Rare Biosphere in Human Gut: A Less Explored Component of Human Gut Microbiota and Its Association with Human Health

2017 ◽  
pp. 133-142 ◽  
Author(s):  
Shrikant S. Bhute ◽  
Saroj S. Ghaskadbi ◽  
Yogesh S. Shouche
Keyword(s):  
Gut Microbiota ◽  
Human Health ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Rare Biosphere

scholarly journals Relationship between Nutrient Intake and Human Gut Microbiota in Monozygotic Twins

Medicina ◽  
2021 ◽  
Vol 57 (3) ◽  
pp. 275
Author(s):  
Natsuko Matsumoto ◽  
Jonguk Park ◽  
Rie Tomizawa ◽  
Hitoshi Kawashima ◽  
Koji Hosomi ◽  
...  
Keyword(s):  
Individual Differences ◽  
Environmental Factors ◽  
Gut Microbiota ◽  
Human Health ◽  
Negative Correlation ◽  
Nutrient Intake ◽  
Monozygotic Twins ◽  
Human Gut ◽  
Positive Correlation ◽  
Human Gut Microbiota

Background and Objectives: The gut microbiota is associated with human health and dietary nutrition. Various studies have been reported in this regard, but it is difficult to clearly analyze human gut microbiota as individual differences are significant. The causes of these individual differences in intestinal microflora are genetic and/or environmental. In this study, we focused on differences between identical twins in Japan to clarify the effects of nutrients consumed on the entire gut microbiome, while excluding genetic differences. Materials and Methods: We selected healthy Japanese monozygotic twins for the study and confirmed their zygosity by matching 15 short tandem repeat loci. Their fecal samples were subjected to 16S rRNA sequencing and bioinformatics analyses to identify and compare the fluctuations in intestinal bacteria. Results: We identified 12 genera sensitive to environmental factors, and found that Lactobacillus was relatively unaffected by environmental factors. Moreover, we identified protein, fat, and some nutrient intake that can affect 12 genera, which have been identified to be more sensitive to environmental factors. Among the 12 genera, Bacteroides had a positive correlation with retinol equivalent intake (rs = 0.38), Lachnospira had a significantly negative correlation with protein, sodium, iron, vitamin D, vitamin B6, and vitamin B12 intake (rs = −0.38, −0.41, −0.39, −0.63, −0.42, −0.49, respectively), Lachnospiraceae ND3007 group had a positive correlation with fat intake (rs = 0.39), and Lachnospiraceae UCG-008 group had a negative correlation with the saturated fatty acid intake (rs = −0.45). Conclusions: Our study is the first to focus on the relationship between human gut microbiota and nutrient intake using samples from Japanese twins to exclude the effects of genetic factors. These findings will broaden our understanding of the more intuitive relationship between nutrient intake and the gut microbiota and can be a useful basis for finding useful biomarkers that contribute to human health.

scholarly journals Does Consumption of Fermented Foods Modify the Human Gut Microbiota?

2020 ◽  
Vol 150 (7) ◽  
pp. 1680-1692 ◽  
Author(s):  
Leah T Stiemsma ◽  
Reine E Nakamura ◽  
Jennifer G Nguyen ◽  
Karin B Michels
Keyword(s):  
Gut Microbiota ◽  
Human Health ◽  
Food Consumption ◽  
Intervention Studies ◽  
Fermented Food ◽  
Fermented Foods ◽  
Human Intervention ◽  
Human Gut ◽  
Gut Dysbiosis ◽  
Human Gut Microbiota

ABSTRACT The human microbiota is a key contributor to many aspects of human health and its composition is largely influenced by diet. There is a growing body of scientific evidence to suggest that gut dysbiosis (microbial imbalance of the intestine) is associated with inflammatory and immune-mediated diseases (e.g., inflammatory bowel disease and asthma). Regular consumption of fermented foods (e.g., kimchi, kefir, etc.) may represent a potential avenue to counter the proinflammatory effects of gut dysbiosis. However, an assessment of the available literature in this research area is lacking. Here we provide a critical review of current human intervention studies that analyzed the effect of fermented foods on the composition and/or function of the human gut microbiota. A total of 19 human intervention studies were identified that met this search criteria. In this review, we discuss evidence that consumption of fermented foods may modify the gut microbiota in humans. Further, there is cursory evidence to suggest that gut microbiota compositional changes mediate associations between fermented food consumption and human health outcomes. Although promising, there remains considerable heterogeneity in the human populations targeted in the intervention studies we identified. Larger longitudinal feeding studies with longer follow-up are necessary to confirm and enhance the current data. Further, future studies should consider analyzing microbiota function as a means to elucidate the mechanism linking fermented food consumption with human health. This review highlights methodologic considerations for intervention trials, emphasizing an expanse of research opportunities related to fermented food consumption in humans.

