Mapping of the benzoate metabolism by human gut microbiome indicates food-derived metagenome evolution

AbstractSodium benzoate is one of the widely used food preservatives and its metabolism in the human body has been studied only with the host perspective. Despite the human gut microbiome being considered as a virtual human organ, its role in benzoate metabolism is yet to be elucidated. The current study uses a multi-omic approach to rationalize the role of human gut microbes in benzoate metabolism. Microbial diversity analysis with multiple features synchronously indicates the dominance of Bacteroidetes followed by Firmicutes, Actinobacteria, and Proteobacteria. Metagenomic exploration highlights the presence of benzoate catabolic protein features. These features were mapped on to the aerobic and anaerobic pathways of benzoate catabolism. Benzoate catabolism assays identified statistically significant metabolites (P < 0.05) associated with the protocatechuate branch of the beta-ketoadipate pathway of the benzoate metabolism. Analysis of the 201 human gut metagenomic datasets across diverse populations indicates the omnipresence of these features. Enrichment of the benzoate catabolic protein features in human gut microbes rationalizes their role in benzoate catabolism, as well as indicates food-derived microbiome evolution.

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Role of dietary fiber in the recovery of the human gut microbiome and its metabolome

Cell Host & Microbe ◽

10.1016/j.chom.2020.12.012 ◽

2021 ◽

Author(s):

Ceylan Tanes ◽

Kyle Bittinger ◽

Yuan Gao ◽

Elliot S. Friedman ◽

Lisa Nessel ◽

...

Keyword(s):

Dietary Fiber ◽

Gut Microbiome ◽

Human Gut ◽

Human Gut Microbiome

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Global and temporal state of the human gut microbiome in health and disease

10.21203/rs.3.rs-339282/v1 ◽

2021 ◽

Author(s):

Saeed Shoaie ◽

Sunjae Lee ◽

Mathieu Almeida ◽

Gholamreza Bidkhori ◽

Nicolas Pons ◽

...

Keyword(s):

Gut Microbiome ◽

Integrative Analysis ◽

Human Gut ◽

Human Gut Microbiome ◽

Health And Disease ◽

One Year ◽

The Stability ◽

Clinical Phenotyping ◽

Sampling Times

Abstract The role of gut microbiota in humans is of great interest, and metagenomics provided the possibilities for extensively analysing bacterial diversity in health and disease. Here we explored the human gut microbiome samples across 19 countries, performing compositional, functional and integrative analysis. To complement these data and analyse the stability of the microbiome, we followed 86 healthy Swedish individuals over one year, with four sampling times and extensive clinical phenotyping. The integrative analysis of temporal microbiome changes shows the existence of two types of species with a tendency to vary in abundance with time, here called outflow and inflow species. Importantly, the former tends to be enriched in disease, while the latter is enriched in health. We suggest that the decrease of disease-associated outflow and the increase of health-associated inflow species with time may be a fundamental albeit previously unrecognized aspect of the homeostasis maintenance in a healthy microbiome.

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Role of Human Gut Microbiome in Health and Disease

Microbiome-Host Interactions ◽

10.1201/9781003037521-9 ◽

2021 ◽

pp. 101-112

Author(s):

Nazar Reehana ◽

Mohamed Yousuff Mohamed Imran ◽

Nooruddin Thajuddin ◽

D. Dhanasekaran

Keyword(s):

Gut Microbiome ◽

Human Gut ◽

Human Gut Microbiome ◽

Health And Disease

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What is the role of cyclic di-GMP signaling within the human gut microbiome?

