Gut Microbiota In Adults Research Articles

The Gut Microbiota in Mild Cognitive Impairment in Community‐Dwelling Older Adults in Taiwan

AbstractBackgroundRecent microbial studies of Alzheimer’s disease and mild cognitive impairment (MCI) have focused on the alterations of gut microbiota in cognitively impaired patients. However, related research remains limited and varies with analytical pipelines. This study aims to examine biodiversity and the differential abundance of gut flora in MCI.MethodThe study sample of 96 older adults was derived from a community‐based prospective cohort study, the Epidemiology of Mild Cognitive Impairment in Taiwan (EMCIT). Among them, 31 were ascertained as MCIs, matched with 65 cognitively normal individuals on age, gender and community. Fecal samples were analyzed by Illumina sequencing of the V3‐V4 regions of the 16S rRNA gene. The divisive amplicon denoising algorithm 2 (DADA2) pipeline was applied to the production of the amplicon sequence variant (ASV) table, and the SILVA database 138.1 was used to assign taxonomies.ResultThere is no significant difference in alpha‐ and beta‐ diversity between MCI and cognitively normal adults after adjusting for age, gender, community, education and hypertension. (Fig. 1). However, the results of linear discriminant analysis (LDA) effect size (LEfSe) showed a differential abundance of ASVs between two groups. Increased abundance of several genera within Firmicutes phylum and reduced abundance of Ruminococcus, Butyricimonas, Oxalobacter are associated with MCI. A ROC curve using these microbial genera of interest can distinguish MCI patients from controls with AUC = 84%. (Fig. 2)ConclusionCompared with cognitively normal older adults, the gut microbiota of older adults with MCI identified from the community was significantly altered, particularly manifesting in enriched genera from the Firmicutes phylum and decreased abundance of genera Ruminococcus, Butyricimonas, Oxalobacter.

Healthy adult gut microbiota sustains its own vitamin B12 requirement in an in vitro batch fermentation model.

Vitamin B12 (cobalamin) is present in the human lower gastrointestinal tract either coming from the unabsorbed dietary fraction or from in situ production of the gut microbiota. However, it is unclear whether the gut microbial communities need exogenous B12 for growth and metabolism, or whether B12 in low and high levels could affect gut community composition and metabolite production. Here, we investigated in vitro B12 production of human fecal microbiota and the effects of different levels of B12 (as cyanocobalamin) on composition and activity. Eight fecal communities from healthy human adults distributed over three enterotypes, dominated by Firmicutes (n = 5), Bacteroides (n = 1) or Prevotella (n = 2) were used to perform batch fermentations in Macfarlane medium supplemented with low B12 medium (Control, 5 ng/ml, within the tested fecal range), no B12 addition (NB12), and high B12 addition (ExtraB12, 2500 ng/ml). The microbiota community composition (qPCR, 16S rRNA metabarcoding), metabolic activity (HPLC-RI), and B12 levels (UHPLC-DAD) were measured after 24 h incubation at 37°C under strict anaerobic conditions. All fecal microbial communities produced B12 in the NB12 condition after 24 h, in the range from 152 ± 4 to 564 ± 25 ng/ml. None of the B12 treatments had an impact on total bacterial growth, community richness, diversity and total metabolite production, compared to the low B12 control. However, a significant increase of propionate was measured in ExtraB12 compared to NB12. Most taxonomic and metabolite changes compared to control incubations were donor-dependent, implying donor-microbiota-specific changes upon B12 treatments. Our in vitro data suggest that healthy human adult gut microbial communities have the capacity to produce B12 at levels fulfilling their own requirements, independently of the initial B12 content tested in the donor's feces. Further, supplementation of exogenous dietary B12 may have limited impact on the healthy human gut microbial community composition and function.

Association of body mass index and intestinal (faecal) Streptococcus in adults in Xining city, China P.R.