scholarly journals Lactobacillus acidophilus Metabolizes Dietary Plant Glucosides and Externalizes Their Bioactive Phytochemicals

mBio ◽  
2017 ◽  
Vol 8 (6) ◽  
Author(s):  
Mia C. Theilmann ◽  
Yong Jun Goh ◽  
Kristian Fog Nielsen ◽  
Todd R. Klaenhammer ◽  
Rodolphe Barrangou ◽  
...  
Keyword(s):  
Microbial Community ◽  
Gut Microbiota ◽  
Human Health ◽  
Lactobacillus Acidophilus ◽  
Transcriptional Analysis ◽  
Taxonomic Group ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Gut Microbial Community

ABSTRACT Therapeutically active glycosylated phytochemicals are ubiquitous in the human diet. The human gut microbiota (HGM) modulates the bioactivities of these compounds, which consequently affect host physiology and microbiota composition. Despite a significant impact on human health, the key players and the underpinning mechanisms of this interplay remain uncharacterized. Here, we demonstrate the growth of Lactobacillus acidophilus on mono- and diglucosyl dietary plant glycosides (PGs) possessing small aromatic aglycones. Transcriptional analysis revealed the upregulation of host interaction genes and identified two loci that encode phosphotransferase system (PTS) transporters and phospho-β-glucosidases, which mediate the uptake and deglucosylation of these compounds, respectively. Inactivating these transport and hydrolysis genes abolished or severely reduced growth on PG, establishing the specificity of the loci to distinct groups of PGs. Following intracellular deglucosylation, the aglycones of PGs are externalized, rendering them available for absorption by the host or for further modification by other microbiota taxa. The PG utilization loci are conserved in L. acidophilus and closely related lactobacilli, in correlation with versatile growth on these compounds. Growth on the tested PG appeared more common among human gut lactobacilli than among counterparts from other ecologic niches. The PGs that supported the growth of L. acidophilus were utilized poorly or not at all by other common HGM strains, underscoring the metabolic specialization of L. acidophilus. These findings highlight the role of human gut L. acidophilus and select lactobacilli in the bioconversion of glycoconjugated phytochemicals, which is likely to have an important impact on the HGM and human host. IMPORTANCE Thousands of therapeutically active plant-derived compounds are widely present in berries, fruits, nuts, and beverages like tea and wine. The bioactivity and bioavailability of these compounds, which are typically glycosylated, are altered by microbial bioconversions in the human gut. Remarkably, little is known about the bioconversion of PGs by the gut microbial community, despite the significance of this metabolic facet to human health. Our work provides the first molecular insights into the metabolic routes of diet relevant and therapeutically active PGs by Lactobacillus acidophilus and related human gut lactobacilli. This taxonomic group is adept at metabolizing the glucoside moieties of select PG and externalizes their aglycones. The study highlights an important role of lactobacilli in the bioconversion of dietary PG and presents a framework from which to derive molecular insights into their metabolism by members of the human gut microbiota. IMPORTANCE Thousands of therapeutically active plant-derived compounds are widely present in berries, fruits, nuts, and beverages like tea and wine. The bioactivity and bioavailability of these compounds, which are typically glycosylated, are altered by microbial bioconversions in the human gut. Remarkably, little is known about the bioconversion of PGs by the gut microbial community, despite the significance of this metabolic facet to human health. Our work provides the first molecular insights into the metabolic routes of diet relevant and therapeutically active PGs by Lactobacillus acidophilus and related human gut lactobacilli. This taxonomic group is adept at metabolizing the glucoside moieties of select PG and externalizes their aglycones. The study highlights an important role of lactobacilli in the bioconversion of dietary PG and presents a framework from which to derive molecular insights into their metabolism by members of the human gut microbiota.

scholarly journals Revealing microbial species diversity using sequence capture by hybridization

