The application of omics techniques to understand the role of the gut microbiota in inflammatory bowel disease

The aetiopathogenesis of inflammatory bowel diseases (IBD) involves the complex interaction between a patient’s genetic predisposition, environment, gut microbiota and immune system. Currently, however, it is not known if the distinctive perturbations of the gut microbiota that appear to accompany both Crohn’s disease and ulcerative colitis are the cause of, or the result of, the intestinal inflammation that characterizes IBD. With the utilization of novel systems biology technologies, we can now begin to understand not only details about compositional changes in the gut microbiota in IBD, but increasingly also the alterations in microbiota function that accompany these. Technologies such as metagenomics, metataxomics, metatranscriptomics, metaproteomics and metabonomics are therefore allowing us a deeper understanding of the role of the microbiota in IBD. Furthermore, the integration of these systems biology technologies through advancing computational and statistical techniques are beginning to understand the microbiome interactions that both contribute to health and diseased states in IBD. This review aims to explore how such systems biology technologies are advancing our understanding of the gut microbiota, and their potential role in delineating the aetiology, development and clinical care of IBD

Increasing culturability of plant microbiome towards core microbiome manipulation and engineering

This study aimed to optimize the use of plant-based culture media for exploration of the plant-associated microbiota and extend the culturability borders to isolate novel bacterial taxa and meticulously characterize the culture-dependent and culture-independent microbiomes in view of the developed plant-based culture media. Throughout the study, we could prove that plant-based culture media are able to support the recovery of previously uncultured plant-associated bacteria, and also support the enrichment of bacterial lineages that belong to the candidate phyla radiation (CPR)

Soil Metagenomics: Concepts and Applications

Soil is a living entity of the Earth, and considered as one of the main reservoir of microbial diversity. Studying the soil microbial diversity is very much necessary, as they play an important role in maintaining the health of soil by recycling the nutrients, creating soil structure and humus. However, the culture dependent approaches fail to provide clear estimates of the diversity and untapped resources. Hence, study of the microbial diversity using culture independent approaches become necessary. The field of metagenomics helps in studying the genomes of the diverse soil organisms collectively in their natural habitat which holds the promising for accessing novel genetic resources. Application of the metagenomics to the soil environment is very challenging due to several difficulties; one of which is co-extraction of humic acid with nucleic acids which hinder downstream high throughout processes. However, applying sequencing methods to soil microbial communities will help in uncovering the hidden resources like novel genes, biomolecules and other valuable products which are yet to be discovered or still unknown. Different culture independent techniques and applications of the metagenomics to study the abundant microflora of the complex and changing environment of soil discussed herein

Synergies of systems biology and synthetic biology in human microbiome studies

A number of studies have shown that the microbial communities of the human body are integral for the maintenance of human health. Advances in next generation sequencing have enabled rapid and large-scale quantification of the composition of microbial communities in health and disease. Microorganisms mediate diverse host responses including metabolic pathways and immune responses. Using a system biology approach to further understand the underlying alterations of the microbiota in physiological and pathological states, can help reveal potential novel therapeutic and diagnostic interventions within the field of synthetic biology. Tools such as biosensors, memory arrays and engineered bacteria can rewire the microbiome environment. In this article, were view the computational tools used to study microbiome communities and the current limitations of these methods. We evaluate how genome-scale metabolic models can advance our understanding of the microbe-microbe and microbe-host interactions. Moreover, we present how synergies between these system biology approaches and synthetic biology can be harnessed in human microbiome studies to improve future therapeutics and diagnostics and highlight important knowledge gaps for future research in these rapidly evolving fields

Systematic Evaluation of Database Builds in Metaproteomics for the Advancement of Microbiome Research

The microscopic life that inhabits a human shares a unique bond with its host. Microbes perform many functions that are vital to the survival of the human species and have long been shown to regulate the absorption of nutrients and to promote immune function. A lack of exposure to certain microbes early in life, excessive antibiotic usage, and improper diet can perturb human microbiomes and lead to disease. Since the emergence of omic sequencing technologies, it has now become possible to measure and monitor the genes and proteins made by these microorganisms to better understand how they contribute to host health or drive potential disease conditions. Early attempts at studying the genomes and proteomes of these environments have revealed that each person may house a unique community of microbial species, each of which contributes distinct and unique functions that separate healthy vs. disbiotic human gut microbiomes. A subfield of the omics known as metaproteomics is now being used to help characterize all proteins found in an environment, and it has been found to show tremendous potential for describing these microbial systems. However, a great deal remains to be done in this field to improve the accuracy and depth of information gained from these investigations. There is currently no accepted standard for determining which genomic databases are best suitable for searching protein sequencing data and it is difficult to know how/ if false positives are being incorporated into the results. The research for this thesis investigated how database curation affects the number of identified proteins and peptides identified from mice gut metaproteome spectra and explored how functional and taxonomic annotation varied according to the database used. The results indicated that translating a high-depth sequenced and assembled metagenome yielded the highest number of identifications while maintaining a low false discovery rate for mice fecal samples and that each database build identified unique and distinct functional and taxonomic information. The goal of this thesis is to better inform the field of metaproteomics and hopefully guide researchers towards a standard practice of using deep metagenome sequencing for database curation, resulting in more thorough coverage of microbiomes with greater confidence