Body mass index (BMI) and gut microbiota show significant interaction, but most studies on the relationship between BMI and gut microbiota have been done in Western countries. Relationships that are also identified in other cultural backgrounds are likely to have functional importance. Hence here we explore gut microbiota in adults living in Xining city (China P.R.) and relate results to subject BMI. Analysis of bacterial 16s rRNA gene was performed on faecal samples from participants with normal-weight (n=24), overweight (n=24), obesity (n=11) and type 2 diabetes (T2D) (n=8). The results show that unweighted but not weighted Unifrac distance was significantly different when gut microbiota composition was compared between the groups. Importantly, the genus Streptococcus was remarkably decreased in both obese subjects and subjects suffering from T2D, as compared to normal-weight subjects. Accordingly, strong association was identified between the genus Streptococcus and BMI and especially Streptococcus salivarius subsp. thermophiles was a major contributor in this respect. As previous studies have shown that Streptococcus salivarius subsp. thermophiles is also negatively associated with obesity in Western cohorts, our results suggest that this species is a potential probiotic for the prevention of obesity and related disorders.

Rationale and study protocol for a randomized controlled feeding study to determine the structural- and functional-level effects of diet-specific interventions on the gut microbiota of non-Hispanic black and white adults

BackgroundColorectal cancer (CRC), the third leading cause of cancer-related deaths in the US, has been associated with an overrepresentation or paucity of several microbial taxa in the gut microbiota, but causality has not been established. Black men and women have among the highest CRC incidence and mortality rates of any racial/ethnic group. This study will examine the impact of the Dietary Approaches to Stop Hypertension (DASH) diet on gut microbiota and fecal metabolites associated with CRC risk. MethodsA generally healthy sample of non-Hispanic Black and white adults (n = 112) is being recruited to participate in a parallel-arm randomized controlled feeding study. Participants are randomized to receive the DASH diet or a standard American diet for a 28-day period. Fecal samples are collected weekly throughout the study to analyze changes in the gut microbiota using 16 s rRNA and selected metagenomics. Differences in bacterial alpha and beta diversity and taxa that have been associated with CRC (Bacteroides, Fusobacterium, Clostridium, Lactobacillus, Bifidobacterium, Ruminococcus, Porphyromonas, Succinivibrio) are being evaluated. Covariate measures include body mass index, comorbidities, medication history, physical activity, stress, and demographic characteristics. ConclusionOur findings will provide preliminary evidence for the DASH diet as an approach for cultivating a healthier gut microbiota across non-Hispanic Black and non-Hispanic White adults. These results can impact clinical, translational, and population-level approaches for modification of the gut microbiota to reduce risk of chronic diseases including CRC.Trial registration: This study was registered on ClinicalTrials.gov, identifier NCT04538482, on September 4, 2020 (https://clinicaltrials.gov/ct2/show/NCT04538482).

Sexual Dimorphism of the Gut Microbiota in the Chinese Alligator and Its Convergence in the Wild Environment.

The gut microbiota forms a complex microecosystem in vertebrates and is affected by various factors. As a key intrinsic factor, sex has a persistent impact on the formation and development of gut microbiota. Few studies have analyzed sexual dimorphism of gut microbiota, particularly in wild animals. We used 16S rRNA gene sequencing to analyze the gut microbiota of juvenile and adult Chinese alligators, and untargeted metabolomics to study serum metabolomes of adult alligators. We observed significant sexual differences in the community diversity in juvenile, but not adult, alligators. In terms of taxonomic composition, the phylum Fusobacteriota and genus Cetobacterium were highly abundant in adult alligators, similar to those present in carnivorous fishes, whereas the gut microbiota composition in juvenile alligators resembled that in terrestrial reptiles, indicating that adults are affected by their wild aquatic environment and lack sex dimorphism in gut microbiota. The correlation analysis revealed that the gut microbiota of adults was also affected by cyanobacteria in the external environment, and this effect was sex-biased and mediated by sex hormones. Overall, this study reveals sexual differences in the gut microbiota of crocodilians and their convergence in the external environment, while also providing insights into host–microbiota interactions in wildlife.

Variation in Gut Microbiota Composition is Associated with Sleep Quality and Cognitive Performance in Older Adults with Insomnia.