2021 ◽  
Vol 7 (12) ◽  
Author(s):  
Sophie Marre ◽  
Cyrielle Gasc ◽  
Camille Forest ◽  
Yacine Lebbaoui ◽  
Pascale Mosoni ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
16S Rdna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Taxonomic Resolution ◽  
Human Gut ◽  
Content Type ◽  
Innovative Strategy ◽  
Human Gut Microbiota ◽  
Rare Biosphere

Targeting small parts of the 16S rDNA phylogenetic marker by metabarcoding reveals microorganisms of interest but cannot achieve a taxonomic resolution at the species level, precluding further precise characterizations. To identify species behind operational taxonomic units (OTUs) of interest, even in the rare biosphere, we developed an innovative strategy using gene capture by hybridization. From three OTU sequences detected upon polyphenol supplementation and belonging to the rare biosphere of the human gut microbiota, we revealed 59 nearly full-length 16S rRNA genes, highlighting high bacterial diversity hidden behind OTUs while evidencing novel taxa. Inside each OTU, revealed 16S rDNA sequences could be highly distant from each other with similarities down to 85 %. We identified one new family belonging to the order Clostridiales , 39 new genera and 52 novel species. Related bacteria potentially involved in polyphenol degradation have also been identified through genome mining and our results suggest that the human gut microbiota could be much more diverse than previously thought.

scholarly journals An extended reconstruction of human gut microbiota metabolism of dietary compounds

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Telmo Blasco ◽  
Sergio Pérez-Burillo ◽  
Francesco Balzerani ◽  
Daniel Hinojosa-Nogueira ◽  
Alberto Lerma-Aguilera ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Human Health ◽  
Metabolic Networks ◽  
16S Rrna Gene Sequencing ◽  
Complex Problem ◽  
Rrna Gene ◽  
Limited Information ◽  
Sequencing Data ◽  
Human Gut ◽  
Human Gut Microbiota

AbstractUnderstanding how diet and gut microbiota interact in the context of human health is a key question in personalized nutrition. Genome-scale metabolic networks and constraint-based modeling approaches are promising to systematically address this complex problem. However, when applied to nutritional questions, a major issue in existing reconstructions is the limited information about compounds in the diet that are metabolized by the gut microbiota. Here, we present AGREDA, an extended reconstruction of diet metabolism in the human gut microbiota. AGREDA adds the degradation pathways of 209 compounds present in the human diet, mainly phenolic compounds, a family of metabolites highly relevant for human health and nutrition. We show that AGREDA outperforms existing reconstructions in predicting diet-specific output metabolites from the gut microbiota. Using 16S rRNA gene sequencing data of faecal samples from Spanish children representing different clinical conditions, we illustrate the potential of AGREDA to establish relevant metabolic interactions between diet and gut microbiota.

scholarly journals Aging progression of human gut microbiota

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Congmin Xu ◽  
Huaiqiu Zhu ◽  
Peng Qiu
Keyword(s):  
Microbial Community ◽  
Gut Microbiota ◽  
Human Health ◽  
Aging Process ◽  
Positive Impact ◽  
Age Groups ◽  
Individual Species ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Age Related

Abstract Background Human 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. Results We 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. Conclusions The 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.

scholarly journals Nutritional Status and the Influence of the Vegan Diet on the Gut Microbiota and Human Health

Medicina ◽  
2020 ◽  
Vol 56 (2) ◽  
pp. 88 ◽  
Author(s):  
Hercules Sakkas ◽  
Petros Bozidis ◽  
Christos Touzios ◽  
Damianos Kolios ◽  
Georgia Athanasiou ◽  
...  
Keyword(s):  
Nutritional Status ◽  
Gut Microbiota ◽  
Human Health ◽  
Dietary Habits ◽  
Metabolic Diseases ◽  
Vegan Diet ◽  
Nutritional Deficiencies ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Medical Disorders

The human gut microbiota is considered a well-known complex ecosystem composed of distinct microbial populations, playing a significant role in most aspects of human health and wellness. Several factors such as infant transitions, dietary habits, age, consumption of probiotics and prebiotics, use of antibiotics, intestinal comorbidities, and even metabolic diseases may continously alter microbiota diversity and function. The study of vegan diet–microbiota interactions is a rapidly evolving field, since plenty of research has been focused on the potential effects of plant-based dietary patterns on the human gut microbiota. It has been reported that well-planned vegan diets and their associated components affect both the bacterial composition and metabolic pathways of gut microbiota. Certain benefits associated with medical disorders but also limitations (including nutritional deficiencies) have been documented. Although the vegan diet may be inadequate in calorific value, it is rich in dietary fiber, polyphenols, and antioxidant vitamins. The aim of the present study was to provide an update of the existing knowledge on nutritional status of vegan diets and the influence of their food components on the human gut microbiota and health.

