scholarly journals Colonic Butyrate-Producing Communities in Humans: an Overview Using Omics Data

mSystems ◽  
2017 ◽  
Vol 2 (6) ◽  
Author(s):  
Marius Vital ◽  
André Karch ◽  
Dietmar H. Pieper
Keyword(s):  
Gut Microbiota ◽  
Functional Group ◽  
Taxonomic Diversity ◽  
Noncommunicable Diseases ◽  
Data Sets ◽  
Omics Data ◽  
Host Interactions ◽  
Functional Capabilities ◽  
Host Health ◽  
Health And Disease

ABSTRACT Studies focusing on taxonomic compositions of the gut microbiota are plentiful, whereas its functional capabilities are still poorly understood. Specific key functions deserve detailed investigations, as they regulate microbiota-host interactions and promote host health and disease. The production of butyrate is among the top targets since depletion of this microbe-derived metabolite is linked to several emerging noncommunicable diseases and was shown to facilitate establishment of enteric pathogens by disrupting colonization resistance. In this study, we established a workflow to investigate in detail the composition of the polyphyletic butyrate-producing community from omics data extracting its biochemical and taxonomic diversity. By combining information from various publicly available data sets, we identified universal ecological key features of this functional group and shed light on its role in health and disease. Our results will assist the development of precision medicine to combat functional dysbiosis. Given the key role of butyrate for host health, understanding the ecology of intestinal butyrate-producing communities is a top priority for gut microbiota research. To this end, we performed a pooled analysis on 2,387 metagenomic/transcriptomic samples from 15 publicly available data sets that originated from three continents and encompassed eight diseases as well as specific interventions. For analyses, a gene catalogue was constructed from gene-targeted assemblies of all genes from butyrate synthesis pathways of all samples and from an updated reference database derived from genome screenings. We demonstrate that butyrate producers establish themselves within the first year of life and display high abundances (>20% of total bacterial community) in adults regardless of origin. Various bacteria form this functional group, exhibiting a biochemical diversity including different pathways and terminal enzymes, where one carbohydrate-fueled pathway was dominant with butyryl coenzyme A (CoA):acetate CoA transferase as the main terminal enzyme. Subjects displayed a high richness of butyrate producers, and 17 taxa, primarily members of the Lachnospiraceae and Ruminococcaceae along with some Bacteroidetes, were detected in >70% of individuals, encompassing ~85% of the total butyrate-producing potential. Most of these key taxa were also found to express genes for butyrate formation, indicating that butyrate producers occupy various niches in the gut ecosystem, concurrently synthesizing that compound. Furthermore, results from longitudinal analyses propose that diversity supports functional stability during ordinary life disturbances and during interventions such as antibiotic treatment. A reduction of the butyrate-producing potential along with community alterations was detected in various diseases, where patients suffering from cardiometabolic disorders were particularly affected. IMPORTANCE Studies focusing on taxonomic compositions of the gut microbiota are plentiful, whereas its functional capabilities are still poorly understood. Specific key functions deserve detailed investigations, as they regulate microbiota-host interactions and promote host health and disease. The production of butyrate is among the top targets since depletion of this microbe-derived metabolite is linked to several emerging noncommunicable diseases and was shown to facilitate establishment of enteric pathogens by disrupting colonization resistance. In this study, we established a workflow to investigate in detail the composition of the polyphyletic butyrate-producing community from omics data extracting its biochemical and taxonomic diversity. By combining information from various publicly available data sets, we identified universal ecological key features of this functional group and shed light on its role in health and disease. Our results will assist the development of precision medicine to combat functional dysbiosis.

scholarly journals Role of Biological Sex in the Cardiovascular-Gut Microbiome Axis

2022 ◽  
Vol 8 ◽  
Author(s):  
Shuangyue Li ◽  
Georgios Kararigas
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
Microbial Composition ◽  
Biological Sex ◽  
Technological Advances ◽  
Host Health ◽  
Health And Disease ◽  
And Function ◽  
Insight Into

There has been a recent, unprecedented interest in the role of gut microbiota in host health and disease. Technological advances have dramatically expanded our knowledge of the gut microbiome. Increasing evidence has indicated a strong link between gut microbiota and the development of cardiovascular diseases (CVD). In the present article, we discuss the contribution of gut microbiota in the development and progression of CVD. We further discuss how the gut microbiome may differ between the sexes and how it may be influenced by sex hormones. We put forward that regulation of microbial composition and function by sex might lead to sex-biased disease susceptibility, thereby offering a mechanistic insight into sex differences in CVD. A better understanding of this could identify novel targets, ultimately contributing to the development of innovative preventive, diagnostic and therapeutic strategies for men and women.

scholarly journals Gut Microbiota Metabolism and Interaction with Food Components

2020 ◽  
Vol 21 (10) ◽  
pp. 3688 ◽  
Author(s):  
Pamela Vernocchi ◽  
Federica Del Chierico ◽  
Lorenza Putignani
Keyword(s):  
Gut Microbiota ◽  
Disease Onset ◽  
Human Gut ◽  
Food Components ◽  
Host Health ◽  
Wide Variability ◽  
Gut Microbe ◽  
A Cell ◽  
Health And Disease ◽  
Biochemical Mechanisms

