Diversity Of Human Gut Microbiota Research Articles

Postbiotic properties of exopolysaccharide produced by Levilactobacillus brevis M-10 isolated from natural fermented sour porridge through in vitro simulated digestion and fermentation.

The simulated digestion and fermentation characteristics in vitro of exopolysaccharide (EPS) of Levilactobacillus brevis M-10 were studied to evaluate its postbiotic properties. The simulated digestion results showed that EPS could not be degraded in saliva but could be very slightly degraded in gastric juice and could be degraded in intestinal juice. The results of simulated fermentation demonstrated that EPS could lower the intestine pH and be utilized by gut microbes to produce short-chain fatty acids such as propionic acid and butyric acid. Meanwhile, EPS significantly raised the diversity of human gut microbiota, and the relative abundances of Phascolarctobacterium were significantly increased, whereas Fusobacterium and Morganella significantly decreased. In conclusion, EPS from L. brevis M-10 was a good postbiotic as inulin. This was the first report about EPS as the postbiotic of L. brevis M-10 screened from broomcorn millet sour porridge in northwestern Shanxi Province, China.

Deciphering the interdependent labyrinth between gut microbiota and the immune system

The human gut microbiome interacts with each other and the host, which has significant effects on health and disease development. Intestinal homeostasis and inflammation are maintained by the dynamic interactions between gut microbiota and the innate and adaptive immune systems. Numerous metabolic products produced by the gut microbiota play a role in mediating cross-talk between gut epithelial and immune cells. In the event of an imbalance between the immune system and microbiota, the body becomes susceptible to infections, and homeostasis is compromised. This review mainly focuses on the interplay between microbes and the immune system, such as, T-cell and B-cell mediated adaptive responses to microbiota and signaling pathways for effective communication between the two. We have also highlighted the role of microbes in the activation of the immune response, the development of memory cells, and how the immune system determines the diversity of human gut microbiota. The review also explains the relationship of commensal microbiota and their relation in the production of immunoglobulins.

Impact of Air Pollution on the Composition and Diversity of Human Gut Microbiota in General and Vulnerable Populations: A Systematic Review.

Recently, growing attention has focused on the impact of air pollution on gut microbiota as a possible mechanism by which air pollutant exposure increased the risk for chronic diseases, as evidenced by in vivo studies demonstrating important exposure-induced alterations in the diversity and relative abundance of gut bacterial taxa. This systematic review provides updated state-of-art findings of studies examining the impact of air pollution on the human gut microbiota. Databases PubMed, Scopus, and Web of Science were searched with the following strategy: “air poll*” AND “gut micro*” OR “intestinal micro*”; moreover, a total of 10 studies were included. Overall, there is the evidence that short-term and long-term exposure to air pollutants have the potential to alter the composition and diversity of gut microbiota; some studies also correlated air pollution exposure to adverse health effects (impaired fasting glucose, adverse pregnancy outcomes, and asthma attacks) via alterations in the composition and/or function of the gut microbiota. However, the evidence on this topic is still scarce, and large cohort studies are needed globally.

Planetary Health and Traditional Medicine: A Potential Synergistic Approach to Tackle Antimicrobial Resistance

Antimicrobials are compounds that impede the activities of bacteria, viruses, parasites, or fungi. Continuous antimicrobial overuse, misuse, and improper use for human, animal, and agricultural purposes are raising concerns about antibiotic residue pollution in the environment, and antibiotic resistance genes (ARGs). Because antimicrobial-resistant diseases are linked to human–-microbial ecosystems, environmental pollution from antibiotic residue and ARGs alters the makeup and diversity of human gut microbiota, putting resistance under selection pressure. This perspective proposes that antibiotic-induced microbiome depletion is linked to environmental quality and has repercussions for human health via the gut microbiome’s sensitive ecosystem. This has stimulated new global efforts and multidisciplinary, integrative approaches to addressing Antimicrobial Resistance (AMR) awareness in communities. Several academic papers published in recent years have shown that medicinal plant extracts are effective against diseases on WHO’s pathogen priority lists (PPL), such as the ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species). Traditional medicine, with its knowledge of medicinal plants, promises to be a valuable source of next-generation powerful antimicrobials. Examples include the recent discovery of Artemisinin, a highly active antimalarial drug derived from Artemisia annua, and the discovery of Taxol, an active chemotherapeutic drug derived from the bark of the Pacific yew, Taxus brevifolia. The connections between small and large ecosystems’ vitality, biodiversity protection, and human health have been acknowledged by Planetary Health principles. To address these intertwined concerns, a Planetary Health and Traditional Medicine approach can be adopted, and antimicrobial resistance can be addressed by expanding the screening of medicinal plants for bioactive compounds.

