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Metagenomic insights to understand the role of polluted river Yamuna in shaping the gut microbial communities of two invasive fish species.. The gastrointestinal microbial community plays a crucial role in host health, immunity, protection, development and provides nutrients to the host. The rising human-induced pollution and heavy metal contamination in all aquatic systems globally has led us to explore the gut microbial diversity of two exotic invasive fish Cyprinus carpio and Oreochromis niloticus from river Yamuna, India. These fishes are aquatic bioindicators with high demographic resilience. Exploring these associations would pave the way for addressing problems that inhabitant fishes are facing due to the increasing pollution load in the River Yamuna. Based on 16S rRNA gene amplicon sequencing, our results deliver comparative information on the gut microbiome of these fishes and highlight connotations between the microbiome of gut and water samples. The gut of C. carpio and O. niloticus was dominated by phyla Proteobacteria whereas Bacteroidetes dominated the water sample. Microbial communities showed predicted roles such as pathogenicity (Escherichia-Shigella, Aeromonas veronii, Vibrio cholerae, Streptococcus iniae, Flavobacterium columnare, Klebsiella pneumoniae, Mycobacterium sp.), probiotic applications (Bacillus velezensis, Lactobacillus plantarum, Enterococcus faecalis, Bifidobacterium longum, Lactococcus lactis, Leuconostoc falkenbergense) and involvement in sewage and organic matter decomposition (Nitrosomonas sp., Methanosaeta harundinacea, Dechloromonas agitata, Thauera humireducens, Zoogloea ramigera). Heavy metal degrading members (Leucobacter chromiireducens, Pseudomonas fluorescens, P. aeruginosa, Klebsiella pneumoniae, and Micrococcus luteus) were detected in gut microbiome samples thus supporting the notion that fish shapes its gut microbiota with changing ecology. Functional profiling showed that microbial communities are specialized in metabolic functions thus reflecting the dietary profile of these invasive fishes. |
Composition and diversity of gut microbiota in Pomacea canaliculata in sexes and between developmental stages.. BACKGROUND: The apple snail, Pomacea canaliculata, is one of the world's 100 worst invasive alien species and vector of some pathogens relevant to human health. METHODS: On account of the importance of gut microbiota to the host animals, we compared the communities of the intestinal microbiota from P. canaliculata collected at different developmental stages (juvenile and adult) and different sexes by using high-throughput sequencing. RESULTS: The core bacteria phyla of P. canaliculata gut microbiota included Tenericutes , Firmicutes , Proteobacteria , Actinobacteria , and Cyanobacteria . The female group possessed the highest richness values, whereas the male group possessed the lowest bacterial richness and diversity compared with the female and juvenile group. Both the developmental stages and sexes had important effects on the composition of the intestinal microbiota of P. canaliculata. By LEfSe analysis, microbes from the phyla Proteobacteria and Actinobacteria were enriched in the female group, phylum Bacteroidetes was enriched in the male group, family Mycoplasmataceae and genus Leuconostoc were enriched in the juvenile group. PICRUSt analysis predicted twenty-four metabolic functions in all samples, including general function prediction, amino acid transport and metabolism, transcription, replication, recombination and repair, carbohydrate transport and metabolism, etc. CONCLUSIONS: This study provided a general understanding of the diversity characteristics of intestinal microbial communities of P. canaliculata, and indicated that developmental stage and gender could both influence the intestinal microbes of P. canaliculata. Further study may focus on the interaction between the gut microbiota and their host. |
Microbial programming of health and disease starts during fetal life.. The pioneer microbiota of the neonatal gut are essential for gut maturation, and metabolic and immunologic programming. Recent research has shown that early bacterial colonization may impact the occurrence of disease later in life (microbial programming). Despite early conflicting evidence, it has long been considered that the womb is a sterile environment and human microbial colonization begins at birth. In the last few years, several findings have reiterated the presence of microbes in infant first stool (meconium) and pointed to the existence of in utero microbial colonization of the infant gut. The dominant bacterial taxa detected in meconium specimens belong to the Enterobacteriaceae family (Escherichia genus) and lactic acid bacteria (notably members of the genera Leuconostoc, Enterococcus, and Lactococcus). Maternal atopy promotes dominance of Enterobacteriaceae in newborn meconium, which in turn may lead to respiratory problems in the infant. This microbial interaction with the host immune system may in fact, originate during fetal life. Our review evaluates the evidence for an intrauterine origin of meconium microbiota, their composition and influences, and potential clinical implications on infant health. |