PurposeInsomnia, a chronic condition affecting 50% of older adults, is often accompanied by cognitive decline. The mechanism underlying this comorbidity is not fully understood. A growing literature suggests the importance of gut microbiota for brain function. We tested associations between sleep quality and cognitive performance with gut microbiota in older adults with insomnia.Patients and MethodsSeventy-two older adults with insomnia (age 73.2 ± 5.73 years, 56 females) provided stool samples for gut microbial sequencing. Microbiota profile was determined using the DADA2 bioinformatics pipeline. Cognition was assessed with the Cambridge Neuropsychological Test Automated Battery. Objective sleep quality was monitored by a two-week actigraphic recording, and participants completed the Insomnia Severity Index (ISI). We used partial canonical correspondence analysis (pCCA) to examine the relative contribution of insomnia, based on actigraphic sleep efficiency (SE) and ISI, and of cognitive status, based on the Multitasking test of Median Reaction Latency (MTTLMD) and the Spatial Working Memory Between Errors (SWMBE), to variance in microbiota composition. We used Pearson correlations to correlate insomnia and cognitive status parameters with microbiota amplicon sequence variants, genera, and families.ResultsThe pCCA revealed that sleep quality and cognitive performance explained a variation of 7.5–7.9% in gut microbiota composition in older adults with insomnia. Correlation analysis demonstrated that Lachnoclostridium (genus) correlates positively with SE (r=0.42; P=0.05) and negatively with MTTLMD (r=−0.29; P=0.03), whereas Blautia (genus) correlates negatively with MTTLMD (r=−0.31; P=0.01).ConclusionFindings demonstrate the associations of sleep quality and cognitive performance with variance in gut microbiota composition and with specific genus abundance in older adults with insomnia. Further studies should validate the findings, determine causal relationships, and evaluate potential interventions for the comorbidity of insomnia and cognitive impairment in older adults with insomnia.

A Cohort Study of the Effects of Daily-Diet Water-Soluble Dietary Fiber on Butyric Acid-Producing Gut Microbiota in Middle-Aged and Older Adults in a Rural Region.

Water-soluble dietary fiber is primarily a substrate for degradation of short chain fatty acids (SCFAs), particularly butyric acid, by gut microbiota. SCFAs have beneficial effects on the whole body. However, epidemiological studies on the association between water-soluble dietary fiber from daily food intake and butyric acid-producing bacteria are inconsistent. The purpose of this study was to determine the association between levels of water-soluble dietary fiber from daily food intake and gut microbiota, particularly butyric acid producers, in middle-aged and older adults in a rural area in Japan. We examined the effects of water-soluble dietary fiber intake on gut microbiota after adjusting for confounding factors. After propensity score matching, 520 subjects (260 in the low-intake group and 260 in the high-intake group) were selected. One year later after a follow-up survey, we re-classified the participants and again compared low- and high-intake groups. As a result, people with a high intake had a higher relative abundance of butyric acid-producing bacteria. It was also revealed that butyric acid-producing bacteria remained high in the group that maintained high intake the next year. We concluded that continuous intake of water-soluble dietary fiber from daily food is necessary to maintain sufficient amounts of butyric acid-producing bacteria.

The Nutritional Links for Gut Microbial Dysbiosis and its Metabolic and Endocrinal Fallouts

