scholarly journals Soil is a key factor influencing gut microbiota and its effect is comparable to that exerted by diet for mice

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 1588 ◽  
Author(s):  
Dongrui Zhou ◽  
Zhimao Bai ◽  
Honglin Zhang ◽  
Na Li ◽  
Zhiyu Bai ◽  
...  

Exposure to an unsanitary environment increases the diversity and alters the composition of gut microbiota. To identify the key element in the unsanitary environment responsible for this phenomenon, we investigated the effect and the extent by which the soil in our environment influenced the composition of gut microbiota. Results show that adding unsterile or sterile soil to bedding, either before birth or after weaning, influences significantly the composition of mice gut microbiota. Specifically, unsterile soil increases the richness and biodiversity of gut microbiota. Interestingly, based on UniFrac distance analysis of 16S rRNA sequences, the impact of soil on gut microbiota is comparable to that exerted by diet. These findings provide a potential new strategy for intervening on the human gut microbial community and preventing disease.

2020 ◽  
Vol 59 (8) ◽  
pp. 3347-3368
Author(s):  
J. R. Swann ◽  
M. Rajilic-Stojanovic ◽  
A. Salonen ◽  
O. Sakwinska ◽  
C. Gill ◽  
...  

AbstractWith the growing appreciation for the influence of the intestinal microbiota on human health, there is increasing motivation to design and refine interventions to promote favorable shifts in the microbiota and their interactions with the host. Technological advances have improved our understanding and ability to measure this indigenous population and the impact of such interventions. However, the rapid growth and evolution of the field, as well as the diversity of methods used, parameters measured and populations studied, make it difficult to interpret the significance of the findings and translate their outcomes to the wider population. This can prevent comparisons across studies and hinder the drawing of appropriate conclusions. This review outlines considerations to facilitate the design, implementation and interpretation of human gut microbiota intervention studies relating to foods based upon our current understanding of the intestinal microbiota, its functionality and interactions with the human host. This includes parameters associated with study design, eligibility criteria, statistical considerations, characterization of products and the measurement of compliance. Methodologies and markers to assess compositional and functional changes in the microbiota, following interventions are discussed in addition to approaches to assess changes in microbiota–host interactions and host responses. Last, EU legislative aspects in relation to foods and health claims are presented. While it is appreciated that the field of gastrointestinal microbiology is rapidly evolving, such guidance will assist in the design and interpretation of human gut microbiota interventional studies relating to foods.


2019 ◽  
Vol 62 (7) ◽  
pp. 985-987
Author(s):  
Qizheng Wu ◽  
Fang Liu ◽  
Yu Song ◽  
Qingyun Meng ◽  
Xunlian Zhang ◽  
...  

mBio ◽  
2017 ◽  
Vol 8 (6) ◽  
Author(s):  
Mia C. Theilmann ◽  
Yong Jun Goh ◽  
Kristian Fog Nielsen ◽  
Todd R. Klaenhammer ◽  
Rodolphe Barrangou ◽  
...  

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.


2020 ◽  
Author(s):  
Clarissa Asha Febinia ◽  
Safarina G. Malik ◽  
Ratna Djuwita ◽  
I Wayan Weta ◽  
Desak Made Wihandani ◽  
...  

Abstract Background: Human living conditions, such as food availability and the built environment, contribute to environmental forces that influence gut microbiota composition. Understanding the impact of the environment on microbiota assembly and its association with human health has multiple potential applications. Indonesia is a densely populated country that has been undergoing a dramatic societal change for the past two decades. It is distinctive in that it occupies an archipelago that imposes diverse geographic and cultural boundaries. The relationship between diet, microbiota, and health is poorly known in Indonesians and represents a natural study for the interaction between ethnogeographic factors and nutrition in microbiota assembly. Results: Here we show the first comprehensive report of the gut microbiota in adults from Bali, Indonesia (n=41). Their microbiotas clustered into two distinct community types: a Prevotella-rich (Type-P) and a Bacteroides-rich (Type-B) community. The Type-P individuals had lower alpha diversity (p <0.001, Shannon) and more incidence of obesity. The two community types are significantly different in their inter-genus co-abundance pattern (p <0.001, ANOSIM, Wilcoxon test). Further analyses with diet and obesity data showed that the presence of two distinct community types in Bali is a significant confounder for identifying health markers. In a multi-country dataset (n=257), the Bali microbiota indicates a transitional state from a subsistent (Prevotella-dominant) to industrial (Bacteroides-dominant) society. The two largest axes in a Principal Coordinate Analysis of weighted UniFrac distance explained the majority of variance between samples across countries (49.1%). Microbial dissimilarity across populations is significantly associated with Prevotella and Bacteriodes abundance (p <0.001, Generalized Additive Model). Conclusion: Our data showed that lifestyle transitions have a strong influence on the frequency of microbiota community types in a population. The Bali microbiota is undergoing a shift towards a Bacteroides-dominant community which reflects the ongoing transition of nutrition, socio-economy, and lifestyle the society. Although enterotypes obscured the detection of health markers, our findings collectively suggest that enterotypes may be useful in future studies for informing population-level stratification in large heterogenetic datasets.