Inorganic Arsenic Exposure and Gut Microbiota in a Birth Cohort from Central Taiwan

BACKGROUND AND AIM: Increasing evidence supports the association between composition and abundance of gut bacteria and human diseases (such as obesity and type 2 diabetes). Certain environmental toxicants, such as inorganic arsenic (iAs), may alter the equilibrium and diversity of human gut microbiota. Reversely, gut microbiota might affect the toxicokinetics of toxicants such as absorption and distribution. As folate-mediated one-carbon metabolism is crucial in fetus and children’s health and development, this study aimed to investigate the associations between iAs exposure, gut microbiota, and folate-related functional pathways in children. METHODS: Eighty children previously recruited in central Taiwan (2012–2014) were followed in 2015–2017. The structured questionnaire was interviewed with urinary sample collected at baseline and follow-up for pregnant women and children, and feces specimens were collected in children aged 3‒4 years. Urinary concentration of iAs species was quantified, and DNA was extracted from feces specimen. The composition and abundance of gut microbiota, and microbial functional profiles were sequenced by whole metagenome shotgun sequencing. We utilize the sum of urinary concentrations of arsenate, arsenate, monomethyl- and dimethyl arsenic acids (ΣiAs) as the index of total iAs exposure. RESULTS:High level of total iAs exposure (upper tertile, ΣiAs ≥ 21.06 μg/L) had a significantly lower abundance of Parabacteroides distasonis but the higher abundance of Roseburia intestinalis and Eubacterium rectale as compared to mid and lower tertile. Total iAs exposure was significantly associated with a decreased abundance of Parabacteroides distasonis (β = -0.021) after adjustment for sex and environmental tobacco smoke. Importantly we also found a significantly decreased function of N10-formyl-tetrahydrofolate biosynthesis (β = -0.040) and folate transformations II (β = -0.040) in relation to total iAs exposure. CONCLUSIONS:Exposure to iAs may alter the abundance of gut microbiota associated with human health, and it also had a negative association with folate-related functions. KEYWORDS: Heavy metals, Microbiome, Epidemiology

Ramadan Fasting Leads to Shifts in Human Gut Microbiota Structured by Dietary Composition.

The structure and diversity of human gut microbiota are directly related to diet, though less is known about the influences of ethnicity and diet-related behaviors, such as fasting (intermittent caloric restriction). In this study, we investigated whether fasting for Ramadan altered the microbiota in Chinese and Pakistani individuals. Using high-throughput 16S rRNA gene sequencing and self-reported dietary intake surveys, we determined that both the microbiota and dietary composition were significantly different with little overlap between ethnic groups. Principal Coordinate Analyses (PCoA) comparison of samples collected from both groups before and after fasting showed partial separation of microbiota related to fasting in the Pakistani group, but not in the Chinese group. Measurement of alpha diversity showed that Ramadan fasting significantly altered the coverage and ACE indices among Chinese subjects, but otherwise incurred no changes among either group. Specifically, Prevotella and Faecalibacterium drove predominance of Bacteroidetes and Firmicutes in the Pakistani group, while Bacteroides (phylum Bacteroidetes) were the most prevalent among Chinese participants both before and after fasting. We observed significant enrichment of some specific taxa and depletion of others in individuals of both populations, suggesting that fasting could affect beta diversity. Notably, Dorea, Klebsiella, and Faecalibacterium were more abundant in the Chinese group after fasting, while Sutterella, Parabacteroides, and Alistipes were significantly enriched after fasting in the Pakistani group. Evaluation of the combined groups showed that genera Coprococcus, Clostridium_XlV, and Lachnospiracea were all significantly decreased after fasting. Analysis of food intake and macronutrient energy sources showed that fat-derived energy was positively associated with Oscillibacter and Prevotella, but negatively associated with Bacteroides. In addition, the consumption of sweets was significantly positively correlated with the prevalence of Akkermansia. Our study indicated that diet was the most significant influence on microbiota, and correlated with ethnic groups, while fasting led to enrichment of specific bacterial taxa in some individuals. Given the dearth of understanding about the impacts of fasting on microbiota, our results provide valuable inroads for future study aimed at novel, personalized, behavior-based treatments targeting specific gut microbes for prevention or treatment of digestive disorders.