The Human Gut Microbiome: The gastro-intestinal tract, skin and genitals, and various other body organs, harbour large and diverse communities of bacteria, viruses, and other microscopic life. In the human gut, a nutrient-rich environment, reside ~ 100 trillion microbes, the vast majority of which is present in the colon. There inhabit microbial members as residents (autochthonous), while others (allochthonous) are from ingested food, water, and other components of the environment. The adult human gut microbiota is dominated by mainly two bacteria, the Bacteroidetes and Firmicutes, and an archea, Metanobrevibacter smithii. The microbial ecosystems throughout the body interact with the molecular processes, which have been linked to various aspects of human physiology. The understanding about microbiota is evolving and presents as an important research avenue. The Gut Biosphere and Ecosystem: In general, the gut microbial communities depend on their specific enzymes and molecules to utilize available nutrients, cell-surface molecular appendages to attach on to their right habitat, to evade bacteriophages, with ability to deal with immune system and avoid washout and genetic mutability to stay well-adapted. The microbiota influences various biological processes and organ physiology, including gastrointestinal processes, energy metabolism and insulin resistance, and thus influence weight gain, development of diabetes, and aging. The intestinal epithelium actively senses various bacteria and plays an essential role in maintaining host-microbial homeostasis at the mucosal interface. On the other hand, the host factors, such as dietary factors influence the host-microbial and microbial-microbial relationships. Microbiota, Health and Disease States: The evidence from clinical studies and animal models shows a link between the gut microbiome and human health. There exists a bidirectional microbiota–gut–brain communication which modulates brain function and behaviours. The research in mice and humans is beginning to establish a link between the composition of microbes in the gut and immune response to tumor cells. Certain metabolites or antigens presented by members of that microbiome may help uplift the sensitivity of immune system to tumour cells, whereas dysbiosis may lead to the loss of antitumor immunity. On the other hand, the gut microbes harbour enzymes and secrete molecules that can influence drug activation, efficacy, and metabolism. Dietary Constituents and Microbiome: The dietary components influence the gut microbiota. It has been documented that a change in diet can alter the degradative activity of the colonic microbiota in vivo and in a physiologically relevant setting influence the expression of various microbial genes. The complex plant polysaccharides in diet are not digested and enter the colon as a potential food source for the gut microorganisms, which harbour a multitude of genes involved in catabolism of carbohydrates. The reduced availability of dietary polysaccharides and fibre can trigger dysbiosis and degradation of intestinal mucin layer and affect intestinal health. The microbial production of short chain fatty acids and other metabolites has been shown to influence immune system.

Green tea extract alters gut microbiota and their metabolism of adults with metabolic syndrome in a host-free human colonic model

BackgroundMetabolic syndrome (MetS) is a common metatoblic disorder that leads to various adverse health outcomes such as diabetes and cardiovascular diseases (CVDs). Recent studies suggested that MetS-associated gut dysbiosis could exacerbate MetS related diseases. Green tea, a popular beverage rich in polyphenols, has showed antioxidant and anti-inflammatory effects in treating MetS through gut modulation. ObjectivesThis study aimed to understand the impact of green tea extract (GTE) on the composition and metabolism of gut microbiota from people with MetS. MethodsWe utilized an in-vitro human colonic model (HCM) to specifically investigate the host-free interactions between GTE and gut microbiota of MetS adults. Fresh fecal samples donated by three adults with MetS were used as gut microbe inoculum in our HCM system. 16S ribosomal RNA sequencing and liquid-chromatography mass spectrometry (LC/MS) combined with QIIME 2, Compound Discoverer 3.1 and MetaboAnalyst 4.0 based data analyses were performed to show the regulating effects of GTE treatment on gut microbial composition and their metabolism. ResultsOur data suggested that GTE treatment in HCM system modified composition of MetS gut microbiota at genus level and led to significant microbiota metabolic profile change.Bioinformatics analysis showed relative abundance of Escherichia and Klebsiella was commonly increased while Bacteroides, Citrobacter, and Clostridium were significantly reduced. All free fatty acids detected were significantly increased in different colon sections. Lipopolysaccharide biosynthesis, methane metabolism, pentose phosphate pathway, purine metabolism, and tyrosine metabolism were regulated by GTE in MetS gut microbiota. In addition, we identified significant associations between altered microbes and microbial metabolites. ConclusionsOverall, our study revealed the impact of GTE treatment on gut microbiota composition and metabolism changes in MetS microbiota in vitro, which may provide information for further mechanistic investigation of GTE in modulating gut dysbiosis in MetS.

Effect of aging on acute pancreatitis through gut microbiota.

