Gut Microbiome Research Research Articles

Challenges and opportunities of strain diversity in gut microbiome research.

Just because two things are related does not mean they are the same. In analyzing microbiome data, we are often limited to species-level analyses, and even with the ability to resolve strains, we lack comprehensive databases and understanding of the importance of strain-level variation outside of a limited number of model organisms. The bacterial genome is highly plastic with gene gain and loss occurring at rates comparable or higher than de novo mutations. As such, the conserved portion of the genome is often a fraction of the pangenome which gives rise to significant phenotypic variation, particularly in traits which are important in host microbe interactions. In this review, we discuss the mechanisms that give rise to strain variation and methods that can be used to study it. We identify that while strain diversity can act as a major barrier in interpreting and generalizing microbiome data, it can also be a powerful tool for mechanistic research. We then highlight recent examples demonstrating the importance of strain variation in colonization, virulence, and xenobiotic metabolism. Moving past taxonomy and the species concept will be crucial for future mechanistic research to understand microbiome structure and function.

Gut microbiome and renal transplantation.

Gut microbiome research has been a surge of interest in many branches of medicine in the last decade. Our main aim is to show ability of microbes to infuence the functions of human body, especially in the immune system, and on the other hand to clarify changes in composition of gut microbiome in the post-transplantation period and their function for the long-term survival of the graft and the patient in the context of the occurrence of a wide range of complications. Kidney transplantation with the subsequent use of immunosuppressants and antibiotics affects the composition of gut microbiome. The subsequent development of dysbiosis significantly increases the risk of acute rejection, interstitial fibrosis and tubular atrophy of the graft, post-transplant diarrhoea, organ´s infections and metabolic complications such as post-transplant diabetes mellitus. Also important is the influence of the microorganisms of the gut microbiome on metabolism of immunosuppressants with the production of less effective components and the subsequent necessity of modifying their levels with a higher risk of underdosing and the occurrence of graft rejection. Support of the composition of the gut microbiome in the post-transplantation period in favor of bacteria producing short chain fatty acids (SCFA) is possible by changing of diet with predominance of fiber, the application of probiotics, prebiotics. According to available studies, it can lead to benefits in term of metabolic compensation, to the induction of donor-specific tolerance and many others, with an overall improvement in the quality of patient and graft survival.

Fecal Microbiome Does Not Represent Whole Gut Microbiome

The current gut microbiome research relies on the fecal microbiome under the assumption that the fecal microbiome represents the microbiome of the entire gastrointestinal (GI) tract. However, there have been growing concerns about using feces as a proxy to study the gut microbiome. Here, we comprehensively analyzed the composition of microbiome and metabolites in the feces and at 14 different locations of GI tracts of genetically homogenous sibling pigs to evaluate the validity of using feces as a proxy to the whole gut microbiome. The composition of intestinal microbes constituting the gut microbiome at each intestinal content and feces and their metabolic compositions were thoroughly investigated through metagenome sequencing and an ultraperformance LC-MS/MS, respectively. The fluctuation in the composition of the microbiome in the stomach and the small intestine became stabilized from the large intestine to feces and was able to be categorized into 3 groups. The taxonomic α-diversities measured by ACE (abundance-based coverage estimator) richness and Shannon diversity indicated that the microbiome in the large intestine was much more diverse than those of the small intestine and feces. The highly independent intestinal microbes in the stomach and the small intestine became flourished in the large intestine and converged into a community with tightly connected networks. β-Diversity analyses by NMDS plots, PCA, and unsupervised hierarchical clustering all showed that the diversities of microbiome compositions were lowest in feces while highest in the large intestine. In accordance with fluctuation of the composition of gut microbiome along with the GI tract, the metabolic composition also completely differed in a location-specific manner along with the GI tract. Comparative analysis of the fecal microbiome and metabolites with those of the whole GI tract indicated that fecal microbiome is insufficient to represent the whole gut microbiome.

