Enrichment or depletion? The impact of stool pretreatment on metaproteomic characterization of the human gut microbiota

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

scholarly journals Considerations for the design and conduct of human gut microbiota intervention studies relating to foods

2020 ◽  
Vol 59 (8) ◽  
pp. 3347-3368
Author(s):  
J. R. Swann ◽  
M. Rajilic-Stojanovic ◽  
A. Salonen ◽  
O. Sakwinska ◽  
C. Gill ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Intestinal Microbiota ◽  
Intervention Studies ◽  
Health Claims ◽  
Host Responses ◽  
Human Gut ◽  
Eligibility Criteria ◽  
Functional Changes ◽  
Human Gut Microbiota ◽  
The Impact

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.

Understanding the impact of chia seed mucilage on human gut microbiota by using the dynamic gastrointestinal model simgi®

2018 ◽  
Vol 50 ◽  
pp. 104-111 ◽  
Author(s):  
Alba Tamargo ◽  
Carolina Cueva ◽  
Laura Laguna ◽  
M.Victoria Moreno-Arribas ◽  
Loreto A. Muñoz
Keyword(s):  
Gut Microbiota ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Chia Seed ◽  
The Impact ◽  
Seed Mucilage

scholarly journals Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides

Science ◽  
2015 ◽  
Vol 350 (6256) ◽  
pp. aac5992 ◽  
Author(s):  
Meng Wu ◽  
Nathan P. McNulty ◽  
Dmitry A. Rodionov ◽  
Matvei S. Khoroshkin ◽  
Nicholas W. Griffin ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Genetic Determinants ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Gene Level ◽  
Transposon Mutants ◽  
Gnotobiotic Mice ◽  
Stability And Resilience

Libraries of tens of thousands of transposon mutants generated from each of four human gut Bacteroides strains, two representing the same species, were introduced simultaneously into gnotobiotic mice together with 11 other wild-type strains to generate a 15-member artificial human gut microbiota. Mice received one of two distinct diets monotonously, or both in different ordered sequences. Quantifying the abundance of mutants in different diet contexts allowed gene-level characterization of fitness determinants, niche, stability, and resilience and yielded a prebiotic (arabinoxylan) that allowed targeted manipulation of the community. The approach described is generalizable and should be useful for defining mechanisms critical for sustaining and/or approaches for deliberately reconfiguring the highly adaptive and durable relationship between the human gut microbiota and host in ways that promote wellness.

scholarly journals The Impact of a Dynamic Working Environment on Human Gut Microbiota

2021 ◽  
Author(s):  
Lu Ling ◽  
Jun Zhou ◽  
Qianlong Meng ◽  
Ziran Zhang ◽  
Wenkun Li ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Clinical Characteristics ◽  
Dietary Habits ◽  
Living Environment ◽  
Working Environment ◽  
Rrna Gene ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Train Drivers ◽  
The Impact

Gut microbiota dysbiosis is associated with a variety of diseases, such as inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS), metabolic diseases, allergic diseases, neurodevelopmental disorders and cancer. The human gut microbiota can be influenced by a variety of factors, including geography, dietary habits, living environment, age and altered lifestyle etc. This study was conducted to explore the gut microbiota compositions in officials who are in a stable working environment and train drivers who are in a dynamic working environment. Microbiota communities in the feces of 80 officials and 88 train drivers were analyzed using Illumina MiSeq sequencing targeting the V3-V4 region of 16S ribosomal RNA (rRNA) gene and ITS1 region of fungi. There were significant differences between the two groups in diversity and richness of gut microbiota, while the microbial community compositions of the two groups were similar. The relationship between gut microbiota and clinical characteristics was investigated. We found that more bacteria and fungi were positively correlated with clinical characteristics. Functional prediction analysis of the gut microbiota between the two groups by PICRUSt2 revealed significant differences between the official group and the train driver group. Elucidating these differences of the microbiome between the two groups will provide a foundation understanding of the impact of a dynamic environment on gut microbiota.

scholarly journals Does geographical variation confound the relationship between host factors and the human gut microbiota: a population-based study in China

BMJ Open ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. e038163
Author(s):  
Shan Sun ◽  
Huijun Wang ◽  
Matthew CB Tsilimigras ◽  
Annie Green Howard ◽  
Wei Sha ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Geographical Variation ◽  
Population Based ◽  
Host Factors ◽  
Secondary Outcome ◽  
Human Gut ◽  
Population Based Study ◽  
Human Gut Microbiota ◽  
Wide Range ◽  
The Impact

ObjectiveThe human gut microbiota plays important roles in human health but is also known to be highly diverse between populations from different regions. Yet most studies inadequately account for this regional diversity in their analyses. This study examines the extent to which geographical variation can act as a confounding variable for studies that associate the microbiota with human phenotypic variation.DesignPopulation-based study.SettingChina.Participants2164 participants from 15 province-level divisions in China.Primary and secondary outcome measuresWe analysed the impact of geographic location on associations between the human gut microbiota and 72 host factors representing a wide variety of environmental-level, household-level and individual-level factors.ResultsWhile the gut microbiota varied across a wide range of host factors including urbanisation, occupation and dietary variables, the geographic region (province/megacity) of the participants explained the largest proportion of the variance (17.9%). The estimated effect sizes for other host factors varied substantially by region with little evidence of a reproducible signal across different areas as measured by permutational multivariate analysis of variance and random forest models.ConclusionsOur results suggest that geographic variation is an essential factor that should be explicitly considered when generalising microbiota-based models to host phenotype across different populations.