BackgroundCompared to younger people, older people have a higher risk and poorer prognosis of acute pancreatitis, but the effect of gut microbiota on acute pancreatitis is still unknown. We aim to investigate the effect of aging gut microbiota on acute pancreatitis and explore the potential mechanism of this phenomenon.MethodsEighteen fecal samples from healthy adult participants, including nine older and nine younger adults were collected. C57BL/6 mice were treated with antibiotics for fecal microbiota transplantation from older and younger participants. Acute pancreatitis was induced by cerulein and lipopolysaccharide in these mice. The effect of the aged gut microbiota was further tested via antibiotic treatment before or after acute pancreatitis induction.ResultsThe gut microbiota of older and younger adults differed greatly. Aged gut microbiota exacerbated acute pancreatitis during both the early and recovery stages. At the same time, the mRNA expression of multiple antimicrobial peptides in the pancreas and ileum declined in the older group. Antibiotic treatment before acute pancreatitis could remove the effect of aging gut microbiota, but antibiotic treatment after acute pancreatitis could not.ConclusionAging can affect acute pancreatitis through gut microbiota which characterizes the deletion of multiple types of non-dominant species. This change in gut microbiota may potentially regulate antimicrobial peptides in the early and recovery stages. The level of antimicrobial peptides has negative correlations with a more severe phenotype.

The microbiome and gut homeostasis.

Changes in the composition of the gut microbiota are associated with many human diseases. So far, however, we have failed to define homeostasis or dysbiosis by the presence or absence of specific microbial species. The composition and function of the adult gut microbiota is governed by diet and host factors that regulate and direct microbial growth. The host delivers oxygen and nitrate to the lumen of the small intestine, which selects for bacteria that use respiration for energy production. In the colon, by contrast, the host limits the availability of oxygen and nitrate, which results in a bacterial community that specializes in fermentation for growth. Although diet influences microbiota composition, a poor diet weakens host control mechanisms that regulate the microbiota. Hence, quantifying host parameters that control microbial growth could help define homeostasis or dysbiosis and could offer alternative strategies to remediate dysbiosis.

Effects of Adding Lean Red Meat to A Vegetarian Diet on Gut Microbiota in Young Adults: A Randomized Controlled Trial

ObjectivesDiet strongly affects human metabolic health, partly by modulating gut microbiota. To date, limited research has assessed the effects of different types of red meat on gut microbiota in human adults. We aim to assess the effects of consuming a healthy US-style eating pattern, without or with unprocessed or processed lean red meats (LRM), on gut microbiota in generally healthy young adults. Secondary outcomes are fecal short-chain fatty acids (SCFAs) and cardiovascular risk factors.MethodsWe conducted a randomized-controlled, crossover trial with three 3-week dietary interventions, each separated by a 5-week washout with a habitual diet. Five females and 7 males (age 26.5 ± 1.5 years old, BMI 23.7 ± 0.9 kg/m2) consumed the following three diets in random order: a healthy lacto-ovo vegetarian diet (LOV), the LOV diet with 3 oz/day of cooked unprocessed LRM, or with 3 oz/day of cooked processed LRM. Fecal and blood samples were collected before and during the last 2 weeks of each diet. We measured changes in fecal microbial community structure using 16S amplicon sequencing targeting the V4 region (primers 515F-806R). Community diversity, structure, and taxonomic composition were computed using mothur v.1.39.3.ResultsAfter consuming a healthy vegetarian diet without or with adding unprocessed or processed LRM, community diversity and structure of gut microbiota were not significantly altered at the phylum level. However, the diets differentially affected bacterial abundances (2 of 14 families and 5 of 42 genera) with varied directionality. Adopting the prescribed healthy eating pattern for 3 weeks did not influence fecal SCFA contents, serum HDL-C or triglycerides concentrations, or blood pressures. Serum total cholesterol and LDL-C concentrations were reduced by diet, independent of LRM intake.ConclusionsThese results suggest adding three ounces per day of unprocessed or processed lean red meats to a healthy vegetarian diet that improved blood lipids and lipoproteins in the short term does not influence the overall gut microbial composition but may influence the abundances of specific families or genera. Further research is warranted to assess potential effects of red meat on gut bacteria.Funding SourcesThe Pork Checkoff, North Dakota Beef Commission, Beef Checkoff, and Foundation for Meat and Poultry Research and Education.