Geography and elevation as drivers of cloacal microbiome assemblages of a passerine bird distributed across Sulawesi, Indonesia

BackgroundEmpirical field studies allow us to view how ecological and environmental processes shape the biodiversity of our planet, but collecting samples in situ creates inherent challenges. The majority of empirical vertebrate gut microbiome research compares multiple host species against abiotic and biotic factors, increasing the potential for confounding environmental variables. To minimize these confounding factors, we focus on a single species of passerine bird found throughout the geologically complex island of Sulawesi, Indonesia. We assessed the effects of two environmental factors, geographic Areas of Endemism (AOEs) and elevation, as well as host sex on the gut microbiota assemblages of the Sulawesi Babbler, Pellorneum celebense, from three different mountains across the island. Using cloacal swabs, high-throughput-amplicon sequencing, and multiple statistical models, we identified the core microbiome and determined the signal of these three factors on microbial composition.ResultsThe five most prevalent bacterial phyla within the gut microbiome of P. celebense were Proteobacteria (32.6%), Actinobacteria (25.2%), Firmicutes (22.1%), Bacteroidetes (8.7%), and Plantomycetes (2.6%). These results are similar to those identified in prior studies of passeriform microbiomes. Overall, microbiota diversity decreased as elevation increased, irrespective of sex or AOE. A single ASV of Clostridium was enriched in higher elevation samples, while lower elevation samples were enriched with the genera Perlucidibaca (Family Moraxellaceae), Lachnoclostridium (Family Lachnospiraceae), and an unidentified species in the Family Pseudonocardiaceae.ConclusionsWhile the core microbiota families recovered here are consistent with other passerine studies, the decreases in diversity as elevation increases has only been seen in non-avian hosts. Additionally, the increased abundance of Clostridium at high elevations suggests a potential microbial response to lower oxygen levels. This study emphasizes the importance of incorporating multiple statistical models and abiotic factors such as elevation in empirical microbiome research, and is the first to describe an avian gut microbiome from the island of Sulawesi.

The gut microbiome and hypertension.

A large body of evidence has emerged in the past decade supporting a role for the gut microbiome in the regulation of blood pressure. The field has moved from association to causation in the last 5 years, with studies that have used germ-free animals, antibiotic treatments and direct supplementation with microbial metabolites. The gut microbiome can regulate blood pressure through several mechanisms, including through gut dysbiosis-induced changes in microbiome-associated gene pathways in the host. Microbiota-derived metabolites are either beneficial (for example, short-chain fatty acids and indole-3-lactic acid) or detrimental (for example, trimethylamine N-oxide), and can activate several downstream signalling pathways via G protein-coupled receptors or through direct immune cell activation. Moreover, dysbiosis-associated breakdown of the gut epithelial barrier can elicit systemic inflammation anddisrupt intestinal mechanotransduction. These alterations activate mechanisms that are traditionally associated with blood pressure regulation, such as the renin-angiotensin-aldosterone system, the autonomic nervous system, and the immune system. Several methodological and technological challenges remain in gut microbiome research, and the solutions involve minimizing confounding factors, establishing causality and acting globally to improve sample diversity. New clinical trials, precision microbiome medicine and computational methods such as Mendelian randomization have the potential to enable leveraging of the microbiome for translational applications to lower blood pressure.

Activity‐Based Protein Profiling – Enabling Phenotyping of Host‐Associated and Environmental Microbiomes

AbstractHost‐associated and environmental microbiomes play central roles in human health, biogeochemical cycling, response to ecosystem change, and agriculture. Scientific approaches that can reveal the functional activities that contribute to observed phenotypes are needed in microbiome research. Broad characterization of the functional activity of microbes within microbiomes is currently hampered by approaches that rely on inference of function from metagenomes or indirect measurements. Activity‐based protein profiling is uniquely positioned to overcome these challenges and reveal the protein‐level mechanisms associated with microbiome phenotypes. In this review we describe the progress made to date using ABPP in gut microbiome, plant‐microbe interaction, and soil microbiome research, and suggest how ABPP data can be coupled with advanced computational methods to enable phenotype prediction and bioengineering of microbiomes for applied purposes.

Association between Dysbiosis in the Gut Microbiota of Primary Osteoporosis Patients and Bone Loss.

