT is capable of ameliorating diarrhea in pre-weaning calves with alterations in their gut microbiota, and that FMT may have a potential role in the improvement of growth performance.

Evaluation of the bacterial community and intestinal development of different genetic lines of chickens.

The gastrointestinal tract (GIT) of each animal species provides a unique niche for specialized intestinal bacterial communities to thrive, and in poultry this is no exception. However, little is known about how the bacterial community varies among these different genetic lines of chickens, especially of those with various growth rates. Therefore, an experiment was conducted to observe and evaluate the changes in the bacterial community and GIT development of a modern multipurpose strain, high-yield strain, and a historic strain, Athens Canadian Random Bred (ACR), of broilers. All birds were fed a standard nonmedicated corn-soybean meal broiler starter diet ad libitum from 0 to 35 d of age. Intestinal measurements and bacterial analysis of the ileum were conducted at 4, 8, 14, 21, and 35 d of age. Bacterial DNA was isolated from the digesta, and the distribution of bacterial 16S rRNA sequence polymorphisms was analyzed by a combination of denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphisms. The multipurpose chicks performed the best from 0 to 14 d of age; however, overall performance was similar for the multipurpose and the high-yield broilers. The ACR birds had the poorest performance at all periods measured. The overall relative weight of the jejunum and ileum was not different between the 3 genetic lines, but the ACR birds had the longest relative jejunum and ileum lengths. Furthermore, the multipurpose birds had the longest villi height, whereas the ACR birds had the shortest villi height in the jejunum and ileum at all measuring periods. Based on denaturing gradient gel electrophoresis, the multipurpose and high-yield broilers had similar bacterial communities at all ages. Regardless of the genetic line of broiler, the bacterial community changed with age. Performance, GIT measurements, and bacterial community of the ACR differed compared with the modern broilers. The results indicate that the different genetic lines of broilers have varying rates of intestinal development, which may affect performance and the bacterial community.

Melatonin attenuates microbiota dysbiosis of jejunum in short-term sleep deprived mice.

Our study demonstrated that sleep deprivation resulted in homeostasis disorder of colon. Our study goes deeper into the positive effects of melatonin on small intestinal microbiota disorder caused by sleep deprivation. We successfully established a multiplatform 72 h sleep deprivation mouse model with or without melatonin supplementation, and analyzed the change of small intestinal microbiota using high-throughput sequencing of the 16S rRNA. We found melatonin supplementation suppressed the decrease of plasma melatonin level in sleep deprivation mice. Meanwhile, melatonin supplementation improved significantly the reduction in OTU numbers and the diversity and richness of jejunal microbiota and the abundance of Bacteroidaeae and Prevotellaceae, as well as an increase in the Firmicutes-to-Bacteroidetes ratio and the content of Moraxellaceae and Aeromonadaceae in the jejunum of sleep deprived-mice. Moreover, melatonin supplementation reversed the change of metabolic pathway in sleep deprived-mice, including metabolism, signal transduction mechanisms and transcription etc, which were related to intestinal health. Furthermore, melatonin supplementation inverted the sleep deprivation-induced a decline of anti-inflammatory cytokines (IL-22) and an increase of the ROS and proinflammatory cytokines (IL-17) in jejunum. These findings suggested that melatonin, similar to a probiotics agent, can reverse sleep deprivation-induced small intestinal microbiota disorder by suppressing oxidative stress and inflammation response.

Faecal microbiota shift during weaning transition in piglets and evaluation of AO blood types as shaping factor for the bacterial community profile.

The host-microbiota interplay is recognized as a key factor for the homeostatic maintenance in animals. In pigs, the weaning transition represents a drastic changes event leading to high risk of gut dysbiosis, which in most cases results in economic losses for swine industry. The blood type antigens expressed on mucosal surfaces can act as receptors for bacterial adhesion and the hypothesis of possible associations between blood groups and intestinal microbial profiles has been tested in human with contrasting results. Nevertheless, no studies testing the blood type as possible shaping factor for gut microbiota are available for pigs. The results of our previous study suggested the porcine AO blood types system as a possible factor influencing the microbiota composition. In the present study, the changes in fecal microbiota of 12 piglets were followed from 7 days after birth to 2 weeks post-weaning, testing the hypothesis that blood types may impact on its structure. No effects attributable to the difference in blood groups were detected, however, the sampling site (faeces) and the low statistical power might have masked the hypothesized impact. The data clearly showed the rearrangement of the bacterial ecosystem triggered by weaning transition; mainly consisting of a shift from a Bacteroidaceae-Enterobacteriaceae dominated community, to a Prevotellaceae-Ruminococcaceae dominated community. The functional analysis by metagenomic predictions suggested a role of the high levels of long-chain fatty acid in swine milk as energy source for Enterobacteriaceae (E. coli), in suckling piglets. This study provides a first insight for further investigations; indicating the need for larger sample size, preferably derived from intestinal mucosa, to test the potential effect of blood groups on gut microbiota profiles, and for analyses aimed at assessing the long-chain fatty acids degradation activity within the intestinal microbiota of suckling piglets, with particular attention to the role of E. coli.

Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana.

BACKGROUND: Gut microbiota from individuals in rural, non-industrialized societies differ from those in individuals from industrialized societies. Here, we use 16S rRNA sequencing to survey the gut bacteria of seven non-industrialized populations from Tanzania and Botswana. These include populations practicing traditional hunter-gatherer, pastoralist, and agropastoralist subsistence lifestyles and a comparative urban cohort from the greater Philadelphia region. RESULTS: We find that bacterial diversity per individual and within-population phylogenetic dissimilarity differs between Botswanan and Tanzanian populations, with Tanzania generally having higher diversity per individual and lower dissimilarity between individuals. Among subsistence groups, the gut bacteria of hunter-gatherers are phylogenetically distinct from both agropastoralists and pastoralists, but that of agropastoralists and pastoralists were not significantly different from each other. Nearly half of the Bantu-speaking agropastoralists from Botswana have gut bacteria that are very similar to the Philadelphian cohort. Based on imputed metagenomic content, US samples have a relative enrichment of genes found in pathways for degradation of several common industrial pollutants. Within two African populations, we find evidence that bacterial composition correlates with the genetic relatedness between individuals. CONCLUSIONS: Across the cohort, similarity in bacterial presence/absence compositions between people increases with both geographic proximity and genetic relatedness, while abundance weighted bacterial composition varies more significantly with geographic proximity than with genetic relatedness.

Assessing the spatial and temporal variability of bacterial communities in two Bardenpho wastewater treatment systems via Illumina MiSeq sequencing.

Next generation sequencing provides new insights into the diversity and ecophysiology of bacteria communities throughout wastewater treatment plants (WWTP), as well as the fate of pathogens in wastewater treatment system. In the present study, we investigated the bacterial communities and human-associated Bacteroidales (HF183) marker in two WWTPs in North America that utilize Bardenpho treatment processes. Although, most pathogens were eliminated during wastewater treatment, some pathogenic bacteria were still observed in final effluents. The HF183 genetic marker demonstrated significant reductions between influent and post-Bardenpho treated samples in each WWTP, which coincided with changes in bacteria relative abundances and community compositions. Consistent with previous studies, the major phyla in wastewater samples were predominantly comprised by Proteobacteria (with Gammaproteobacteria and Alphaproteobacteria among the top two classes), Actinobacteria, Bacteroidetes, and Firmicutes. Dominant genera were often members of Proteobacteria and Firmicutes, including several pathogens of public health concern, such as Pseudomonas, Serratia, Streptococcus, Mycobacterium and Arcobacter. Pearson correlations were calculated to observe the seasonal variation of relative abundances of gene sequences at different levels based on the monthly average temperature. These findings profile how changes in bacterial communities can function as a robust method for monitoring wastewater treatment quality and performance for public and environmental health purposes.

Enrichment of intracellular sulphur cycle -associated bacteria in intertidal benthic foraminifera revealed by 16S and aprA gene analysis.

Benthic foraminifera are known to play an important role in marine carbon and nitrogen cycles. Here, we report an enrichment of sulphur cycle -associated bacteria inside intertidal benthic foraminifera (Ammonia sp. (T6), Haynesina sp. (S16) and Elphidium sp. (S5)), using a metabarcoding approach targeting the 16S rRNA and aprA -genes. The most abundant intracellular bacterial groups included the genus Sulfurovum and the order Desulfobacterales. The bacterial 16S OTUs are likely to originate from the sediment bacterial communities, as the taxa found inside the foraminifera were also present in the sediment. The fact that 16S rRNA and aprA -gene derived intracellular bacterial OTUs were species-specific and significantly different from the ambient sediment community implies that bacterivory is an unlikely scenario, as benthic foraminifera are known to digest bacteria only randomly. Furthermore, these foraminiferal species are known to prefer other food sources than bacteria. The detection of sulphur-cycle related bacterial genes in this study suggests a putative role for these bacteria in the metabolism of the foraminiferal host. Future investigation into environmental conditions under which transcription of S-cycle genes are activated would enable assessment of their role and the potential foraminiferal/endobiont contribution to the sulphur-cycle.