Red Raspberry and Fructo-Oligosaccharide Supplementation, Metabolic Biomarkers, and the Gut Microbiota in Adults with Prediabetes: A Randomized Crossover Clinical Trial

BackgroundEvidence suggests that the gut microbiota and cardiometabolic status are associated, suggesting dietary interventions that alter the microbiota may affect metabolic health. ObjectivesWe investigated whether supplementation with (poly)phenol-dense red raspberries (RRB), alone or with a fructo-oligosaccharide (FOS) prebiotic, would improve biomarkers of cardiometabolic risk in individuals with prediabetes (PreDM) and insulin resistance (IR) and whether the effects are related to modulation of the gut microbiota. MethodsAdults with PreDM-IR (n = 26; mean ± SEM age, 35 ± 2 years; fasting glucose, 5.7 ± 0.1 mmol/L; HOMA-IR, 3.3 ± 0.3) or who were metabolically healthy (reference group; n = 10; age, 31 ± 3 years; fasting glucose, 5.1 ± 0.2 mmol/L; HOMA-IR, 1.1 ± 0.1) participated in a randomized crossover trial with two 4-week supplementation periods, in which they consumed either RRB (125 g fresh equivalents) daily or RRB + 8g FOS daily, separated by a 4-week washout. The primary outcome variable was the change in the gut microbiota composition, assessed by shotgun sequencing before (baseline) and at the end of each supplementation period. Secondary outcomes were changes in glucoregulation, lipid metabolism, anti-inflammatory status, and anthropometry. The trial is registered at ClinicalTrials.gov, NCT03049631. ResultsIn PreDM-IR, RRB supplementation reduced hepatic-IR (−30.1% ± 14.6%; P = 0.04) and reduced plasma total and LDL cholesterol [−4.9% ± 1.8% (P = 0.04) and −7.2% ± 2.3% (P = 0.003), respectively] from baseline. Adding FOS (RRB + FOS) improved β-cell function [insulin secretion rate, +70.2% ± 32.8% (P = 0.02); Disposition Index, +94.4% ± 50.2% (P = 0.04)], but had no significant effect on plasma cholesterol compared to baseline. RRB increased Eubacterium eligens (2-fold) and decreased Ruminococcus gnavus (−60% ± 34%), whereas RRB + FOS increased Bifidobacterium spp. (4-fold) and decreased Blautia wexlerae (−23% ± 12%) from baseline (all P values ≤ 0.05). R. gnavus was positively correlated with hepatic-IR, and E. eligens and Bifidobacterium catenulatum were negatively correlated with cholesterol concentrations (P ≤ 0.05). ConclusionsIncreased Bifidobacterium spp., concurrently with reduced R. gnavus, was associated with metabolic improvements in adults with PreDM-IR, warranting further research on the mechanisms involved in (poly)phenol/FOS-microbial interactions with host metabolism.

Making a meal out of bugs

Making a meal out of bugs

Composition and Diversity of Gut Bacterial Community in Different Life Stages of a Leaf Beetle Gastrolina depressa.

Insect gut bacteria have a significant impact on host biology, which has a favorable or negative impact on insect fitness. The walnut leaf beetle (Gastrolina depressa) is a notorious pest in China, causing severe damage to Juglandaceae trees including Juglans regia and Pterocarya rhoifolia. To date, however, we know surprisingly little about the gut microbiota of G. depressa. This study used a high-throughput sequencing platform to investigate the gut bacterial community of G. depressa throughout its life cycle, including the 1st, 2nd, and 3rd instar larvae, as well as male, female, and pre-pregnant female adults. Our results showed that the diversity of the gut bacterial community in larvae was generally higher than that in adults, and young larvae (1st and 2nd larvae) possessed the most diversified and abundant community. Principal coordinate analysis results showed that the gut microbiota of adults cluster together, which is independent of the 1st and 2nd instar larvae. The main phyla were Proteobacteria and Firmicutes in the microbial community of G. depressa, while the dominant genera were Enterobacter, Rosenbergiella, Erwinia, Pseudomonas, and Lactococcus. The gut bacteria of G. depressa were mostly enriched in metabolic pathways (carbohydrate metabolism and amino acid metabolism) as revealed by functional prediction. This study contributes to a better knowledge of G. depressa's gut microbiota and its potential interactions with the host insect, facilitating the development of a microbial-based pest management strategy.