In recent decades, gut microbiome research has experienced significant growth, driven by technological advances that enable quantifying bacterial taxa with greater precision. Age, diet, and living environment have emerged as three key factors influencing gut microbes. Dysbiosis, resulting from alterations in these factors, may lead to changes in bacterial metabolites that regulate pro- and anti-inflammatory processes and consequently impact bone health. Restoration of a healthy microbiome signature could mitigate inflammation and potentially reduce bone loss associated with osteoporosis or experienced by astronauts during spaceflight. However, current research is hindered by contradictory findings, insufficient sample sizes, and inconsistency in experimental conditions and controls. Despite progress in sequencing technology, defining a healthy gut microbiome across global populations remains elusive. Challenges persist in identifying accurate gut bacterial metabolics, specific taxa, and their effects on host physiology. We suggest greater attention be directed towards this issue in Western countries as the cost of treating osteoporosis in the United States reaches billions of dollars annually, with expenses projected to continue rising.

Pouch bacteria: an understudied and potentially important facet of marsupial reproduction

Australia is home to a rich biodiversity of marsupials that are found nowhere else. Unfortunately, many of these species are currently threatened with extinction due to introduced feral predators and other anthropogenic factors. There is growing recognition that host-associated microorganisms can play important roles for animal health, with billions of dollars currently being invested into human gut microbiome research and the development of microbiome-based therapeutics to improve human health. Can microorganisms also be harnessed to stem the tide of marsupial extinctions? In this review, we provide an overview of some of the challenges facing Australia’s marsupials, and our current understanding of the microbiology of the marsupial pouch. We also propose outstanding research questions pertaining to the marsupial pouch, which, if addressed, may provide actionable knowledge and novel microbial therapies that could help stem the tide of marsupial extinctions in Australia.

Application of emerging technologies for gut microbiome research.

Microbiome is associated with a wide range of diseases. The gut microbiome is also a dynamic reflection of health status, which can be modified, thus representing great potential to exploit the mechanisms that influence human physiology. Recent years have seen a dramatic rise in gut microbiome studies, which has been enabled by the rapidly evolving high-throughput sequencing methods (i.e. 16S rRNA sequencing and shotgun sequencing). As the emerging technologies for microbiome research continue to evolve (i.e. metatranscriptomics, metabolomics, culturomics, synthetic biology), microbiome research has moved beyond phylogenetic descriptions and towards mechanistic analyses. In this review, we highlight different approaches to study the microbiome, in particular, the current limitations and future promise of these techniques. This review aims to provide clinicians with a framework for studying the microbiome, as well as to accelerate the adoption of these techniques in clinical practice.

Advancing dietary assessment in human gut microbiome research: review and gap analysis

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The gut microbiome in human health and disease-Where are we and where are we going? A bibliometric analysis.

There are trillions of microbiota in our intestinal tract, and they play a significant role in health and disease via interacting with the host in metabolic, immune, neural, and endocrine pathways. Over the past decades, numerous studies have been published in the field of gut microbiome and disease. Although there are narrative reviews of gut microbiome and certain diseases, the whole field is lack of systematic and quantitative analysis. Therefore, we outline research status of the gut microbiome and disease, and present insights into developments and characteristics of this field to provide a holistic grasp and future research directions. An advanced search was carried out in the Web of Science Core Collection (WoSCC), basing on the term "gut microbiome" and its synonyms. The current status and developing trends of this scientific domain were evaluated by bibliometric methodology. CiteSpace was used to perform collaboration network analysis, co-citation analysis and citation burst detection. A total of 29,870 articles and 13,311 reviews were retrieved from the database, which involve 42,900 keywords, 176 countries/regions, 19,065 institutions, 147,225 authors and 4,251 journals. The gut microbiome and disease research is active and has received increasing attention. Co-cited reference analysis revealed the landmark articles in the field. The United States had the largest number of publications and close cooperation with other countries. The current research mainly focuses on gastrointestinal diseases, such as inflammatory bowel disease (IBD), ulcerative colitis (UC) and Crohn's disease (CD), while extra-intestinal diseases are also rising, such as obesity, diabetes, cardiovascular disease, Alzheimer's disease, Parkinson's disease. Omics technologies, fecal microbiota transplantation (FMT) and metabolites linked to mechanism would be more concerned in the future. The gut microbiome and disease has been a booming field of research, and the trend is expected to continue. Overall, this research field shows a multitude of challenges and great opportunities.