Dysbiosis of intestinal homeostasis contribute to Whitmania pigra edema disease.. Whitmania pigra is widely used in traditional Chinese medicine. However, W. pigra is being threatened by an edema disease with unknown causes (WPE). In this study, a comprehensive exploration of virome, microbiome, and metabolome aberrations in the intestine of W. pigra was performed to address the aetiology of WPE. Virome analysis indicated that eukaryotic viruses did not contribute to WPE, whereas an expansion of Caudovirales was observed in WPE. Compared to the control, the microbial richness and diversity in diseased W. pigra decreased remarkably. Nine genera, including Aeromonas, Anaerotruncus, Vibrio, Proteocatella, Acinetobacter, and Brachyspira were overrepresented in WPE, whereas eleven genera, including Bifidobacterium, Phascolarctobacterium, Lactobacillus, Bacillus and AF12, were enriched in healthy individuals. Furthermore, certain metabolites, especially amino acids, short-chain fatty acids, and bile acids, were found to be linked to intestinal microbiota alterations in WPE. An integration of the microbiome and metabolome in WPE found that dysbiosis of the gut microbiota or metabolites caused WPE. Notably, W. pigra accepted intestinal microbiota transplantation from WPE donors developed WPE clinical signs eventually, and the dysbiotic intestinal microbiota can be recharacterized in this recipient W. pigra. Strikingly, pathological features of metanephridium and uraemic toxin enrichment in the gut indicated a putative interconnection between the gut and metanephridium in WPE, which represents the prototype of the gut-kidney axis in mammals. These finding exemplify the conservation of "microecological Koch's postulates" from annelids to insects and other vertebrates, which provides a direction of prevention and treatment for WPE and opens a new insight into the pathogenesis of aquatic animal diseases from an ecological perspective. |
Composition of the gut microbiota in patients with inflammatory bowel disease in Saudi Arabia: A pilot study.. CONCLUSIONS: The results of this study provide an overview of the variations in microbiota diversity present in Saudi IBD patients compared to healthy controls. RESULTS: The key finding was three negative bacterial biomarkers, Paraprevotellaceae, the Muribaculaceae families of Bacteroidetes phylum, and the Leuconostocaceae family of Firmicutes phylum, which had a higher relative abundance in healthy individuals compared to IBD patients. It was also found that primary microbiota signatures at certain genera and species levels, including Prevotella copri, Bifidobacterium adolescentis, Ruminococcus callidus, Coprococcus sp., Ruminococcus gnavus, Dorea formicigenerans, Leuconostoc, Dialister, Catenibacterium, Eubacterium biforme, and Lactobacillus mucosae, were absent in almost all IBD patients, while Veillonella dispar was absent in all healthy individuals. METHODS: After obtaining an informed consent, fecal samples were collected from 11 participants with IBD (patients) and 10 healthy individuals (controls). The bacterial components of the microbial population were identified by next-generation sequencing of partial 16S rRNA. Statistically significant dissimilarities were observed between samples for all metrics. BACKGROUND: Inflammatory bowel disease (IBD) is a chronic intestinal inflammatory condition attributed to a complex interaction between imbalances in the gut microbiome, environmental conditions, and a deregulated immune response. The aim of the study was to investigate the composition of the gut microbiome of Saudi patients with IBD. |
Feeding with Sustainably Sourdough Bread Has the Potential to Promote the Healthy Microbiota Metabolism at the Colon Level.. The contribution of sustainably food processing to healthy intestinal microbial functions is of recent acquisition. The sourdough fermentation fits well with the most sustainable bread making. We manufactured baker's yeast (BYB) and sourdough breads, which first underwent to an in-depth characterization. According to nutritional questionnaires, we selected 40 volunteers adhering to the Mediterranean diet. Data on their fecal microbiota and metabolome allowed the selection of two highly representative fecal donors to separately run the Twin Mucosal-SHIME (Twin M-SHIME) under 2-week feeding with BYB and t-SB30. Bread feeding did not affect the microbial composition at phylum and family levels of both donors, in all Twin M-SHIME colon tracts, and lumen and mucosal compartments. The genus core microbiota showed few significant fluctuations, which regarded the relative abundances of Lactobacillus and Leuconostoc according to feeding with BYB and t-SB30, respectively. Compared with BYB, the content of all short chain fatty acids (SCFA), and isovaleric and 2-methylbutyric acids significantly increased with t-SB30 feeding. This was evident for all Twin M-SHIME colon tracts and both donors. The same was found for the content of Asp, Thr, Glu, GABA, and Orn. The bread characterization made possible to identify the main features responsible for this metabolic response. Compared with BYB, t-SB30 had much higher contents of resistant starch, peptides, and free amino acids, and an inhomogeneous microstructure. We used the most efficient approach to investigate a staple food component, excluding interferences from other dietary factors and attenuating human physiology overlaps. The daily consumption of sourdough bread may promote the healthy microbiota metabolism at colon level. |
Probiotics for the prevention of pediatric antibiotic-associated diarrhea.. BACKGROUND: Antibiotics are frequently prescribed in children. They alter the microbial balance within the gastrointestinal tract, commonly resulting in antibiotic-associated diarrhea (AAD). Probiotics may prevent AAD via restoration of the gut microflora. OBJECTIVES: The primary objectives were to assess the efficacy and safety of probiotics (any specified strain or dose) used for the prevention of AAD in children. SEARCH METHODS: MEDLINE, EMBASE, CENTRAL, CINAHL, AMED, and the Web of Science were searched along with specialized registers including the Cochrane IBD/FBD review group, CISCOM (Centralized Information Service for Complementary Medicine), NHS Evidence, the International Bibliographic Information on Dietary Supplements as well as trial registries. Letters were sent to authors of included trials, nutraceutical and pharmaceutical companies, and experts in the field requesting additional information on ongoing or unpublished trials. Conference proceedings, dissertation abstracts, and reference lists from included and relevant articles were also searched. SELECTION CRITERIA: Randomized, parallel, controlled trials in children receiving antibiotics, that compare probiotics to placebo, active alternative