Adaptation of the gut pathobiont Enterococcus faecalis to deoxycholate and taurocholate bile acids

Enterococcus faecalis is a natural inhabitant of the human gastrointestinal tract. This bacterial species is subdominant in a healthy physiological state of the gut microbiota (eubiosis) in adults, but can become dominant and cause infections when the intestinal homeostasis is disrupted (dysbiosis). The relatively high concentrations of bile acids deoxycholate (DCA) and taurocholate (TCA) hallmark eubiosis and dysbiosis, respectively. This study aimed to better understand how E. faecalis adapts to DCA and TCA. We showed that DCA impairs E. faecalis growth and possibly imposes a continuous adjustment in the expression of many essential genes, including a majority of ribosomal proteins. This may account for slow growth and low levels of E. faecalis in the gut. In contrast, TCA had no detectable growth effect. The evolving transcriptome upon TCA adaptation showed the early activation of an oligopeptide permease system (opp2) followed by the adjustment of amino acid and nucleotide metabolisms. We provide evidence that TCA favors the exploitation of oligopeptide resources to fuel amino acid needs in limiting oligopeptide conditions. Altogether, our data suggest that the combined effects of decreased DCA and increased TCA concentrations can contribute to the rise of E. faecalis population during dysbiosis.

Neonatal immune challenge influences the microbiota and behaviour in a sexually dimorphic manner

There is comorbidity between anxiety disorders and gastrointestinal disorders, with both linked to adverse early life events. The microbiome gut-brain-axis, a bidirectional communication system, is plastic throughout the neonatal period and is a possible mediator of this relationship. Here, we used a well-established neonatal rodent immune activation model to investigate the long-term effect of neonatal lipopolysaccharide (LPS) exposure on adult behaviour and the relationship to microbiome composition. Wistar rats were injected with LPS (0.05 mg/kg) or saline (equivolume) on postnatal days 3 and 5. In adulthood, behavioural tests were performed to assess anxiety-like behaviour, and microbiota sequencing was performed on stool samples. There were distinctly different behavioural phenotypes for LPS-exposed males and females. LPS-exposed males displayed typical anxiety-like behaviours with significantly decreased social interaction (F(1,22) = 7.576, p = 0.009) and increased defecation relative to saline controls (F(1,23) = 8.623, p = 0.005). LPS-exposed females displayed a different behavioural phenotype with significantly increased social interaction (F(1,22) = 6.094, p = 0.018), and exploration (F(1,24) = 6.359, p = 0.015), compared to saline controls. With respect to microbiota profiling data, Bacteroidota was significantly increased for LPS-exposed females (F(1,14) = 4.931p = 0.035) and Proteobacteria was decreased for LPS-exposed rats of both sexes versus controls (F(1,30) = 4.923p = 0.035). Furthermore, alterations in predicted functional pathways for neurotransmitters in faeces were observed with a decrease in the relative abundance of D-glutamine and D-glutamate metabolism in LPS exposed females compared to control females (p < 0.05). This suggests that neonatal immune activation alters both later life behaviour and adult gut microbiota in sex-specific ways. These findings highlight the importance of sex in determining the impact of neonatal immune activation on social behaviour and the gut microbiota.

Pectin with various degrees of esterification differentially alters gut microbiota and metabolome of healthy adults

AbstractPectin with various degrees of esterification (DE) leads to different food processing directions and has the distinct potential for modulating human health. Investigations of pectin–gut microbiota interactions may contribute towards better understanding of the structure–function mechanism. In this study, in vitro batch fermentation (artificial colon model) was used to illustrate the differential impacts of pectin with different DE on the gut microbiota and metabolome of healthy adults. The results indicated that low‐esterified pectin L13 showed better‐sustained abilities in terms of the diversity of microbiota and promoted the abundance of Clostridiaceae and Lachnospiraceae at family levels, and Bacteroides and Lachnospira at genus levels. High‐esterified pectin H121 induced less Enterococcus and Clostridium. Data from untargeted metabolomics revealed the alterations of intracellular metabolites including fatty acids, amino acids, and organic molecules by various types of pectins. Inositol was the unique intracellular metabolite that was significantly upregulated by low‐esterified pectin L13. All types of pectins could increase the level of acetic acid, but butyric acid was only enriched by pectin L13.

