Taxonomic Composition Of Gut Microbiota Research Articles

The Interplay between Gut Microbiota and Cognitive Functioning in the Healthy Aging Population: A Systematic Review.

The gut microbiota in healthy older individuals typically show a decrease in beneficial bacteria like Bifidobacterium and Lactobacillus, alongside an increase in pro-inflammatory microbes such as Enterobacteriaceae and Clostridia. These changes contrast with younger and middle-aged individuals and appear to correlate with cognitive status. Although there is extensive research on gut microbiota and cognitive functions in cognitively impaired elderly individuals, its impact on cognitively healthy elderly populations has not been extensively studied. A comprehensive literature search was conducted across PubMed, EBSCO, Web of Science, and Scopus databases to identify studies exploring the relationship between gut microbiota composition and cognitive functioning in healthy older adults. During the literature screening process, each record was initially assessed by its title, abstract, and keywords to exclude articles that did not align with the scope of this review. Three authors independently screened and retrieved the records. The inclusion criteria included: (1) publication in peer-reviewed journals; (2) studies involving neurologically, cognitively, and medically healthy populations; (3) participants identified as older adults, defined for this review as individuals aged 45 years and older due to the limited number of records; (4) analysis of gut microbiota; and (5) assessment of cognitive function. Subsequently, full texts were analyzed to determine eligibility. The exclusion criteria encompassed: (1) incorrect publication type; (2) inappropriate sample population; (3) unsuitable study design; (4) absence of one or more inclusion criteria; and (5) studies based on animal research. A risk of bias assessment was performed for each included study using the Joanna Briggs Institute (JBI) checklist, ensuring all selected studies met established quality standards. A total of 6 eligible research articles from a possible 1752 published until March 2024 were identified and included. We categorized the included studies into two groups based on their focus: the taxonomic composition of gut microbiota and the alpha diversity, which is the variety of organisms within a sample. Additionally, two methods were identified for assessing cognition: neuropsychological tests and physiological measurements, notably electroencephalography (EEG). The studies show varying results regarding the abundance of specific bacterial taxa and their cognitive associations. Notably, the relationship between certain bacteria and cognition may vary when analyzed at different taxonomic levels, such as phylum versus family. Changes in gut microbiota composition in the elderly, even without a cognitive impairment diagnosis, could potentially serve as early biological markers for Alzheimer's disease or other dementias before mild cognitive impairment appears.

Layer chicken microbiota: a comprehensive analysis of spatial and temporal dynamics across all major gut sections

BackgroundThe gut microbiota influences chicken health, welfare, and productivity. A diverse and balanced microbiota has been associated with improved growth, efficient feed utilisation, a well-developed immune system, disease resistance, and stress tolerance in chickens. Previous studies on chicken gut microbiota have predominantly focused on broiler chickens and have usually been limited to one or two sections of the digestive system, under controlled research environments, and often sampled at a single time point. To extend these studies, this investigation examined the microbiota of commercially raised layer chickens across all major gut sections of the digestive system and with regular sampling from rearing to the end of production at 80 weeks. The aim was to build a detailed picture of microbiota development across the entire digestive system of layer chickens and study spatial and temporal dynamics.ResultsThe taxonomic composition of gut microbiota differed significantly between birds in the rearing and production stages, indicating a shift after laying onset. Similar microbiota compositions were observed between proventriculus and gizzard, as well as between jejunum and ileum, likely due to their anatomical proximity. Lactobacillus dominated the upper gut in pullets and the lower gut in older birds. The oesophagus had a high proportion of Proteobacteria, including opportunistic pathogens such as Gallibacterium. Relative abundance of Gallibacterium increased after peak production in multiple gut sections. Aeriscardovia was enriched in the late-lay phase compared to younger birds in multiple gut sections. Age influenced microbial richness and diversity in different organs. The upper gut showed decreased diversity over time, possibly influenced by dietary changes, while the lower gut, specifically cecum and colon, displayed increased richness as birds matured. However, age-related changes were inconsistent across all organs, suggesting the influence of organ-specific factors in microbiota maturation.ConclusionAddressing a gap in previous research, this study explored the microbiota across all major gut sections and tracked their dynamics from rearing to the end of the production cycle in commercially raised layer chickens. This study provides a comprehensive understanding of microbiota structure and development which help to develop targeted strategies to optimise gut health and overall productivity in poultry production.