Obesity Measures and Dietary Parameters as Predictors of Gut Microbiota Phyla in Healthy Individuals.

The dynamics and diversity of human gut microbiota that can remarkably influence the wellbeing and health of the host are constantly changing through the host’s lifetime in response to various factors. The aim of the present study was to determine a set of parameters that could have a major impact on classifying subjects into a single cluster regarding gut bacteria composition. Therefore, a set of demographical, environmental, and clinical data of healthy adults aged 25–50 years (117 female and 83 men) was collected. Fecal microbiota composition was characterized using Illumina MiSeq 16S rRNA gene amplicon sequencing. Hierarchical clustering was performed to analyze the microbiota data set, and a supervised machine learning model (SVM; Support Vector Machines) was applied for classification. Seventy variables from collected data were included in machine learning analysis. The agglomerative clustering algorithm suggested the presence of four distinct community types of most abundant bacterial phyla. Each cluster harbored a statistically significant different proportion of bacterial phyla. Regarding prediction, the most important features classifying subjects into clusters were measures of obesity (waist to hip ratio, BMI, and visceral fat index), total body water, blood pressure, energy intake, total fat, olive oil intake, total fiber intake, and water intake. In conclusion, the SVM model was shown as a valuable tool to classify healthy individuals based on their gut microbiota composition.

Aging progression of human gut microbiota

BackgroundHuman gut microbiota are important for human health and have been regarded as a “forgotten organ”, whose variation is closely linked with various factors, such as host genetics, diet, pathological conditions and external environment. The diversity of human gut microbiota has been correlated with aging, which was characterized by different abundance of bacteria in various age groups. In the literature, most of the previous studies of age-related gut microbiota changes focused on individual species in the gut community with supervised methods. Here, we aimed to examine the underlying aging progression of the human gut microbial community from an unsupervised perspective.ResultsWe obtained raw 16S rRNA sequencing data of subjects ranging from newborns to centenarians from a previous study, and summarized the data into a relative abundance matrix of genera in all the samples. Without using the age information of samples, we applied an unsupervised algorithm to recapitulate the underlying aging progression of microbial community from hosts in different age groups and identify genera associated to this progression. Literature review of these identified genera indicated that for individuals with advanced ages, some beneficial genera are lost while some genera related with inflammation and cancer increase.ConclusionsThe multivariate unsupervised analysis here revealed the existence of a continuous aging progression of human gut microbiota along with the host aging process. The identified genera associated to this aging process are meaningful for designing probiotics to maintain the gut microbiota to resemble a young age, which hopefully will lead to positive impact on human health, especially for individuals in advanced age groups.

Comparative analysis of human and animal gut microbiota diversity and soil microbiota diversity in Xilinguole pasture