Association between residential greenness and gut microbiota in Chinese adults

BackgroundA growing body of studies have reported the health benefits of greenness. However, less is known about the potential beneficial effects of residential greenness on gut microbiota, which is essential to human health. In this study, we aim to examine the association between residential greenness and gut microbiota in a population-based cohort study. MethodsWe included 1758 participants based on the China Multi-Ethnic Cohort (CMEC) study and collected their stool samples for 16S sequencing to derive gut microbiota data. Residential greenness was estimated using the satellite-based data on enhanced vegetation index (EVI) and the normalized differential vegetation index (NDVI) in circular buffers of 250 m, 500 m, and 1000 m. The relationships between residential greenness levels and the composition of gut microbiota, measured by standardized α-diversity and taxonomic composition, were assessed using linear regression and Spearman correlation weighted by generalized propensity scores. ResultsHigher greenness levels were significantly positively associated with standardized α-diversity. Per interquartile range (IQR) increase of EVI and NDVI in the circular buffer of 250 m were associated with the increments of 0.995(95% confidence interval (CI): 0.212–1.778) and 0.653(95% CI: 0.160–1.146) in the standardized Shannon index. For the taxonomic composition of gut microbiota, higher greenness levels were significantly correlated with 29 types of microbial taxonomic composition. NDVI in the circular buffer of 250 m was associated with increased Firmicutes (r = 0.102, adjusted p value = 0.004), which was the dominant composition in the gut microbiota. ConclusionsIncreased amounts of residential greenness may support healthy gut microbiota by benignly altering their composition. These findings suggested that green spaces should be designed to support diverse gut microbiota and ultimately optimize health benefits.

Metagenomic strain detection with SameStr: identification of a persisting core gut microbiota transferable by fecal transplantation

BackgroundThe understanding of how microbiomes assemble, function, and evolve requires metagenomic tools that can resolve microbiota compositions at the strain level. However, the identification and tracking of microbial strains in fecal metagenomes is challenging and available tools variably classify subspecies lineages, which affects their applicability to infer microbial persistence and transfer.ResultsWe introduce SameStr, a bioinformatic tool that identifies shared strains in metagenomes by determining single-nucleotide variants (SNV) in species-specific marker genes, which are compared based on a maximum variant profile similarity. We validated SameStr on mock strain populations, available human fecal metagenomes from healthy individuals and newly generated data from recurrent Clostridioides difficile infection (rCDI) patients treated with fecal microbiota transplantation (FMT). SameStr demonstrated enhanced sensitivity to detect shared dominant and subdominant strains in related samples (where strain persistence or transfer would be expected) when compared to other tools, while being robust against false-positive shared strain calls between unrelated samples (where neither strain persistence nor transfer would be expected). We applied SameStr to identify strains that are stably maintained in fecal microbiomes of healthy adults over time (strain persistence) and that successfully engraft in rCDI patients after FMT (strain engraftment). Taxonomy-dependent strain persistence and engraftment frequencies were positively correlated, indicating that a specific core microbiota of intestinal species is adapted to be competitive both in healthy microbiomes and during post-FMT microbiome assembly. We explored other use cases for strain-level microbiota profiling, as a metagenomics quality control measure and to identify individuals based on the persisting core gut microbiota.ConclusionSameStr provides for a robust identification of shared strains in metagenomic sequence data with sufficient specificity and sensitivity to examine strain persistence, transfer, and engraftment in human fecal microbiomes. Our findings identify a persisting healthy adult core gut microbiota, which should be further studied to shed light on microbiota contributions to chronic diseases.Bmxg3NA25n3myfWhCsfsJVVideo abstract