prophylaxis, or no treatment and measure the incidence of diarrhea secondary to antibiotic use were considered for inclusion. DATA COLLECTION AND ANALYSIS: Study selection, data extraction as well as methodological quality assessment using the risk of bias instrument was conducted independently and in duplicate by two authors. Dichotomous data (incidence of diarrhea, adverse events) were combined using a pooled risk ratio (RR) or risk difference (RD), and continuous data (mean duration of diarrhea, mean daily stool frequency) as mean difference (MD), along with their corresponding 95% confidence interval . For overall pooled results on the incidence of diarrhea, sensitivity analyses included available case versus extreme-plausible analyses and random- versus fixed-effect models. To explore possible explanations for heterogeneity, a priori subgroup analysis were conducted on probiotic strain, dose, definition of antibiotic-associated diarrhea, as well as risk of bias. We also conducted post hoc subgroup analyses by patient diagnosis, single versus multi-strain, industry sponsorship, and inpatient status. The overall quality of the evidence supporting the outcomes was evaluated using the GRADE criteria. MAIN RESULTS: Twenty-three studies met the inclusion criteria. Trials included treatment with either Bacillus spp., Bifidobacterium spp., Clostridium butyricum, Lactobacilli spp., Lactococcus spp., Leuconostoc cremoris, Saccharomyces spp., orStreptococcus spp., alone or in combination. Eleven studies used a single strain probiotic, four combined two probiotic strains, three combined three probiotic strains, one combined four probiotic strains, two combined seven probiotic strains, one included ten probiotic strains, and one study included two probiotic arms that used three and two strains respectively. The risk of bias was determined to be high or unclear in 13 studies and low in 10 studies. Available case (patients who did not complete the studies were not included in the analysis) results from 22/23 trials reporting on the incidence of diarrhea show a precise benefit from probiotics compared to active, placebo or no treatment control. The incidence of AAD in the probiotic group was 8% compared to 19% in the control group = 55%, 3898 participants). A GRADE analysis indicated that the overall quality of the evidence for this outcome was moderate. This benefit remained statistically significant in an extreme plausible sensitivity analysis, where the incidence of AAD in the probiotic group was 14% compared to 19% in the control group = 63%, 4529 participants). None of the 16 trials that reported on adverse events documented any serious adverse events attributable to probiotics. Meta-analysis excluded all but an extremely small non-significant difference in adverse events between treatment and control . The majority of adverse events were in placebo, standard care or no treatment group. Adverse events reported in the studies include rash, nausea, gas, flatulence, abdominal bloating, abdominal pain, vomiting, increased phlegm, chest pain, constipation, taste disturbance, and low appetite. AUTHORS' CONCLUSIONS: Moderate quality evidence suggests a protective effect of probiotics in preventing AAD. Our pooled estimate suggests a precise probiotic effect with a NNT of 10. Among the various probiotics evaluated, Lactobacillus rhamnosus or Saccharomyces boulardii at 5 to 40 billion colony forming units/day may be appropriate given the modest NNT and the likelihood that adverse events are very rare. It is premature to draw conclusions about the efficacy and safety of other probiotic agents for pediatric AAD. Although no serious adverse events were observed among otherwise healthy children, serious adverse events have been observed in severely debilitated or immuno-compromised children with underlying risk factors including central venous catheter use and disorders associated with bacterial/fungal translocation. Until further research has been conducted, probiotic use should be avoided in pediatric populations at risk for adverse events. Future trials would benefit from a standard and valid outcomes to measure AAD. |
The effect of a multispecies probiotic on microbiota composition in a clinical trial of patients with diarrhea-predominant irritable bowel syndrome.. BACKGROUND: Although probiotics are increasingly used in irritable bowel syndrome (IBS), their mechanism of action has not been elucidated sufficiently. We aimed to evaluate the impact of a multispecies probiotic on enteric microbiota composition in women with diarrhea-predominant-IBS (IBS-D) and to determine whether these effects are associated with changes in IBS symptoms or inflammatory markers. METHODS: In a double-blind, placebo-controlled study, Rome III IBS-D women completed a two-week run-in period and eligible women were assigned at random to a probiotic capsule or an indistinguishable placebo, twice daily for 8 weeks. IBS symptoms and stool consistency were rated daily by visual analogue scales and the Bristol stool scale. High sensitivity C-reactive protein, fecal calprotectin and microbial composition were tested at baseline and at 4 and 8 weeks. Microbial sequencing of the 16S rRNA was performed and data were analyzed to compare patients who responded to treatment with those who did not. KEY RESULTS: 172 IBS-D patients were recruited and 107 eligible patients were allocated to the intervention or placebo group. Compared to placebo, BIO-25 did not result in changes in microbial diversity or taxa proportions, except for higher relative proportions of Lactobacillus in the BIO-25 group . Symptomatic responders to BIO-25 showed a reduction in the proportion of Bilophila posttreatment. Patients with beneficial inflammatory-marker changes had higher baseline proportions of Faecalibacterium, Leuconostoc , and Odoribacter compared to corresponding non-responders. CONCLUSIONS & INFERENCES: Identifying patients with a more amenable microbiome at treatment initiation may result in better treatment response. |