scholarly journals Glycan complexity dictates microbial resource allocation in the large intestine

2015 ◽  
Vol 6 (1) ◽  
Author(s):  
Artur Rogowski ◽  
Jonathon A. Briggs ◽  
Jennifer C. Mortimer ◽  
Theodora Tryfona ◽  
Nicolas Terrapon ◽  
...  
Keyword(s):  
Resource Allocation ◽  
Gut Microbiota ◽  
Large Intestine ◽  
Side Chains ◽  
Dietary Carbohydrates ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Bacteroides Ovatus ◽  
Complex Carbohydrates

Abstract The structure of the human gut microbiota is controlled primarily through the degradation of complex dietary carbohydrates, but the extent to which carbohydrate breakdown products are shared between members of the microbiota is unclear. We show here, using xylan as a model, that sharing the breakdown products of complex carbohydrates by key members of the microbiota, such as Bacteroides ovatus, is dependent on the complexity of the target glycan. Characterization of the extensive xylan degrading apparatus expressed by B. ovatus reveals that the breakdown of the polysaccharide by the human gut microbiota is significantly more complex than previous models suggested, which were based on the deconstruction of xylans containing limited monosaccharide side chains. Our report presents a highly complex and dynamic xylan degrading apparatus that is fine-tuned to recognize the different forms of the polysaccharide presented to the human gut microbiota.

The impact of Crohn's disease genes on healthy human gut microbiota: a pilot study

Gut ◽  
2013 ◽  
Vol 62 (6) ◽  
pp. 952.1-954 ◽  
Author(s):  
Christopher Quince ◽  
Elin E Lundin ◽  
Anna N Andreasson ◽  
Dario Greco ◽  
Joseph Rafter ◽  
...  
Keyword(s):  
Crohn’S Disease ◽  
Pilot Study ◽  
Crohn's Disease ◽  
Gut Microbiota ◽  
Disease Genes ◽  
Human Gut ◽  
Healthy Human ◽  
Human Gut Microbiota ◽  
The Impact

scholarly journals Quantifying the Impact of Human Leukocyte Antigen on the Human Gut Microbiota

mSphere ◽  
2021 ◽  
Author(s):  
Stijn P. Andeweg ◽  
Can Keşmir ◽  
Bas E. Dutilh
Keyword(s):  
Gut Microbiota ◽  
Human Leukocyte Antigen ◽  
Human Leukocyte ◽  
Colonization Resistance ◽  
Human Gut ◽  
Leukocyte Antigen ◽  
Human Gut Microbiota ◽  
The Impact ◽  
Uptake Of Nutrients

The microorganisms that live in the digestive tracts of humans, known as the gut microbiota, are essential for hosts’ survival, as they support crucial functions. For example, they support the host in facilitating the uptake of nutrients and give colonization resistance against pathogens.

scholarly journals Compositional and Functional Differences in the Human Gut Microbiome Correlate with Clinical Outcome following Infection with Wild-Type Salmonella enterica Serovar Typhi

mBio ◽  
2018 ◽  
Vol 9 (3) ◽  
Author(s):  
Yan Zhang ◽  
Arthur Brady ◽  
Cheron Jones ◽  
Yang Song ◽  
Thomas C. Darton ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Clinical Outcomes ◽  
Salmonella Enterica ◽  
Enteric Pathogens ◽  
Wild Type ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Functional Differences ◽  
And Function ◽  
The Impact

ABSTRACT Insights into disease susceptibility as well as the efficacy of vaccines against typhoid and other enteric pathogens may be informed by better understanding the relationship between the effector immune response and the gut microbiota. In the present study, we characterized the composition (16S rRNA gene profiling) and function (RNA sequencing [RNA-seq]) of the gut microbiota following immunization and subsequent exposure to wild-type Salmonella enterica serovar Typhi in a human challenge model to further investigate the central hypothesis that clinical outcomes may be linked to the gut microbiota. Metatranscriptome analysis of longitudinal stool samples collected from study subjects revealed two stable patterns of gene expression for the human gut microbiota, dominated by transcripts from either Methanobrevibacter or a diverse representation of genera in the Firmicutes phylum. Immunization with one of two live oral attenuated vaccines against S.  Typhi had minimal effects on the composition or function of the gut microbiota. It was observed that subjects harboring the methanogen-dominated transcriptome community at baseline displayed a lower risk of developing symptoms of typhoid following challenge with wild-type S.  Typhi. Furthermore, genes encoding antioxidant proteins, metal homeostasis and transport proteins, and heat shock proteins were expressed at a higher level at baseline or after challenge with S.  Typhi in subjects who did not develop symptoms of typhoid. These data suggest that functional differences relating to redox potential and ion homeostasis in the gut microbiota may impact clinical outcomes following exposure to wild-type S.  Typhi. IMPORTANCE S.  Typhi is a significant cause of systemic febrile morbidity in settings with poor sanitation and limited access to clean water. It has been demonstrated that the human gut microbiota can influence mucosal immune responses, but there is little information available on the impact of the human gut microbiota on clinical outcomes following exposure to enteric pathogens. Here, we describe differences in the composition and function of the gut microbiota in healthy adult volunteers enrolled in a typhoid vaccine trial and report that these differences are associated with host susceptibility to or protection from typhoid after challenge with wild-type S . Typhi. Our observations have important implications in interpreting the efficacy of oral attenuated vaccines against enteric pathogens in diverse populations.

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