The human gut contains trillions of microbes that play a central role in host biology, including the provision of key nutrients from the diet. Food is a major source of precursors for metabolite production; in fact, diet modulates the gut microbiota (GM) as the nutrients, derived from dietary intake, reach the GM, affecting both the ecosystem and microbial metabolic profile. GM metabolic ability has an impact on human nutritional status from childhood. However, there is a wide variability of dietary patterns that exist among individuals. The study of interactions with the host via GM metabolic pathways is an interesting field of research in medicine, as microbiota members produce myriads of molecules with many bioactive properties. Indeed, much evidence has demonstrated the importance of metabolites produced by the bacterial metabolism from foods at the gut level that dynamically participate in various biochemical mechanisms of a cell as a reaction to environmental stimuli. Hence, the GM modulate homeostasis at the gut level, and the alteration in their composition can concur in disease onset or progression, including immunological, inflammatory, and metabolic disorders, as well as cancer. Understanding the gut microbe–nutrient interactions will increase our knowledge of how diet affects host health and disease, thus enabling personalized therapeutics and nutrition.

scholarly journals A global omics data sharing and analytics marketplace: Case study of a rapid data COVID-19 pandemic response platform

2020 ◽  
Author(s):  
Ibrahim Farah ◽  
Giada Lalli ◽  
Darrol Baker ◽  
Axel Schumacher
Keyword(s):  
Data Sharing ◽  
Biomarker Discovery ◽  
Disease Outbreaks ◽  
Ease Of Use ◽  
Diagnostic Tools ◽  
Data Sets ◽  
Omics Data ◽  
Host Interactions ◽  
Healthcare Data ◽  
Global Pandemic

AbstractUnder public health emergencies, particularly an early epidemic, it is fundamental that genetic and other healthcare data is shared across borders in both a timely and accurate manner before the outbreak of a global pandemic. However, although the COVID-19 pandemic has created a tidal wave of data, most patient data is siloed, not easily accessible, and due to low sample size, largely not actionable. Based on the precision medicine platform Shivom, a novel and secure data sharing and data analytics marketplace, we developed a versatile pandemic preparedness platform that allows healthcare professionals to rapidly share and analyze genetic data. The platform solves several problems of the global medical and research community, such as siloed data, cross-border data sharing, lack of state-of-the-art analytic tools, GDPR-compliance, and ease-of-use. The platform serves as a central marketplace of ‘discoverability’. The platform combines patient genomic & omics data sets, a marketplace for AI & bioinformatics algorithms, new diagnostic tools, and data-sharing capabilities to advance virus epidemiology and biomarker discovery. The bioinformatics marketplace contains some preinstalled COVID-19 pipelines to analyze virus- and host genomes without the need for bioinformatics expertise. The platform will be the quickest way to rapidly gain insight into the association between virus-host interactions and COVID-19 in various populations which can have a significant impact on managing the current pandemic and potential future disease outbreaks.

Gastrointestinal Microbiota and Colon Cancer

2016 ◽  
Vol 34 (3) ◽  
pp. 244-250 ◽  
Author(s):  
Georgina L. Hold
Keyword(s):  
Gut Microbiota ◽  
Good Health ◽  
Cancer Development ◽  
Gastrointestinal Microbiota ◽  
Human Gut ◽  
Microbial Biofilms ◽  
Functional Capabilities ◽  
Health Burden ◽  
Host Health

The human gut microbiota plays a major role in the development and maintenance of good health. Many recent studies have attempted to define links between microbiota residents, their function and the development of colorectal cancer (CRC). Gut microbiota drive the development of inflammation within the colon and such inflammation is implicated in colonic neoplastic development. Although the precise mechanisms through which the microbiota is involved in cancer development remain elusive, the message is clear: the microbiota contributes to cancer risk by influencing a number of key host processes. It is also recognized that we have the ability to influence the role of the gut microbiota by considering our nutritional intake. We have always known that ‘we are what we eat' but it is also true that ‘they (our gut microbiota) are what we eat'. We therefore have a huge opportunity to positively influence our health through microbial manipulation. There is now a clear need to move past defining the constituents of the gastrointestinal microbiota and to focus more on understanding the functional capabilities of the resident microbial community and how this impacts on host health. One such emerging concept is the development of microbial biofilms which can form in the gut in conjunction with CRC tissue. By better understanding of the interaction between the host and its resident microbiota, in the context of health and cancer development, we will open new therapeutic and diagnostic opportunities for reducing the CRC global health burden.

scholarly journals Gut Microbial Alterations in Diarrheal Baer's Pochards (Aythya baeri)

2021 ◽  
Vol 8 ◽  
Author(s):  
Li Xi ◽  
Xinxi Qin ◽  
Yumin Song ◽  
Jincheng Han ◽  
Zhiqiang Li ◽  
...  
Keyword(s):  
Statistical Analysis ◽  
Gut Microbiota ◽  
Internal Transcribed Spacer ◽  
Fungal Diversity ◽  
High Throughput Sequencing ◽  
Microbial Structure ◽  
Composition And Structure ◽  
Host Health ◽  
Health And Disease ◽  
The Relationship