scholarly journals Colonization Ability and Impact on Human Gut Microbiota of Foodborne Microbes From Traditional or Probiotic-Added Fermented Foods: A Systematic Review

2021 ◽  
Vol 8 ◽  
Author(s):  
Marianna Roselli ◽  
Fausta Natella ◽  
Paola Zinno ◽  
Barbara Guantario ◽  
Raffaella Canali ◽  
...  
Keyword(s):  
Systematic Review ◽  
Gut Microbiota ◽  
Human Health ◽  
Fermented Foods ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Colonization Ability ◽  
Scientific Results ◽  
Gut Microorganisms ◽  
Study Designs

A large subset of fermented foods act as vehicles of live environmental microbes, which often contribute food quality assets to the overall diet, such as health-associated microbial metabolites. Foodborne microorganisms also carry the potential to interact with the human gut microbiome via the food chain. However, scientific results describing the microbial flow connecting such different microbiomes as well as their impact on human health, are still fragmented. The aim of this systematic review is to provide a knowledge-base about the scientific literature addressing the connection between foodborne and gut microbiomes, as well as to identify gaps where more research is needed to clarify and map gut microorganisms originating from fermented foods, either traditional or added with probiotics, their possible impact on human gut microbiota composition and to which extent foodborne microbes might be able to colonize the gut environment. An additional aim was also to highlight experimental approaches and study designs which could be better standardized to improve comparative analysis of published datasets. Overall, the results presented in this systematic review suggest that a complex interplay between food and gut microbiota is indeed occurring, although the possible mechanisms for this interaction, as well as how it can impact human health, still remain a puzzling picture. Further research employing standardized and trans-disciplinary approaches aimed at understanding how fermented foods can be tailored to positively influence human gut microbiota and, in turn, host health, are therefore of pivotal importance.

scholarly journals Escherichia coli Exopolysaccharides Induced by Ceftriaxone Regulated Human Gut Microbiota in vitro

2021 ◽  
Vol 12 ◽  
Author(s):  
Baiyuan Li ◽  
Huahai Chen ◽  
Linyan Cao ◽  
Yunfei Hu ◽  
Dan Chen ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Gut Microbiota ◽  
Human Health ◽  
Molar Ratio ◽  
Composition Analysis ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Human Gut ◽  
Human Gut Microbiota

A stable intestinal microflora is an essential prerequisite for human health. This study investigated the interaction between Escherichia coli exopolysaccharides (named EPS-m2) and the human gut microbiota (HGM) in vitro. The EPS-m2 was produced by E. coli WM3064 when treated with ceftriaxone. The monosaccharide composition analysis revealed that EPS-m2 is composed of glucuronic acid, glucose, fucose, galactose/N-acetyl glucosamine, arabinose, xylose, and ribose with a molar ratio of approximately 77:44:29:28:2:1:1. The carbohydrates, protein, and uronic acids contents in EPS-m2 was 78.6 ± 0.1%, 4.38 ± 0.11%, and 3.86 ± 0.09%, respectively. In vitro batch fermentation experiments showed that 77% of EPS-m2 could be degraded by human fecal microbiota after 72 h of fermentation. In reverse, 16S rRNA gene sequencing analysis showed that EPS-m2 increased the abundance of Alistipes, Acinetobacter, Alloprevotella, Howardella, and Oxalobacter; GC detection illustrated that EPS-m2 enhanced the production of SCFAs. These findings indicated that EPS-m2 supplementation could regulate the HGM and might facilitate modulation of human health.

In vitro study of the interaction between human gut microbiota and herbal extracts using willow bark extract as an example

Planta Medica ◽  
2016 ◽  
Vol 81 (S 01) ◽  
pp. S1-S381
Author(s):  
EM Pferschy-Wenzig ◽  
K Koskinen ◽  
C Moissl-Eichinger ◽  
R Bauer
Keyword(s):  
Gut Microbiota ◽  
In Vitro Study ◽  
Vitro Study ◽  
Bark Extract ◽  
Herbal Extracts ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Willow Bark
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