Microbiome Science and Medicine ◽

10.2478/micsm-2014-0001 ◽

2014 ◽

Vol 1 (1) ◽

Cited By ~ 2

Author(s):

Rachel M. Rudlaff ◽

Christopher M. Waters

Keyword(s):

Gut Microbiome ◽

Diguanylate Cyclase ◽

Human Gut ◽

Base Pairs ◽

Metagenomic Dna ◽

Human Gut Microbiome ◽

Commensal Species ◽

Stool Samples ◽

Specific Species

AbstractThere is currently little understanding of the role of the bacterial second messenger cyclic di-GMP (c-di-GMP) in the human gut microbiome. C-di-GMP is synthesized by highly conserved diguanylate cyclase (DGC) enzymes and degraded by highly conserved phosphodiesterase (PDE) enzymes. To begin to assess the prevalence of c-di-GMP signaling in the gut microbiome, we found on average 1.0 DGC and 0.8 PDE enzymes per million base pairs of metagenomic DNA derived from stool samples. Specific species encoding substantial numbers of GGDEF and EAL domains were the commensal species

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Examining the Effects of an Anti-Salmonella Bacteriophage Preparation, BAFASAL®, on Ex-Vivo Human Gut Microbiome Composition and Function Using a Multi-Omics Approach

Viruses ◽

10.3390/v13091734 ◽

2021 ◽

Vol 13 (9) ◽

pp. 1734

Author(s):

Janice Mayne ◽

Xu Zhang ◽

James Butcher ◽

Krystal Walker ◽

Zhibin Ning ◽

...

Keyword(s):

Food Chain ◽

Gut Microbiome ◽

Food Industry ◽

Ex Vivo ◽

Human Gut ◽

Microbiome Composition ◽

Human Gut Microbiome ◽

And Function ◽

The Impact

Salmonella infections (salmonellosis) pose serious health risks to humans, usually via food-chain contamination. This foodborne pathogen causes major food losses and human illnesses, with significant economic impacts. Overuse of antibiotics in the food industry has led to multidrug-resistant strains of bacteria, and governments are now restricting their use, leading the food industry to search for alternatives to secure food chains. Bacteriophages, viruses that infect and kill bacteria, are currently being investigated and used as replacement treatments and prophylactics due to their specificity and efficacy. They are generally regarded as safe alternatives to antibiotics, as they are natural components of the ecosystem. However, when specifically used in the industry, they can also make their way into humans through our food chain or exposure, as is the case for antibiotics. In particular, agricultural workers could be repeatedly exposed to bacteriophages supplemented to animal feeds. To our knowledge, no studies have investigated the effects of such exposure to bacteriophages on the human gut microbiome. In this study, we used a novel in-vitro assay called RapidAIM to investigate the effect of a bacteriophage mixture, BAFASAL®, used in poultry farming on five individual human gut microbiomes. Multi-omics analyses, including 16S rRNA gene sequencing and metaproteomic, revealed that ex-vivo human gut microbiota composition and function were unaffected by BAFASAL® treatment, providing an additional measure for its safety. Due to the critical role of the gut microbiome in human health and the known role of bacteriophages in regulation of microbiome composition and function, we suggest assaying the impact of bacteriophage-cocktails on the human gut microbiome as a part of their safety assessment.

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The Human Gut Phageome: Origins and Roles in the Human Gut Microbiome

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.643214 ◽

2021 ◽

Vol 11 ◽

Author(s):

Eleanor M. Townsend ◽

Lucy Kelly ◽

George Muscatt ◽

Joshua D. Box ◽

Nicole Hargraves ◽

...

Keyword(s):

Gut Microbiome ◽

Adult Life ◽

Microbial Populations ◽

Human Gut ◽

Bacterial Populations ◽

Human Gut Microbiome ◽

Microbiome Research ◽

Health And Disease ◽

Over Time

The investigation of the microbial populations of the human body, known as the microbiome, has led to a revolutionary field of science, and understanding of its impacts on human development and health. The majority of microbiome research to date has focussed on bacteria and other kingdoms of life, such as fungi. Trailing behind these is the interrogation of the gut viruses, specifically the phageome. Bacteriophages, viruses that infect bacterial hosts, are known to dictate the dynamics and diversity of bacterial populations in a number of ecosystems. However, the phageome of the human gut, while of apparent importance, remains an area of many unknowns. In this paper we discuss the role of bacteriophages within the human gut microbiome. We examine the methods used to study bacteriophage populations, how this evolved over time and what we now understand about the phageome. We review the phageome development in infancy, and factors that may influence phage populations in adult life. The role and action of the phageome is then discussed at both a biological-level, and in the broader context of human health and disease.