Chronic intestinal spirochaetosis and Giardia lamblia infection mimicking eosinophilic enterocolitis.. Human intestinal spirochaetosis is caused by the colonisation of the luminal membrane of the colon and rectum by anaerobic spirochaetes belonging to the genus Brachyspira. The common method used for its diagnosis is routine haematoxylin and eosin staining of colonic and rectal biopsy samples. The clinical spectrum of human intestinal spirochaetosis is heterogeneous, ranging from asymptomatic colonisation to symptoms such as chronic mucosal diarrhoea, rectal bleeding, and abdominal pain. In this Grand Round, we present a detailed report of the endoscopic and histological evaluation and clinical and therapeutic management of an immunocompetent patient with chronic watery diarrhoea caused by intestinal spirochaetosis followed by infection with Giardia lamblia. The initial histological picture mimicked other causes of chronic diarrhoea, such as inflammatory bowel disease, microscopic colitis, and eosinophilic enterocolitis, leading to a delay in diagnosis and treatment. A full course of metronidazole led to the remission of symptoms and to the complete eradication of pathogens as shown by the follow-up histological assessment. This case report highlights the need to consider intestinal spirochaetosis in the differential diagnosis of chronic watery diarrhoea, even when immunodeficiency or other probable risk factors are not present. |
Human intestinal spirochetosis mimicking ulcerative colitis.. Human intestinal spirochetosis (HIS) is a colorectal infection caused by the Brachyspira species of intestinal spirochetes, whose pathogenicity in humans remains unclear owing to the lack of or mild symptoms. We monitored the 5-year clinical course of a woman diagnosed with HIS in whom ulcerative colitis (UC) had been suspected. Following a positive fecal occult blood test, she underwent a colonoscopic examination at a local clinic where she was diagnosed with "right-sided" UC concomitant with incidentally detected HIS, and was referred to our hospital. Colonoscopic, histopathological, and cytological examination revealed localized erosive colitis in the ascending and the right transverse colon concomitant with HIS resembling skip lesions of UC. Initially, we chose the wait-and-watch approach; however, she gradually developed bloody diarrhea. Metronidazole improved her abdominal symptoms, as well as her colonoscopic and histopathological findings, suggesting that HIS was responsible for her colorectal inflammation. This case reveals a possible pro-inflammatory role of HIS, difficulties in diagnosing HIS in chronic proctocolitis, and a possible inclusion of some HIS cases in "UC". HIS could mimic UC and might be included in differential diagnoses for UC. Antibiotic administration is necessary following the detection of HIS, particularly in patients demonstrating an atypical presentation of UC. |
Multi-omics analyses of serum metabolome, urine metabolome and gut microbiome reveal dysregulated glycerophospholipid metabolism in subacute cadmium-exposed wistar rats.. Data is limited on intestinal microbiota and metabolites in healthy residents exposed to cadmium (Cd), a population uniquely susceptible to Cd toxicity through contaminated foods. In this study, the 16 S rRNA gene sequencing, serum metabolomics and urine metabolomics were performed to examine the alterations of gut microbiota and metabolomics profile of wistar rats exposed to Cd. These findings indicated that Cd exposure markedly altered the structure of gut microbial community, reduced significantly microbiome diversity, and identified 5 phyla and 6 genera with significant changes. Specifically, the levels of Pseudoxanthomonas and Anaerovibrio upregulated and that of Akkermansia, Brachyspira, Aggregatibacter and SMB53 reduced in rats treated with Cd. Metabolomics profiles of the urine and serum of Cd-treated rats revealed that the abundance of glycerophospholipid metabolites and their derivatives were markedly altered. Glycerophospholipid metabolic pathways that were markedly enriched in metabolomics in both samples was also significantly predicted in gut microbiota analysis. Further, interaction analysis predicted that there might be a relationship between the differential glycerophospholipid metabolites and affected bacteria genera induced by Cd. These results suggested that subacute Cd could disrupt the intestinal microecologica equilibrium and glycerophospholipid metabolic homeostasis, and also provided potential differential microbiota and glycerophospholipid biomarkers between subacute Cd-exposed rats and healthy rats. |
Maternal fecal microbiome predicts gestational age, birth weight and neonatal growth in rural Zimbabwe.. BACKGROUND: Preterm birth and low birth weight (LBW) affect one in ten and one in seven livebirths, respectively, primarily in low-income and middle-income countries (LMIC) and are major predictors of poor child health outcomes. However, both have been recalcitrant to public health intervention. The maternal intestinal microbiome may undergo substantial changes during pregnancy and may influence fetal and neonatal health in LMIC populations. METHODS: Within a subgroup of 207 mothers and infants enrolled in the SHINE trial in rural Zimbabwe, we performed shotgun metagenomics on 351 fecal specimens provided during pregnancy and at 1-month post-partum to investigate the relationship between the pregnancy gut microbiome and infant gestational age, birth weight, 1-month length-, and weight-for-age z-scores using extreme gradient boosting machines. FINDINGS: Pregnancy gut microbiome taxa and metabolic functions predicted birth weight and WAZ at 1 month more accurately than gestational age and LAZ. Blastoscystis sp, Brachyspira sp and Treponeme carriage were high compared to Western populations. Resistant starch-degraders were important predictors of birth outcomes. Microbiome capacity for environmental sensing, vitamin B metabolism, and signalling predicted increased infant birth weight and neonatal growth; while functions involved in biofilm formation in response to nutrient starvation predicted reduced birth weight and growth. INTERPRETATION: The pregnancy gut microbiome in rural Zimbabwe is characterized by resistant starch-degraders and may be an important metabolic target to improve birth weight. FUNDING: Bill and Melinda Gates Foundation, UK Department for International Development, Wellcome Trust, Swiss Agency for Development and Cooperation, US National Institutes of Health, and UNICEF. |