Heterogeneity and lyophilization comparison of stool processing for gastrointestinal bile acid measurement by LC-MS/MS

Fecal bile acid (BA) analysis is an emerging area of gut microbiome research. However, sample preparation procedures for fecal BA analysis are not standardized. Current fecal BA analysis often utilizes either original or lyophilized aliquot, and fecal BA result difference between these two processing steps remains not systematically investigated. Moreover, the distribution pattern of fecal BA in the collected stool sample also remains unclear but affects interpretation of fecal BA for downstream experiments. To address these two questions regarding effect of lyophilization on fecal BA and fecal heterogeneity, fourteen separate BAs were quantified from 60 aliquots obtained from 10 clinical fecal samples using liquid chromatography-tandem mass spectrometry (LC-MS/MS). BA concentrations in the lyophilized sample were typically 2–4 folds higher than those in the original sample, but were almost identical using a water-adjusted lyophilized BA concentration. The fecal BA compositional profile and four BA ratios were similar utilizing either the original or lyophilized samples. BA concentrations were similar among different aliquots of differing starting mass except for the relatively trace-level BA. Therefore, it is suggested that fecal BA concentrations should be presented as the original sample concentration or water-adjusted lyophilization concentration to allow comparisons between studies. A single aliquot (20–100 mg) of stool can be used to reflect the concentrations in the entire sample. These results help to standardize analyses in this emerging field.

Westlake Gut Project: A consortium of microbiome epidemiology for the gut microbiome and health research in China

Microbiome epidemiology is an emerging field for the discovery of novel disease biomarkers or intervention targets in human epidemiological studies. The determinants and consequences of human microbiome variations, especially for the gut microbiome, are both important and unsolved research questions, while the majority of findings of prior research are based on small-scale human studies with limited statistical power and a lack of replication/generalizability across different populations. Here, we initiated the Westlake Gut (WeGut) project, a consortium of gut microbiome-based human cohort studies in China. The WeGut project aims to provide a platform for the integration of gut microbiome data across different cohort studies, including two major components: 1) cohorts for healthy ageing and 2) cohorts for healthy pregnancy. The WeGut consortium includes seven core/foundation cohorts involving over 32,000 participants with gut microbiome and rich phenotype data across 17 provinces/megacities in China. Within the WeGut framework, we hope to disentangle the interplay among diet, lifestyle factors, host genetics and the gut microbiome in human health and explore the role of the gut microbiome for the precision prevention of chronic diseases in Chinese populations.

Diversity-scaling analysis of human breast milk microbiomes from population perspective.

Quantitative measuring the population-level diversity-scaling of human microbiomes is different from conventional approach to traditional individual-level diversity analysis, and it is of obvious significance. For example, it is well known that individuals are of significant heterogeneity with their microbiome diversities, and the population-level analysis can effectively capture such kind of individual differences. Here we reanalyze a dozen datasets of 2,115 human breast milk microbiome (BMM) samples with diversity-area relationship (DAR) to tackle the previous questions. Our focus on BMM is aimed to offer insights for supplementing the gut microbiome research from nutritional perspective. DAR is an extension to classic species-area relationship, which was discovered in the 19th century and established as one of a handful fundamental laws in community ecology. Our DAR modeling revealed the following numbers, all approximately: (i) The population-level potential diversity of BMM is 1,108 in terms of species richness (number of total species), and 67 in terms of typical species. (ii) On average, an individual carry 17% of population-level diversity in terms of species richness, and 61% in terms of typical species. (iii) The similarity (overlap) between individuals according to pair-wise diversity overlap (PDO) should be approximately 76% in terms of total species, and 92% in terms of typical species, which symbolizes the inter-individual heterogeneity. (iv) The average individual (alpha-) diversity of BMM is approximately 188 (total-species) and 37 (typical-species). (v) To deal with the potential difference among 12 BMM datasets, we conducted DAR modeling separately for each dataset, and then performed permutation tests for DAR parameters. It was found that the DAR scaling parameter that measures inter-individual heterogeneity in diversity is invariant (constant), but the population potential diversity is different among 30% of the pair-wise comparison between 12 BMM datasets. These results offer comprehensive biodiversity analyses of the BMM from host individual, inter-individual, and population level perspectives.

The Skin and Gut Microbiome in Hidradenitis Suppurativa: Current Understanding and Future Considerations for Research and Treatment.