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Diversity and Distribution of Sulfur Metabolism 1 in the Human Gut Microbiome and its Association with Colorectal Cancer

10.21203/rs.3.rs-809984/v1 ◽

2021 ◽

Author(s):

Patricia G. Wolf ◽

Elise S. Cowley ◽

Adam Breister ◽

Sarah Matatov ◽

Luke Lucio ◽

...

Keyword(s):

Colorectal Cancer ◽

Sulfate Reduction ◽

Gut Microbiome ◽

Sulfur Metabolism ◽

Human Gut ◽

Human Gut Microbiome ◽

Metabolic Genes ◽

Comprehensive Knowledge ◽

Potential Trigger

Abstract Background: Microbial sulfidogenesis produces genotoxic hydrogen sulfide (H2S) in the human gut using inorganic (sulfate) and organic (taurine/cysteine/methionine) substrates, however the majority of studies have focused on sulfate reduction using dissimilatory sulfite reductases (Dsr). Recent evidence implicates microbial sulfidogenesis as a potential trigger of colorectal cancer (CRC), highlighting the need for comprehensive knowledge of sulfur metabolism within the human gut.Results: Here we show that microbial sulfur metabolism is more abundant and diverse than previously studied and is statistically associated with CRC. Using ~17,000 bacterial genomes from publicly available stool metagenomes, we studied the diversity of sulfur metabolic genes in 667 participants across different health statuses: healthy, adenoma, and carcinoma. Sulfidogenic genes were harbored by 142 bacterial genera and both organic and inorganic sulfidogenic genes were associated with carcinoma. Significantly, anaerobic sulfite reductases were twice as abundant as dsr, demonstrating that this enzyme is likely a more important contributor to sulfate reduction in the human gut. We identified twelve potential pathways for reductive taurine metabolism and discovered novel genera harboring these pathways. Finally, prevalence of metabolic genes for organic sulfur indicate that these understudied substrates may be the most abundant source of microbially derived H2S.Conclusions: Our findings significantly expand knowledge of microbial sulfur metabolism in the human gut. We show that microbial sulfur metabolism in the human gut is more prevalent than previously known, irrespective of health status (i.e., in both healthy and diseased states). Our results significantly increase the diversity of pathways and bacteria that are associated with microbial sulfur metabolism in the human gut. Overall, our results have implications for understanding the role of the human gut microbiome and its potential contributions to the pathogenesis of CRC.

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The gut mycobiome: a novel player in chronic liver diseases

Journal of Gastroenterology ◽

10.1007/s00535-020-01740-5 ◽

2020 ◽

Author(s):

Lu Jiang ◽

Peter Stärkel ◽

Jian-Gao Fan ◽

Derrick Eugene Fouts ◽

Petra Bacher ◽

...

Keyword(s):

Human Health ◽

Gut Microbiome ◽

Liver Diseases ◽

Therapeutic Targets ◽

Chronic Liver Diseases ◽

Human Gut ◽

Human Gut Microbiome ◽

The Impact ◽

Potential Use

Abstract The human gut microbiome (bacteria, fungi, viruses, and archaea) is a complex and diverse ecosystem. It plays an important role in human health, but is involved in several intestinal and extraintestinal diseases. Most research to date has focused on the role of bacteria, while studies focusing on fungi (also referred to as “mycobiome” or “fungome”) are still in its infancy. In this review, we focus on the existing literature available about the gut mycobiome with an emphasis on compositional mycobiome changes associated with liver diseases, the impact on pathogenesis of disease, and its potential use as therapeutic targets. We also provide insights into current methodologies of studying mycobiome, and we highlight the interkingdom interactions in the context of disease and how they affect health of the host. Herein, by focusing on the gut mycobiome, this review provides novel insights and directions for liver research.

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