An Investigation into the Etiological Agents of Swine Dysentery in Australian Pig Herds.. Swine dysentery (SD) is a mucohemorrhagic colitis, classically seen in grower/finisher pigs and caused by infection with the anaerobic intestinal spirochete Brachyspira hyodysenteriae. More recently, however, the newly described species Brachyspira hampsonii and Brachyspira suanatina have been identified as causing SD in North America and/or Europe. Furthermore, there have been occasions where strains of B. hyodysenteriae have been recovered from healthy pigs, including in multiplier herds with high health status. This study investigated whether cases of SD in Australia may be caused by the newly described species; how isolates of B. hyodysenteriae recovered from healthy herds compared to isolates from herds with disease; and how contemporary isolates compare to those recovered in previous decades, including in their plasmid gene content and antimicrobial resistance profiles. In total 1103 fecal and colon samples from pigs in 97 Australian herds were collected and tested. Of the agents of SD only B. hyodysenteriae was found, being present in 34 of the herds, including in 14 of 24 herds that had been considered to be free of SD. Multilocus sequence typing applied to 96 isolates from 30 herds and to 53 Australian isolates dating from the 1980s through the early 2000s showed that they were diverse, distinct from those reported in other countries, and that the 2014/16 isolates generally were different from those from earlier decades. These findings provided evidence for ongoing evolution of B. hyodysenteriae strains in Australia. In seven of the 20 herds where multiple isolates were available, two to four different sequence types (STs) were identified. Isolates with the same STs also were found in some herds with epidemiological links. Analysis of a block of six plasmid virulence-associated genes showed a lack of consistency between their presence or absence and their origin from herds currently with or without disease; however, significantly fewer isolates from the 2000s and from 2014/16 had this block of genes compared to isolates from the 1980s and 1990s. It is speculated that loss of these genes may have been responsible for the occurrence of milder disease occurring in recent years. In addition, fewer isolates from 2014/16 were susceptible to the antimicrobials lincomycin, and to a lesser extent tiamulin, than those from earlier Australian studies. Four distinct multi-drug resistant strains were identified in five herds, posing a threat to disease control. |
Gut microbiome alterations in patients with wheat-dependent exercise-induced anaphylaxis.. The intestinal microbiota plays a critical role in food allergy development. However, little is known regarding the structure and composition of the intestinal microbiota in patients with wheat-dependent exercise-induced anaphylaxis (WDEIA). We examined the gut microbiota alterations in patients with WDEIA and the microbiota's association with WDEIA. Fecal samples were collected from 25 patients with WDEIA and 25 healthy controls. Environmental exposure factors were obtained, serum total IgE, IgE specific to wheat, gluten, and ω-5 gliadin were measured. Fecal samples were profiled using 16S rRNA gene sequencing. The relative abundances of the bacterial genera Blautia , Erysipelatoclostridium , Akkermansia and Lachnospiraceae_NK4A136_group were significantly increased, while those of Lactobacillus and Dialister were significantly decreased in subjects with WDEIA. The microbial diversity did not differ between WDEIA patients and healthy controls. IgE specific to ω-5 gliadin was positively associated with the Oscillospira and negatively associated with Leuconostoc . Total IgE levels were significantly negatively correlated with Bifidobacterium . The gut microbiome compositions in WDEIA patients differed from those of healthy controls. We identified a potential association between the gut microbiome and WDEIA development. Our findings may suggest new methods for preventing and treating WDEIA. |
Dietary fibers with low hydration properties exacerbate diarrhea and impair intestinal health and nutrient digestibility in weaned piglets.. BACKGROUND: This study aimed to investigate the hydration properties of different-source fibrous materials by comparing their water-binding capacity (WBC), water swelling capacity (WSC), viscosity, and in vivo effects of selected samples on growth performance, nutrient digestibility, diarrhea, and intestinal health in weaned piglets. METHODS: A total of 13 commercially available fibrous materials were first compared in chemical composition and in vitro hydration property. Subsequently, 40 weaned piglets were randomized to five experimental dietary groups : control diet (a basal diet without dietary fiber, CON), basal diet supplemented with 5% microcrystalline cellulose (MCC), 5% wheat bran (WB), 5% Moringa oleifera leaf powder (MOLP), or 5% sugar beet pulp (SBP), followed by analyzing their growth performance and diarrhea rate in a 28-d experiment. After the feeding experiment, anaesthetized piglets were killed, and their intestinal and colon content or plasma samples were analyzed in nutrient digestibility, intestinal morphology, intestinal barrier, short-chain fatty acids (SCFAs), and bacterial population. RESULTS: In vitro studies showed low hydration properties for WB and MCC, while medium hydration properties for MOLP and SBP. In vivo studies indicated that compared with medium hydration property groups, low hydration property