Association between Taxonomic Composition of Gut Microbiota and Host Single Nucleotide Polymorphisms in Crohn's Disease Patients from Russia.

Crohn's disease (CD) is a chronic relapsing inflammatory bowel disease of unknown etiology. Genetic predisposition and dysbiotic gut microbiota are important factors in the pathogenesis of CD. In this study, we analyzed the taxonomic composition of the gut microbiota and genotypes of 24 single nucleotide polymorphisms (SNP) associated with the risk of CD. The studied cohorts included 96 CD patients and 24 healthy volunteers from Russia. Statistically significant differences were found in the allele frequencies for 8 SNPs and taxonomic composition of the gut microbiota in CD patients compared with controls. In addition, two types of gut microbiota communities were identified in CD patients. The main distinguishing driver of bacterial families for the first community type are Bacteroidaceae and unclassified members of the Clostridiales order, and the second type is characterized by increased abundance of Streptococcaceae and Enterobacteriaceae. Differences in the allele frequencies of the rs9858542 (BSN), rs3816769 (STAT3), and rs1793004 (NELL1) were also found between groups of CD patients with different types of microbiota communities. These findings confirm the complex multifactorial nature of CD.

Invited review: Effect of subacute ruminal acidosis on gut health of dairy cows.

Subacute ruminal acidosis (SARA) is assumed to be a common disease in high-yielding dairy cows. Despite this, the epidemiological evidence is limited by the lack of survey data. The prevalence of SARA has mainly been determined by measuring the pH of ruminal fluid collected using rumenocentesis. This may not be sufficiently accurate, because the symptoms of SARA are not solely due to ruminal pH depression, and ruminal pH varies among sites in the rumen, throughout a 24-h period, and among days. The impact of SARA has mainly been studied by conducting SARA challenges in cows, sheep, and goats based on a combination of feed restriction and high-grain feeding. The methodologies of these challenges vary considerably among studies. Variations include differences in the duration and amount of grain feeding, type of grain, amount and duration of feed restriction, number of experimental cows, and sensitivity of cows to SARA challenges. Grain-based SARA challenges affect gut health. These effects include depressing the pH in, and increasing the toxin content of, digesta. They also include altering the taxonomic composition of microbiota, reducing the functionality of the epithelia throughout the gastrointestinal tract (GIT), and a moderate inflammatory response. The effects on the epithelia include a reduction in its barrier function. Effects on microbiota include reductions in their richness and diversity, which may reduce their functionality and reflect dysbiosis. Changes in the taxonomic composition of gut microbiota throughout the GIT are evident at the phylum level, but less evident and more variable at the genus level. Effects at the phylum level include an increase in the Firmicutes to Bacteroidetes ratio. More studies on the effects of a SARA challenge on the functionality of gut microbiota are needed. The inflammatory response resulting from grain-based SARA challenges is innate and moderate and mainly consists of an acute phase response. This response is likely a combination of systemic inflammation and inflammation of the epithelia of the GIT. The systemic inflammation is assumed to be caused by translocation of immunogenic compounds, including bacterial endotoxins and bioamines, through the epithelia into the interior circulation. This translocation is increased by the increase in concentrations of toxins in digesta and a reduction of the barrier function of epithelia. Severe SARA can cause rumenitis, but moderate SARA may activate an immune response in the epithelia of the GIT. Cows grazing highly fermentable pastures with high sugar contents can also have a low ruminal pH indicative of SARA. This is not accompanied by an inflammatory response but may affect milk production and gut microbiota. Grain-based SARA affects several aspects of gut health, but SARA resulting from grazing high-digestible pastures and insufficient coarse fiber less so. We need to determine which method for inducing SARA is the most representative of on-farm conditions.

Association between residential greenness and gut microbiota in Chinese adults.