Current Insight into Culture-Dependent and Culture- Independent Methods in Discovering Ascomycetous Taxa

This research was funded by the National Natural Science Foundation of China (No. NSFC 31950410558, NSFC 31760013), the State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medicial University (No. FAMP201906K); Science and Technology Department of Guizhou Province (QKHRCPT [2017]5101) and High-Level Talent Recruitment Plan of Yunnan Provinces ("Young Talents" Program and "High-End Foreign Experts" Program).Nalin N. Wijayawardene and Dong-Qin Dai gratefully acknowledge Paul M. Kirk, Sandhya Jayasekara, Shalini Rajakaruna, D. Siril A. Wijesundara, Steve L. Stephenson, R.P. Prabat K. Jayasinghe, Samantha C. Karunarathne, Faruk Selcuk, Makbule Erdogdu and Kevin D. Hyde for their suggestions and support.Culture techniques are vital in both traditional and modern fungal taxonomy. Establishing sexual-asexual links and synanamorphs, extracting DNA and secondary metabolites are mainly based on cultures. However, it is widely accepted that a large number of species are not sporulating in nature while others cannot be cultured. Recent ecological studies based on culture-independent methods revealed these unculturable taxa, i.e., dark taxa. Recent fungal diversity estimation studies suggested that environmental sequencing plays a vital role in discovering missing species. However, Sanger sequencing is still the main approach in determining DNA sequences in culturable species. In this paper, we summarize culture-based and culture-independent methods in the study of ascomycetous taxa. High-throughput sequencing of leaf endophytes, leaf litter fungi and fungi in aquatic environments is important to determine dark taxa. Nevertheless, currently, naming dark taxa is not recognized by the ICN, thus provisional naming of them is essential as suggested by several studies.National Natural Science Foundation of China (NSFC) NSFC 31950410558- NSFC 31760013State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medicial University FAMP201906KScience and Technology Department of Guizhou Province QKHRCPT [2017]5101High-Level Talent Recruitment Plan of Yunnan Province

Chapter 12: Human Microbiome Analysis

Humans are essentially sterile during gestation, but during and after birth, every body surface, including the skin, mouth, and gut, becomes host to an enormous variety of microbes, bacterial, archaeal, fungal, and viral. Under normal circumstances, these microbes help us to digest our food and to maintain our immune systems, but dysfunction of the human microbiota has been linked to conditions ranging from inflammatory bowel disease to antibiotic-resistant infections. Modern high-throughput sequencing and bioinformatic tools provide a powerful means of understanding the contribution of the human microbiome to health and its potential as a target for therapeutic interventions. This chapter will first discuss the historical origins of microbiome studies and methods for determining the ecological diversity of a microbial community. Next, it will introduce shotgun sequencing technologies such as metagenomics and metatranscriptomics, the computational challenges and methods associated with these data, and how they enable microbiome analysis. Finally, it will conclude with examples of the functional genomics of the human microbiome and its influences upon health and disease

Characterization of Human Gut Microbiota Dynamics Using Model Communities in Gnotobiotic Mice

The human gut is colonized by a diverse array of microbes, collectively referred to as the microbiota. The microbiota\u27s complexity poses significant challenges in characterizing the rules dictating its assembly, inferring the functional roles of its component species, and understanding how communities sense and respond to changes in their habitat. We developed defined, representative model communities comprised of sequenced human gut bacteria that could be characterized in a highly controlled manner in gnotobiotic mice, plus a suite of scalable molecular tools for assaying community properties. These tools were first used to evaluate how the microbiota is impacted by probiotic bacterial strains found in fermented milk products: FMP). Introduction of a consortium of five FMP strains resulted in only minimal changes in the structural configuration of a 15-member model microbiota. However, RNA-Seq and follow-up mass spectrometry revealed numerous functional responses, many related to carbohydrate metabolism. Results from a study performed in monozygotic twin pairs confirmed many of our observations in the model microbiota, showing that lessons learned from preclinical models can inform the design and interpretation of human studies. In a second set of experiments, we evaluated the impact of food on both a model community and its constituent taxa by feeding gnotobiotic mice oscillating diets of disparate composition. In addition to prompt and reversible structural reconfigurations suggesting rules-based diet effects, we noted consistent, staggered changes in the representation of many functions within the metatranscriptome related to carbohydrate and amino acid metabolism. One prominent community member, Bacteroides cellulosilyticus WH2, was identified as an adaptive forager that tailors its versatile carbohydrate utilization strategy to the dietary polysaccharides available. The specific carbohydrates that trigger expression of many of this organism\u27s 113 predicted polysaccharide utilization loci were identified by RNA-Seq analysis during in vitro growth on 31 distinct carbohydrate substrates, aiding our interpretation of in vivo RNA-Seq and high resolution proteomics data. These results offer insight into how gut microbes adapt to dietary perturbations, both at a community level and from the perspective of a well-adapted symbiont with exceptional saccharolytic capabilities, and illustrate the value of studying defined models of the human gut microbiota