groups showed exacerbated diarrhea, impaired intestinal health, and reduced apparent fecal digestibility of dry matter, gross energy, acid detergent fiber, and neutral detergent fiber; decreased SCFAs concentration and relative levels of Lactobacillus and Bifidobacterium, but increased levels of Escherichia coli and Brachyspira hyodysenteriae in colon contents. Additionally, SBP showed optimal performance in reducing diarrhea and increasing SCFAs production. Correlation analysis revealed a positive correlation of fiber hydration properties with in vitro SCFAs production, and diarrhea index and nutrient digestibility were negatively and positively correlated with SCFAs levels in the colon contents of weaned piglets, respectively. CONCLUSIONS: Different-source dietary fibers varied in their hydration properties and impacts on diarrhea, microbial composition and SCFAs production in weaned piglets. WB and MCC could exacerbate diarrhea and impair nutrient digestibility, probably because their low hydration properties were detrimental to gut microbial homeostasis and fermentation. Our findings provide new ideas for rational use of fiber resources in weaned piglets. |
Consumption of a Leuconostoc holzapfelii-enriched synbiotic beverage alters the composition of the microbiota and microbial extracellular vesicles.. Synbiotics, the combination of probiotics and prebiotics, are known to confer health benefits via intestinal microbiota modulation. However, significant intestinal microbiota alterations can be difficult to determine in intervention studies based on solely bacterial stool metagenomic analysis. Intestinal microbiota constituents secrete 20-200-nm-sized extracellular vesicles (EVs) containing microbial DNA, proteins, and lipids that are distributed throughout the body, providing an alternative target for microbiota metagenomic analysis. Here, we determined the impact of a synbiotic beverage enriched with the kimchi-derived bacterium Leuconostoc holzapfelii (L. holzapfelii) on the intestinal microbiota and local and circulatory microbiota-derived EV composition of healthy Korean adults. We isolated microbial DNA from stool bacteria, stool EVs, and urinary EVs and conducted next-generation sequencing of the 16S rDNA V3-V4 regions before and after synbiotic consumption. The species diversity of circulating urinary EVs was significantly increased after synbiotic consumption, while stool bacterial and EV diversity remained unchanged. Furthermore, we found that while a single genus was decreased among the stool bacteria constituents, stool EVs and urinary EVs showed significant alterations in four and eight genera, respectively. Blood chemistry assays revealed that synbiotic consumption significantly lowered aspartate aminotransferase (AST) serum levels, particularly in subjects with starting levels above the normal range . In conclusion, the L. holzapfelii-enriched synbiotic beverage greatly altered serum AST levels and microbial EV composition in urine and stool, while only minor changes were observed in the gut microbiota composition. Based on these findings, we suggest the potential use of microbiota-derived EVs as surrogate markers in future predictive diagnosis studies. |
Probiotics for the Prevention of Pediatric Antibiotic-Associated Diarrhea.. UNLABELLED: Goldenberg JZ, Lytvyn L, Steurich J, Parkin P, Mahant S, Johnston BC. Probiotics for the prevention of pediatric antibiotic-associated diarrhea.Cochrane Database Syst Rev2015, Issue 12. Art. No.: CD004827. http://dx.doi.org/10.1002/14651858.CD004827.pub4. BACKGROUND: Antibiotics are frequently prescribed in children. They alter the microbial balance within the gastrointestinal tract, commonly resulting in antibiotic-associated diarrhea (AAD). Probiotics may prevent AAD via restoration of the gut microflora. OBJECTIVES: The primary objectives were to assess the efficacy and safety of probiotics (any specified strain or dose) used for the prevention of AAD in children. SEARCH METHODS: MEDLINE, EMBASE, CENTRAL, CINAHL, AMED, and the Web of Science were searched along with specialized registers including the Cochrane IBD/FBD review group, CISCOM (Centralized Information Service for Complementary Medicine), NHS Evidence, the International Bibliographic Information on Dietary Supplements, as well as trial registries. Letters were sent to authors of included trials, nutraceutical and pharmaceutical companies, and experts in the field requesting additional information on ongoing or unpublished trials. Conference proceedings, dissertation abstracts, and reference lists from included and relevant articles were also searched. SELECTION CRITERIA: Randomized, parallel, controlled trials in children receiving antibiotics, that compare probiotics to placebo, active alternative prophylaxis, or no treatment and measure the incidence of diarrhea secondary to antibiotic use were considered for inclusion. DATA COLLECTION AND ANALYSIS: Study selection, data extraction, and methodological quality assessment using the risk of bias instrument were conducted independently and in duplicate by two authors. Dichotomous data (incidence of diarrhea and adverse events) were combined using a pooled risk ratio (RR) or risk difference (RD), and continuous data (mean duration of diarrhea and mean daily stool frequency) as mean difference (MD), along with their corresponding 95% confidence interval . For overall pooled results on the incidence of diarrhea, sensitivity analyses included available case versus extreme-plausible analyses and random- versus fixed-effect models. To explore possible explanations for heterogeneity, a priori subgroup analysis was conducted on probiotic strain, dose, definition of antibiotic-associated diarrhea, and risk of bias. We also conducted post hoc subgroup analyses by patient diagnosis, single versus multi-strain, industry sponsorship, and inpatient status. The overall quality of the evidence supporting the outcomes was evaluated using the GRADE criteria. MAIN RESULTS: Overall, 23 studies met the inclusion criteria. Trials