A 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. We 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 250m, 500m, and 1000m. 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. Higher greenness levels were significantly positively associated with standardized α-diversity. Per interquartile range (IQR) increase of EVI and NDVI in the circular buffer of 250m 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 250m was associated with increased Firmicutes (r=0.102, adjusted p value=0.004), which was the dominant composition in the gut microbiota. Increased 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.

Gut microbiota profile in patients with nonalcoholic fatty liver disease and presumed nonalcoholic steatohepatitis.

Background:The main composition of intestinal microbiota in nonalcoholic fatty liver disease (NAFLD) and nonalcoholic steatohepatitis (NASH) patients has not yet been elucidated. In this, case-control study, we identified differences of intestinal microbiota in male patients with NAFLD, presumed NASH, and healthy controls.Materials and Methods:We compared gut microbial composition of 25 patients with NAFLD, 13 patients with presumed NASH, and 12 healthy controls. Demographic information as well as clinical, nutritional, and physical activity data was gathered. Stool and blood samples were collected to perform the laboratory analysis. The taxonomic composition of gut microbiota was assessed using V4 regions of microbial small subunit ribosomal Ribonucleic acid genes sequencing of stool samples.Results:Firmicutes, Actinobacteria, and Bacteroidetes were the most frequently phyla in all groups. Our results revealed that Veillonella was the only genus with significantly different amounts in presumed NASH patients compared with patients with NAFLD (P = 2.76 × 10−6, q = 2.07 × 10−4, logFC = 5.52).Conclusion:This pilot study was the first study to compare gut microbial composition in patients with NAFLD and presumed NASH in the Middle East. Given the potential effects of gut microbiota on the management and prevention of NAFLD, larger, prospective studies are recommended to confirm this study's findings.

Lung and Gut Microbiota Changes Associated with Pseudomonas aeruginosa Infection in Mouse Models of Cystic Fibrosis.

Cystic fibrosis (CF) disease leads to altered lung and gut microbiomes compared to healthy subjects. The magnitude of this dysbiosis is influenced by organ-specific microenvironmental conditions at different stages of the disease. However, how this gut-lung dysbiosis is influenced by Pseudomonas aeruginosa chronic infection is unclear. To test the relationship between CFTR dysfunction and gut-lung microbiome under chronic infection, we established a model of P. aeruginosa infection in wild-type (WT) and gut-corrected CF mice. Using 16S ribosomal RNA gene, we compared lung, stool, and gut microbiota of C57Bl/6 Cftr tm1UNCTgN(FABPCFTR) or WT mice at the naïve state or infected with P. aeruginosa. P. aeruginosa infection influences murine health significantly changing body weight both in CF and WT mice. Both stool and gut microbiota revealed significantly higher values of alpha diversity in WT mice than in CF mice, while lung microbiota showed similar values. Infection with P. aeruginosa did not changed the diversity of the stool and gut microbiota, while a drop of diversity of the lung microbiota was observed compared to non-infected mice. However, the taxonomic composition of gut microbiota was shown to be influenced by P. aeruginosa infection in CF mice but not in WT mice. This finding indicates that P. aeruginosa chronic infection has a major impact on microbiota diversity and composition in the lung. In the gut, CFTR genotype and P. aeruginosa infection affected the overall diversity and taxonomic microbiota composition, respectively. Overall, our results suggest a cross-talk between lung and gut microbiota in relation to P. aeruginosa chronic infection and CFTR mutation.

Associations Between Gut Microbiota and Asthma Endotypes: A Cross-Sectional Study in South China Based on Patients with Newly Diagnosed Asthma.