The structure and composition of gut microbiota correlate with the occurrence and development of host health and disease. Diarrhea can cause alterations in gut microbiota in animals, and the changes in the gut microbial structure and composition may affect the development of diarrhea. However, there is a scarcity of information on the effects of diarrhea on gut fungal composition and structure, particularly in Baer's pochard (Aythya baeri). The current study was performed for high-throughput sequencing of the fungal-specific internal transcribed spacer 1 (ITS-1) to detect the differences of gut mycobiota in healthy and diarrheal Baer's pochard. Results showed that the gut mycobiota not only decreased significantly in diversity but also in structure and composition. Statistical analysis between two groups revealed a significant decrease in the abundance of phylum Rozellomycota, Zoopagomycota, Mortierellomycota, and Kickxellomycota in diarrheal Baer's pochard. At the genus levels, fungal relative abundance changed significantly in 95 genera, with 56 fungal genera, such as Wickerhamomyces, Alternaria, Penicillium, Cystofilobasidium, and Filobasidium, increasing significantly in the gut of the diarrheal Baer's pochard. In conclusion, the current study revealed the discrepancy in the gut fungal diversity and community composition between the healthy and diarrheal Baer's pochard, laying the basis for elucidating the relationship between diarrhea and the gut mycobiota in Baer's pochard.

scholarly journals The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

2016 ◽  
Vol 1 (10) ◽  
Author(s):  
Ilias Lagkouvardos ◽  
Rüdiger Pukall ◽  
Birte Abt ◽  
Bärbel U. Foesel ◽  
Jan P. Meier-Kolthoff ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Intestinal Bacteria ◽  
Future Research ◽  
Bacterial Strains ◽  
Host Interactions ◽  
Functional Potential ◽  
Health And Disease ◽  
Mouse Intestine ◽  
Reference Strains ◽  
Insight Into

Abstract Intestinal bacteria influence mammalian physiology, but many types of bacteria are still uncharacterized. Moreover, reference strains of mouse gut bacteria are not easily available, although mouse models are extensively used in medical research. These are major limitations for the investigation of intestinal microbiomes and their interactions with diet and host. It is thus important to study in detail the diversity and functions of gut microbiota members, including those colonizing the mouse intestine. To address these issues, we aimed at establishing the Mouse Intestinal Bacterial Collection (miBC), a public repository of bacterial strains and associated genomes from the mouse gut, and studied host-specificity of colonization and sequence-based relevance of the resource. The collection includes several strains representing novel species, genera and even one family. Genomic analyses showed that certain species are specific to the mouse intestine and that a minimal consortium of 18 strains covered 50–75% of the known functional potential of metagenomes. The present work will sustain future research on microbiota–host interactions in health and disease, as it will facilitate targeted colonization and molecular studies. The resource is available at www.dsmz.de/miBC.

scholarly journals The Impact of Dietary Fiber on Gut Microbiota in Host Health and Disease

2018 ◽  
Vol 23 (6) ◽  
pp. 705-715 ◽  
Author(s):  
Kassem Makki ◽  
Edward C. Deehan ◽  
Jens Walter ◽  
Fredrik Bäckhed
Keyword(s):  
Gut Microbiota ◽  
Dietary Fiber ◽  
Host Health ◽  
Health And Disease ◽  
The Impact

scholarly journals Probiotics, gut microbiota, and their influence on host health and disease

2016 ◽  
Vol 61 (1) ◽  
pp. 1600240 ◽  
Author(s):  
Borja Sánchez ◽  
Susana Delgado ◽  
Aitor Blanco-Míguez ◽  
Anália Lourenço ◽  
Miguel Gueimonde ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Host Health ◽  
Health And Disease

scholarly journals The Microbiota-Bone-Allergy Interplay

2021 ◽  
Vol 19 (1) ◽  
pp. 282
Author(s):  
Maria Maddalena Sirufo ◽  
Francesca De Pietro ◽  
Alessandra Catalogna ◽  
Lia Ginaldi ◽  
Massimo De Martinis
Keyword(s):  
Immune System ◽  
Gut Microbiota ◽  
Bone Metabolism ◽  
Hormonal Status ◽  
Negative Effects ◽  
Host Interactions ◽  
Treatment And Prevention ◽  
Wide Range ◽  
Health And Disease ◽  
Practical Implications

Emerging knowledge suggests an increasing importance of gut microbiota in health and disease. Allergy and bone metabolism are closely interconnected, and the possible negative effects of common therapies are not the only aspects of this relationship. The immune system is influenced by the microbiota-host interactions, and several pieces of evidence suggest the existence of an interplay between microbiota, bone metabolism, and allergies. Understanding these inter-relationships is essential for the development of new potential strategies of treatment and prevention targeting microbiota. A wide range of substances and germs, prebiotics and probiotics, are capable of influencing and modifying the microbiota. Prebiotics and probiotics have been shown in several studies to have different actions based on various factors such as sex, hormonal status, and age. In this review, we summarize the latest knowledge on the topic, and we discuss practical implications and the need for further studies.

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