included treatment with either Bacillus spp., Bifidobacterium spp., Clostridium butyricum, Lactobacilli spp., Lactococcus spp., Leuconostoc cremoris, Saccharomyces spp., or Streptococcus spp., alone or in combination. Eleven studies used a single-strain probiotic, four combined two probiotic strains, three combined three probiotic strains, one combined four probiotic strains, two combined seven probiotic strains, one included ten probiotic strains, and one study included two probiotic arms that used three and two strains, respectively. The risk of bias was determined to be high or unclear in 13 studies and low in 10 studies. Available case (patients who did not complete the studies were not included in the analysis) results from 22/23 trials reporting on the incidence of diarrhea show a precise benefit from probiotics compared to active, placebo, or no treatment control. The incidence of AAD in the probiotic group was 8% compared to 19% in the control group . A GRADE analysis indicated that the overall quality of the evidence for this outcome was moderate. This benefit remained statistically significant in an extreme-plausible sensitivity analysis, where the incidence of AAD in the probiotic group was 14% compared to 19% in the control group . None of the 16 trials that reported on adverse events documented any serious adverse events attributable to probiotics. Meta-analysis excluded all but an extremely small non-significant difference in adverse events between treatment and control . The majority of adverse events were in placebo, standard care, or no treatment group. Adverse events reported in the studies include rash, nausea, gas, flatulence, abdominal bloating, abdominal pain, vomiting, increased phlegm, chest pain, constipation, taste disturbance, and low appetite. AUTHORS׳ CONCLUSIONS: Moderate quality evidence suggests a protective effect of probiotics in preventing AAD. Our pooled estimate suggests a precise probiotic effect with an NNT of 10. Among the various probiotics evaluated, Lactobacillus rhamnosus or Saccharomyces boulardii at 5-40 billion colony-forming units/day may be appropriate given the modest NNT and the likelihood that adverse events are very rare. It is premature to draw conclusions about the efficacy and safety of other probiotic agents for pediatric AAD. Although no serious adverse events were observed among otherwise healthy children, serious adverse events have been observed in severely debilitated or immunocompromised children with underlying risk factors including central venous catheter use and disorders associated with bacterial/fungal translocation. Until further research has been conducted, probiotic use should be avoided in pediatric populations at risk for adverse events. Future trials would benefit from a standard and valid outcomes to measure AAD. |
Composition of the gut microbiota in patients with inflammatory bowel disease in Saudi Arabia: A pilot study.. CONCLUSIONS: The results of this study provide an overview of the variations in microbiota diversity present in Saudi IBD patients compared to healthy controls. RESULTS: The key finding was three negative bacterial biomarkers, Paraprevotellaceae, the Muribaculaceae families of Bacteroidetes phylum, and the Leuconostocaceae family of Firmicutes phylum, which had a higher relative abundance in healthy individuals compared to IBD patients. It was also found that primary microbiota signatures at certain genera and species levels, including Prevotella copri, Bifidobacterium adolescentis, Ruminococcus callidus, Coprococcus sp., Ruminococcus gnavus, Dorea formicigenerans, Leuconostoc, Dialister, Catenibacterium, Eubacterium biforme, and Lactobacillus mucosae, were absent in almost all IBD patients, while Veillonella dispar was absent in all healthy individuals. METHODS: After obtaining an informed consent, fecal samples were collected from 11 participants with IBD (patients) and 10 healthy individuals (controls). The bacterial components of the microbial population were identified by next-generation sequencing of partial 16S rRNA. Statistically significant dissimilarities were observed between samples for all metrics. BACKGROUND: Inflammatory bowel disease (IBD) is a chronic intestinal inflammatory condition attributed to a complex interaction between imbalances in the gut microbiome, environmental conditions, and a deregulated immune response. The aim of the study was to investigate the composition of the gut microbiome of Saudi patients with IBD. |
Brassica rapa L. polysaccharide mitigates hypobaric hypoxia-induced oxidation and intestinal damage via microbiome modulation.. The high-altitude, low-pressure, and hypoxia environment poses a significant threat to human health, particularly causing intestinal damage and disrupting gut microbiota. This study investigates the protective effects of Brassica rapa L. crude polysaccharides (BRP) on intestinal damage in mice exposed to hypobaric hypoxic conditions. Results showed that oxidative stress and inflammation levels were elevated in the hypoxia group, while BRP intervention significantly increased antioxidant enzyme activities (SOD, GSH-Px, T-AOC) and reduced inflammatory markers . BRP also restored intestinal barrier function by enhancing claudin-1, occludin, and ZO-1 expression. Notably Chromatographic and metagenomic analyses revealed that BRP enriched butyrate levels, promoted beneficial bacteria like Akkermansia muciniphila and Leuconostoc lactis, and upregulated L-arginine biosynthesis II and L-methionine biosynthesis III pathways to enhance antioxidant activity. Fecal microbiota transfer experiments confirmed the role of gut microbiota in mediating BRP's protective effects, providing valuable insights into prebiotic-based therapeutic strategies for hypobaric hypoxia-induced intestinal damage. |