As an important part of ecosystem, microbes are widely distributed in various habitats. In recent years, more and more attention has been paid to the study on gut microbiota. The gut microbiota and their metabolites influence human and animal nutrition processing, metabolic balance, immune function, gastrointestinal development and other physiological activities. With the deepening of studies on human and animal gut microbiota, it has been found that some factors, such as diet, age, gender, and living environment, impacting on the composition of gut microbiota, while the differences among animal species have more significant influence on the gut microbiota composition. In relatively primitive grassland ecosystems, soil microbes interact with human and animal activities. On the one hand, microbes in the soil environment are the driving forces for the transformation and circulation of organic matter and nutrients. The improvement of soil microbial community diversity is beneficial for the soil fertility. On the other hand, human and animal activities will affect the diversity of soil microbial community. Although there are a lot of researches on soil microbiota, animal and human gut microbiota, their differences in diversity and composition within the same environment have not been studied. The advent of sequencing technology provides an effective mean for the accurate and comprehensive understanding of microbes, especially for the study of uncultivable microorganisms. The PacBio single-molecule real-time (SMRT) technology is advantageous in producing long sequence reads with high accuracy. Based on sequencing the full length 16S rRNA genes, the microbiota composition can be identified to the species level. Therefore, it is an effective approach for studying microbial diversity. We collected 56 stool and soil samples from Xilinguole, including 6, 10, 11, 9, and 10 stool samples from human, goat, cattle, horse, and sheep, respectively, as well as 10 soil samples. Genomic DNA was extracted from the samples. After DNA extraction and quality check, the 16S rRNA genes of all samples were amplified from the genomic DNA. The PCR products were sequenced using the PacBio RS II instrument. The QIIME software (V1.7) was used to analyze the sequencing data, and the R software (version 3.5.0) was used to further analyze and visualize the results. Firstly, it was found that the gut microbiota diversity of human was significantly lower than other samples ( P 0.01). The overall composition of the human and animal gut microbiota were dominated by the Firmicutes and Bacteroidetes phyla. However, the soil microbiota was dominated by Proteobacteria and Acidobacteria. At the genus level, the sheep, goat and cattle gut microbiota were dominated by Clostridium , Bacteroides , and Oscillibacter , while the horse gut microbiota was mainly composed of Clostridium , Eubacterium , and Treponema . The soil microbiota was composed mainly of Blastocatella and Bacillus . The human gut microbiota comprised much of Veillonella , Clostridium , Escherichia/Shigella . At the species level, the human gut microbiota mainly contained Escherichia/Shigella , dysenteriae , Streptococcus salivarius . The sheep, goat, cattle, and horse gut microbiota were dominated by Oscillibacter valericigenes and Eubacterium coprostanoligenes . The major species in soil were Blastocatella fastidiosa and Bacillus longiquaesitum . Moreover, principal coordinate analysis (PCoA) and hierarchical clustering analysis showed some differences in the microbiota structure among human gut, animal gut and soil samples. The gut microbiota structure was similar among cattle, goats and sheep. They were more different from the samples collected from human, horse and soil. We classified all samples into four clusters. Cluster 1 only included human samples; cluster 2 comprised the horse samples; cluster 3 was consisted of the sheep, goat, and cattle samples; while cluster 4 contained only the soil samples. Lastly, we identified the discriminatory OTUs and assigned them taxonomically to the species level. In conclusion, there were significant differences between animal gut microbiota and soil microbiota. The soil microbiota was more complex. As an omnivore, human gut microbiota diversity was significantly lower than other herbivorous animal (namely cattle, goat, horse and sheep). Although cattle, sheep, goat and horses are all herbivorous animals, the distinct features of the digestive systems could contribute to the difference in gut microbiota composition of horse from those of sheep, goat and cattle. This study revealed the differences of gut microbiota diversity between human and other animals, as well as from the soil microbial community. This work has laid a theoretical foundation for further studies on microbial diversity in different habitats.

Distal gut microbiota of adolescent children is different from that of adults

Human intestinal microbiota plays a number of important roles in human health and is also implicated in several gastrointestinal disorders. Although the diversity of human gut microbiota in adults and in young children has been examined, few reports of microbiota composition are available for adolescents. In this work, we used Microbiota Array for high-throughput analysis of distal gut microbiota in adolescent children 11-18 years of age. Samples obtained from healthy adults were used for comparison. Adolescent and adult groups could be separated in the principal components analysis space based on the relative species abundance of their distal gut microbiota. All samples were dominated by class Clostridia. A core microbiome of 46 species that were detected in all examined samples was established; members of genera Ruminococcus, Faecalibacterium, and Roseburia were well represented among core species. Comparison of intestinal microbiota composition between adolescents and adults revealed a statistically significantly higher abundance of genera Bifidobacterium and Clostridium among adolescent samples. The number of detected species was similar between sample groups, indicating that it was the relative abundances of the genera and not the presence or absence of a specific genus that differentiated adolescent and adult samples. In summary, contrary to the current belief, this study suggests that the gut microbiome of adolescent children is different from that of adults.