2021 ◽  
pp. 71-100
Author(s):  
Sebastian Wardak

The human digestive tract is the living environment for billions of cells of various microorganisms that are part of the human microflora. The use of modern molecular biology techniques, such as NGS (Next Generation Sequencing), made it possible to study the microorganisms inhabiting the intestines and to understand their impact on human health. The gut microbiota plays a significant role in the synthesis and metabolism of many nutrients and metabolites, including short-chain fatty acids (SCFA), amino acids, lipids, bile acids and vitamins. Many factors such as diet, age, climate, and socioeconomic conditions influence the diversity of the microbiota. Rapid changes in the composition of the microbiota (disturbance of homeostasis) can lead to dysbiosis - a condition associated not only with intestinal disorders, but also with numerous extraintestinal diseases. The present work is a review of current reports on: research techniques used to analyze microbiota, the impact of various factors on its diversity and the impact of microbiota on our health.


Author(s):  
Akhlash P. Singh

The human gut is the complex microbial ecosystem comprises more than 100 trillion microbes also known as microbiota. The gut microbiota does not only include about 400–500 types of bacterial strains, but it also contains archaea, bacteriophage, fungi, and protozoa species. In order to complete the characterization of the gut microbial community, we need the help of many culture-dependent and culture-independent genomic technologies. Recently, next-generation sequencing (NGS), mediated metagenomics that rely on 16S rRNA gene amplification, and whole-genome sequencing (WGS) have provided us deep knowledge related to important interactions such as host-microbiota and microbe-microbe interactions under various perturbation inside the gut. But, we still lack complete knowledge related to unique gene products encoded by gut meta-genome. Hence, it required the application of high-throughput “omics-based” methods to support metagenomics. Currently, a combination of high-throughput culturing and microfluidics assays is providing a new method to characterize non-amenable bacterial strains from the gut environment. The recent additions of artificial intelligence and deep learning to the area of microbiome studies have enhanced the capability of identification of thousand microbes simultaneously. Given above, it is necessary to apply new genome editing tools that can be used to design the personalized microflora which can be used to cure lifestyle-related diseases.


2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Antonio Palomba ◽  
Alessandro Tanca ◽  
Marcello Abbondio ◽  
Rosangela Sau ◽  
Monica Serra ◽  
...  

AbstractDiet is a key factor influencing gut microbiota (GM) composition and functions, which in turn affect host health. Among dietary regimens, time-restricted (TR) feeding has been associated to numerous health benefits. The impact of TR feeding on the GM composition has been mostly explored by means of metagenomic sequencing. To date, however, little is known about the modulation of GM functions by this dietary regimen. Here, we analyzed the effects of TR feeding on GM functions by evaluating protein expression changes in a rat model through a metaproteomic approach. We observed that TR feeding has a relevant impact on GM functions, specifically leading to an increased abundance of several enzymes involved in carbohydrate and protein metabolism and expressed by Lactobacillus spp. and Akkermansia muciniphila. Taken together, these results contribute to deepening our knowledge about the key relationship between diet, GM, and health.


PROTEOMICS ◽  
2015 ◽  
Vol 15 (20) ◽  
pp. 3474-3485 ◽  
Author(s):  
Alessandro Tanca ◽  
Antonio Palomba ◽  
Salvatore Pisanu ◽  
Maria Filippa Addis ◽  
Sergio Uzzau

2018 ◽  
Vol 50 ◽  
pp. 104-111 ◽  
Author(s):  
Alba Tamargo ◽  
Carolina Cueva ◽  
Laura Laguna ◽  
M.Victoria Moreno-Arribas ◽  
Loreto A. Muñoz

Microbiology ◽  
2010 ◽  
Vol 156 (11) ◽  
pp. 3224-3231 ◽  
Author(s):  
R. A. Kemperman ◽  
S. Bolca ◽  
L. C. Roger ◽  
E. E. Vaughan

Polyphenols, ubiquitously present in the food we consume, may modify the gut microbial composition and/or activity, and moreover, may be converted by the colonic microbiota to bioactive compounds that influence host health. The polyphenol content of fruit and vegetables and derived products is implicated in some of the health benefits bestowed on eating fruit and vegetables. Elucidating the mechanisms behind polyphenol metabolism is an important step in understanding their health effects. Yet, this is no trivial assignment due to the diversity encountered in both polyphenols and the gut microbial composition, which is further confounded by the interactions with the host. Only a limited number of studies have investigated the impact of dietary polyphenols on the complex human gut microbiota and these were mainly focused on single polyphenol molecules and selected bacterial populations. Our knowledge of gut microbial genes and pathways for polyphenol bioconversion and interactions is poor. Application of specific in vitro or in vivo models mimicking the human gut environment is required to analyse these diverse interactions. A particular benefit can now be gained from next-generation analytical tools such as metagenomics and metatranscriptomics allowing a wider, more holistic approach to the analysis of polyphenol metabolism. Understanding the polyphenol–gut microbiota interactions and gut microbial bioconversion capacity will facilitate studies on bioavailability of polyphenols in the host, provide more insight into the health effects of polyphenols and potentially open avenues for modulation of polyphenol bioactivity for host health.


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