Effect of dietary nucleosides and yeast extracts on composition and metabolic activity of infant gut microbiota in PolyFermS colonic fermentation models.. Nucleotides (NT) and nucleosides (NS) are added to infant formula to mimic the content of breast milk, but little is known about their impact on infant gut microbiota. In this study, we tested the effect of NS and of yeast extracts (YE) with different NT content using PolyFermS continuous fermentation models mimicking formula-fed, healthy and enteropathogen-contaminated infant gut microbiota. Microbiota composition, short-chain fatty acid (SCFA) formation and gene expression were determined. NS, and to a larger extend YE modulated microbiota composition and increased metabolic activity in both models. Anaerococcus, Peptoniphilus, Fusobacterium, Lactobacillus/Pediococcus/Leuconostoc and Veillonella were enhanced when YE and/or NS were added. The production of SCFA increased with the level of supplied NT equivalents. Addition of NS and YE reduced colonization of Salmonella compared to control periods. Gene expression analysis confirmed taxonomical changes and indicated functional responses to YE. Transcripts related to NT and sulfur metabolism and iron acquisition increased while biosynthesis of co-factors and vitamins decreased after YE addition. Elevated butyrate formation correlated with increased transcripts encoding key enzymes of the two major butyrate synthesis pathways. Our results uncover a strong dose-dependent modulation of NS and YE on infant gut microbiota composition and metabolic activity. |
A diet of U.S. military food rations alters gut microbiota composition and does not increase intestinal permeability.. Interactions between gut microbes and dietary components modulate intestinal permeability (IP) and inflammation. Recent studies have reported altered fecal microbiota composition together with increased IP and inflammation in individuals consuming military food rations in austere environments, but could not isolate effects of the diet from environmental factors. To determine how the U.S. Meal, Ready-to-Eat food ration affects fecal microbiota composition, IP and inflammation, 60 adults were randomized to consume their usual ad libitum diet for 31 days (CON) or a strictly controlled Meal, Ready-to-Eat-only diet for 21 days followed by their usual diet for 10 days (MRE). In both groups, fecal microbiota composition was measured before, during and after the intervention period. IP and inflammation [high-sensitivity C-reactive protein (hsCRP)] were measured on days 0, 10, 21 and 31. Longitudinal changes in fecal microbiota composition differed between groups , and fecal samples collected from MRE during INT were identified with 88% accuracy using random forest models. The genera making the strongest contribution to that prediction accuracy included multiple lactic acid bacteria (Lactobacillus, Lactococcus, Leuconostoc), which demonstrated lower relative abundance in MRE, and several genera known to dominate the ileal microbiota (Streptococcus, Veillonella, Clostridium), the latter two demonstrating higher relative abundance in MRE. IP and hsCRP were both lower in MRE relative to CON on day 21 but did not differ otherwise. Findings demonstrate that a Meal, Ready-to-Eat ration diet alters fecal microbiota composition and does not increase IP or inflammation. |
Profile of gut microbiota and serum metabolites associated with metabolic syndrome in a remote island most afflicted by obesity in Japan.. Numerous studies have revealed distinct differences in the profiles of gut microbiota between non-obese and obese individuals. To date, however, little is known if any disparities in the community of gut microbiota exist between metabolically healthy obese (MHO) and metabolically unhealthy obese (MUO) subjects. We therefore aimed to comprehensively characterize the gut microbiota and circulating metabolites in serum from both MHO and MUO residing in the remote island, Kumejima, where the prevalence of obesity is one of the highest in Japan, and explored possible correlations between the gut microbiota profile and markers of metabolic syndrome. Results revealed that MUO showed significantly higher levels of genera such as g_Succinivibrio, g_Granulicatella, g_Brachyspira, g_Oribacterium and g_Atopobium in comparison to MHO. Moreover, abundance of g_Succinivibrio, g_Brachyspira and g_Atopobium were positively correlated with value of fasting insulin, HOMA-R, circulating triglycerides, diastolic blood pressure, BMI, body weight, waist circumference and HbA1c. In addition, MUO compared to MHO showed an imbalance of serum metabolites, with a significant elevation in 2-oxoisovaleric acid, pyruvic acid, 2-hydroxybutyric acid, and creatine. Our data highlight unmet needs in precision approaches for the treatment of obesity, targeting the gut microbiota profile and serum metabolites in a distinct population affected by obesity. |
Leucnostoc and Brachyspira Microbiome Findings
This dataset contains scientific findings about bacteria in the human gut microbiome in health and ulcerative colitis.
Dataset Structure
The dataset follows the same structure as TinyStories, with a single 'text' field containing scientific findings from research papers.
Example:
Metagenomic insights to understand the role of polluted river Yamuna in shaping the gut microbial communities of two invasive fish species.. The gastrointestinal microbial community plays a crucial role in host health, immunity, protection, development and provides nutrients to the host. The rising human-induced pollution and heavy metal contamination in all aquatic systems globally has led us to explore the gut microbial diversity of two exotic invasive fish Cyprinus carpio and Oreochromis nilo...
Dataset Creation
This dataset was created by extracting findings from PubMed abstracts focused on the role of bacteria in the human gut microbiome in health and ulcerative colitis. Only studies using human fecal/stool samples were included.
Usage
This dataset can be used to train models to understand the relationship between bacteria and human gut health.
from datasets import load_dataset
dataset = load_dataset("polejowska/microbiome-leuconostoc-brachyspira")
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