ObjectiveThis study aimed to investigate the gut microbiome profile in different inflammatory phenotypes of treatment-naive newly diagnosed asthmatic adults, to gain insight on the associations between intestinal microbiota and phenotypic features that characterize asthma heterogeneity to develop new treatments for asthma.MethodsFresh stool samples were obtained from 20 healthy subjects and 47 newly diagnosed asthmatic patients prior to any interventions. The asthmatics were divided into allergic and non-allergic cohorts. Intestinal microbiota was analyzed by 16S rRNA next-generation sequencing. Demographic and clinical parameters were collected. Alpha and beta diversity analysis were calculated to detect differences within sample phylotype richness and evenness between controls and asthmatic patients. Statistically significant differences between samples were analyzed for all used metrics, and features of gut bacterial community structure were evaluated in relation to extensive clinical characteristics of asthmatic patients.ResultsGut microbial compositions were significantly different between asthmatic and healthy groups. Alpha-diversity of the gut microbiome was significantly lower in asthmatics than in controls. The microbiome between allergic and non-allergic asthmatic patients were also different, and 28 differential species were identified. PPAR signaling pathway, carotenoid biosynthesis, and flavonoid biosynthesis were significantly positively correlated with allergy-associated clinical index, including FENO value, blood eosinophil counts, and serum IgE and IL-4 levels. A combination of Ruminococcus bromii, Brevundimonas vesicularis, and Clostridium disporicum showed an AUC of 0.743 in the specific allergic/non-allergic cohort. When integrating C. disporicum, flavone, flavonol biosynthesis, and serum IL-4 values, the AUC achieved 0.929 to classify asthmatics. At the same time, C. colinum and its associated functional pathway exhibited an AUC of 0.78 to distinguish allergic asthmatics from those without allergies.ConclusionWe demonstrated a distinct taxonomic composition of gut microbiota in different asthmatic phenotypes, highlighting their significant relationships. Our study may support considerations of intestinal microbial signatures in delineating asthma phenotypes.

Study Protocol - Impact of Lactobacillus rhamnosus GG on Allergic Reactions and Gut Microbiota Composition in Children with Cow’s Milk Allergy A Single-Center, Randomized, Double-Blinded, Placebo-Controlled, Phase II – MILK ALLERGY Trial

Background: IgE-mediated reactions constitute 70% of cow's milk-induced allergic reactions (AR). There is no established treatment. Recent evidence suggests that immunomodulation with probiotics represents a safe novel strategy, influencing immunity and inducing tolerance to milk protein antigens by action on human gut microbiota. Current evidence focuses most on the infant population. Objective: We will study the impact of Lactobacillus rhamnosus GG (LGG), compared to placebo, as an effective agent to improve ARs upon exposure to cow's milk in children from 5 to 10 years of age. Methods: This will be a phase II, single-center, randomized, double-blinded, placebo-controlled study, where a total of 200 participants will be treated for 12 months, with either; LGG or placebo, randomly allocated at 1:1. A double-blinded placebo-controlled food challenge (DBPCFC) with cow's milk will be used before and after the intervention. Results will be graded using the PRACTALL scoring system. The primary outcome will be binary – 'passing' by the absence of any AR, or a decrease from the baseline results or 'not passing' the DBPCFC after treatment. Secondary outcomes will include covariate adjustment and subgroup analysis by affected body systems and severity of ARs. Secondary analyses will include a comparison of the proportions of the taxonomic composition of gut microbiota, and quality of life, with baseline measurements. Conclusion: This trial will contribute to filling knowledge gaps about cow's milk allergy management using LGG in this specific population as an affordable and accessible non-pharmacological agent with few recorded side effects. If proven to be efficacious, it has the potential to decrease the worldwide prevalence of CMA and the resulting systemic, familial, and personal burdens.

Dynamic Changes in Microbiome Composition Following Mare's Milk Intake for Prevention of Collateral Antibiotic Effect.

IntroductionProbiotics and prebiotics are widely used for recovery of the human gut microbiome after antibiotic treatment. High antibiotic usage is especially common in children with developing microbiome. We hypothesized that dry Mare’s milk, which is rich in biologically active substances without containing live bacteria, could be used as a prebiotic in promoting microbial diversity following antibiotic treatment in children. The present pilot study aims to determine the impacts of dry Mare’s milk on the diversity of gut bacterial communities when administered during antibiotic treatment and throughout the subsequent recovery phase.MethodsSix children aged 4 to 5 years and diagnosed with bilateral bronchopneumonia were prescribed cephalosporin antibiotics. During the 60 days of the study, three children consumed dry Mare’s milk whereas the other three did not. Fecal samples were collected daily during antibiotic therapy and every 5 days after antibiotic therapy. Total DNA was isolated and taxonomic composition of gut microbiota was analyzed by 16S rRNA amplicon sequencing. To assess the immune status of the gut, stool samples were analyzed by bead-based multiplex assays.ResultsMare’s milk treatment seems to prevent the bloom of Mollicutes, while preventing the loss of Coriobacteriales. Immunological analysis of the stool reveals an effect of Mare’s milk on local immune parameters under the present conditions.

Altered Gut Microbiota Taxonomic Compositions of Patients With Sepsis in a Pediatric Intensive Care Unit.

Background: The gut is thought to play an important role in the pathogenesis of sepsis. Changes in the gut microbiota are closely related to the occurrence and development of human diseases, but few studies have focused on taxonomic composition of gut microbiota in septic patients. Knowledge of changes in the gut microbiota is a key issue in intensive care. Clinicians must understand how an altered gut microbiota affects the susceptibility and prognosis of septic patients.Measurements and Main Results: In the single-center case control study, 20 septic patients and 20 healthy children were recruited. The taxonomic composition of gut microbiota was determined via 16S rRNA gene sequencing. Gut microbiota diversity in children with sepsis was significantly reduced compared with that in healthy children. The taxonomic composition of gut microbiota can effectively distinguish children with sepsis from healthy children. Thirteen taxa of gut microbiota were significantly increased in the guts of children with sepsis compared with those of healthy children. The increased abundances of Enterococcaceae, Enterococcus, and Enterococcus durans in gut of septic patients were significantly positively correlated with blood inflammation indicators CRP and WBC. The abundances of seven bacteria were significantly decreased in the guts of septic children compared with those of healthy children. The decreased abundance of Bifidobacteriales in gut of septic patients is significantly negatively correlated with blood inflammation index WBC. A machine-learning classifier was built for distinguishing sepsis and achieved the AUC value of 81.25%. It shows that the composition of gut microbiota has certain potential for diagnosis of sepsis.Conclusions: Gut microbiota alterations in septic patients exhibit proliferation of opportunistic pathogenic bacteria, the massive reduction of the commensal flora, and the significant decrease in the diversity of the gut microbiota. Dysbiosis may also account for some changes in the inflammation indexes.

Characterization of Gut Microbiome in Korean Patients with Metabolic Associated Fatty Liver Disease.

Metabolic associated fatty liver disease (MAFLD) is a new concept where the presence of both fatty liver and metabolic abnormality are necessary for diagnosis. Several studies have reported that altered gut microbiome is closely associated with metabolic diseases and non-alcoholic fatty liver disease. However, the studies on MAFLD population are scarce. This prospective study aimed to identify differences in gut microbiome between patients with MAFLD and healthy controls in Korean population. In this study, patients with MAFLD and age, sex-matched healthy controls were included, and their stool samples were collected. Taxonomic composition of gut microbiota was analyzed using 16S ribosomal ribonucleic acid pyrosequencing. Twenty-two MAFLD patients and 44 healthy controls were included. Taxonomic diversity was lower in patients with MAFLD in the aspect of alpha and beta diversity. The differences were also found at phylum, class, family, and genus levels between the two groups. Phylum Proteobacteria, family Enterobactereriaceae, genus Citrobacter abundance was significantly increased and genus Faecalibacterium was significantly decreased in patients with MAFLD. In addition, butyrate-producing bacteria were decreased and ethanol-producing bacteria were increased in patients with MAFLD. The composition of gut microbiome was different between MAFLD and healthy controls in Korean population. This could offer potential targets for therapeutic intervention in MAFLD.

The severity of nonalcoholic fatty liver disease is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota.

Several animal studies have emphasized the role of gut microbiota in nonalcoholic fatty liver disease (NAFLD). However, data about gut dysbiosis in human NAFLD remain scarce in the literature, especially studies including the whole spectrum of NAFLD lesions. We aimed to evaluate the association between gut dysbiosis and severe NAFLD lesions, that is, nonalcoholic steatohepatitis (NASH) and fibrosis, in a well-characterized population of adult NAFLD. Fifty-seven patients with biopsy-proven NAFLD were enrolled. Taxonomic composition of gut microbiota was determined using 16S ribosomal RNA gene sequencing of stool samples. Thirty patients had F0/F1 fibrosis stage at liver biopsy (10 with NASH), and 27 patients had significant F≥2 fibrosis (25 with NASH). Bacteroides abundance was significantly increased in NASH and F≥2 patients, whereas Prevotella abundance was decreased. Ruminococcus abundance was significantly higher in F≥2 patients. By multivariate analysis, Bacteroides abundance was independently associated with NASH and Ruminococcus with F≥2 fibrosis. Stratification according to the abundance of these two bacteria generated three patient subgroups with increasing severity of NAFLD lesions. Based on imputed metagenomic profiles, Kyoto Encyclopedia of Genes and Genomes pathways significantly related to NASH and fibrosis F≥2 were mostly related to carbohydrate, lipid, and amino acid metabolism. NAFLD severity associates with gut dysbiosis and a shift in metabolic function of the gut microbiota. We identified Bacteroides as independently associated with NASH and Ruminococcus with significant fibrosis. Thus, gut microbiota analysis adds information to classical predictors of NAFLD severity and suggests novel metabolic targets for pre-/probiotics therapies.

Effect of Long‐Term Dietary Selenium Deprivation and Aging on Gut Microbiota in Short Telomere Mice

Gut microbiota represent an important bridge between dietary intake and host metabolism. Selenium (Se) is implicated in aging and age-related degenerations, but the role of gut microbiota in such linkage is not understood. Feces were collected from male Terc-/- premature aging mice at 18 and 24 months of age after being fed a Se-deficient diet or the diet supplemented with Se (0.15 ppm as selenate) since weanling. Metagenomic analyses of PCR-amplified V3-V4 regions of the 16S rRNA gene were performed through a MiSeq platform. Results from a classic multidimensional scaling graph plotted on the basis of Pearson covariance distance matrix demonstrated that the taxonomic composition of gut microbiota changed with age and dietary Se deprivation.The relative abundance of phyla Bacteroidetes was increased while Firmicutes, Actinobacteria and Proteobacteria were decreased as a result of dietary Se deficiency or aging. Analyses of aggregate microbiotic composition at species level based on Shannon diversity index demonstrated that the total microbial diversity was increased while the probiotic Bifidobacterium quantity was decreased by Se deprivation or aging. Taken together, nutritional Se may prevent age-dependent compositional changes of gut microbiota.

The inconstant gut microbiota of Drosophila species revealed by 16S rRNA gene analysis

The gut microorganisms in some animals are reported to include a core microbiota of consistently associated bacteria that is ecologically distinctive and may have coevolved with the host. The core microbiota is promoted by positive interactions among bacteria, favoring shared persistence; its retention over evolutionary timescales is evident as congruence between host phylogeny and bacterial community composition. This study applied multiple analyses to investigate variation in the composition of gut microbiota in drosophilid flies. First, the prevalence of five previously described gut bacteria (Acetobacter and Lactobacillus species) in individual flies of 21 strains (10 Drosophila species) were determined. Most bacteria were not present in all individuals of most strains, and bacterial species pairs co-occurred in individual flies less frequently than predicted by chance, contrary to expectations of a core microbiota. A complementary pyrosequencing analysis of 16S rRNA gene amplicons from the gut microbiota of 11 Drosophila species identified 209 bacterial operational taxonomic units (OTUs), with near-saturating sampling of sequences, but none of the OTUs was common to all host species. Furthermore, in both of two independent sets of Drosophila species, the gut bacterial community composition was not congruent with host phylogeny. The final analysis identified no common OTUs across three wild and four laboratory samples of D. melanogaster. Our results yielded no consistent evidence for a core microbiota in Drosophila. We conclude that the taxonomic composition of gut microbiota varies widely within and among Drosophila populations and species. This is reminiscent of the patterns of bacterial composition in guts of some other animals, including humans.