Hidradenitis suppurativa (HS) is a chronic, inflammatory skin disease comprising painful abscesses, deep nodules, fistulas, and scarring predominantly in the axilla and groin. Bacterial colonization of HS lesions has been well characterized and may lead to chronic infection of lesions. While disease pathogenesis of HS is not fully understood, there is increasing evidence that microbial dysbiosis may be occurring in numerous locations, including the skin and gut. The skin-gut microbiome has been proposed as a mechanism by which inflammatory skin disorders, including HS, can be exacerbated. This is evidenced by HS patients being significantly more likely to develop inflammatory bowel disease as well as the well documented cutaneous manifestations in inflammatory bowel disease. In this review, we discuss the current literature regarding HS skin and gut microbiome research. Furthermore, we discuss further considerations for microbiome research in HS, including the potential role of bacterial metabolites in disease progression and future therapeutic avenues like probiotics.

MetaProClust-MS1: an MS1 Profiling Approach for Large-Scale Microbiome Screening.

ABSTRACTMetaproteomics is used to explore the functional dynamics of microbial communities. However, acquiring metaproteomic data by tandem mass spectrometry (MS/MS) is time-consuming and resource-intensive, and there is a demand for computational methods that can be used to reduce these resource requirements. We present MetaProClust-MS1, a computational framework for microbiome feature screening developed to prioritize samples for follow-up MS/MS. In this proof-of-concept study, we tested and compared MetaProClust-MS1 results on gut microbiome data, from fecal samples, acquired using short 15-min MS1-only chromatographic gradients and MS1 spectra from longer 60-min gradients to MS/MS-acquired data. We found that MetaProClust-MS1 identified robust gut microbiome responses caused by xenobiotics with significantly correlated cluster topologies of comparable data sets. We also used MetaProClust-MS1 to reanalyze data from both a clinical MS/MS diagnostic study of pediatric patients with inflammatory bowel disease and an experiment evaluating the therapeutic effects of a small molecule on the brain tissue of Alzheimer’s disease mouse models. MetaProClust-MS1 clusters could distinguish between inflammatory bowel disease diagnoses (ulcerative colitis and Crohn’s disease) using samples from mucosal luminal interface samples and identified hippocampal proteome shifts of Alzheimer’s disease mouse models after small-molecule treatment. Therefore, we demonstrate that MetaProClust-MS1 can screen both microbiomes and single-species proteomes using only MS1 profiles, and our results suggest that this approach may be generalizable to any proteomics experiment. MetaProClust-MS1 may be especially useful for large-scale metaproteomic screening for the prioritization of samples for further metaproteomic characterization, using MS/MS, for instance, in addition to being a promising novel approach for clinical diagnostic screening.IMPORTANCE Growing evidence suggests that human gut microbiome composition and function are highly associated with health and disease. As such, high-throughput metaproteomic studies are becoming more common in gut microbiome research. However, using a conventional long liquid chromatography (LC)-MS/MS gradient metaproteomics approach as an initial screen in large-scale microbiome experiments can be slow and expensive. To combat this challenge, we introduce MetaProClust-MS1, a computational framework for microbiome screening using MS1-only profiles. In this proof-of-concept study, we show that MetaProClust-MS1 identifies clusters of gut microbiome treatments using MS1-only profiles similar to those identified using MS/MS. Our approach allows researchers to prioritize samples and treatments of interest for further metaproteomic analyses and may be generally applicable to any proteomic analysis. In particular, this approach may be especially useful for large-scale metaproteomic screening or in clinical settings where rapid diagnostic evidence is required.

Gut-on-chip for ecological and causal human gut microbiome research

There is a growing interest to understand if and how the gut microbiome is causally linked to the pathogenesis and/or progression of diseases. While in vitro cell line models are commonly used for studying specific aspects of the host-microbe interaction, gnotobiotic murine models are considered the preferred platform for studying causality in microbiome research. Nevertheless, findings from animal studies provide limited opportunity for delineating various areas of interest to the human gut microbiome research. Gut-on-chips are biomimetics recapitulating intestinal physiology which enable investigation of bidirectional effects of the host and microbiome. We posit that they could advance causal and ecological gut microbiome research in three major areas: (i) diet-microbiome and drug-microbiome interaction; (ii) microbiome-targeted therapeutics pharmacoecology; and (iii) mechanistic studies of gut microbiome and microbiome-targeted intervention in extraintestinal pathologies.

The heart and gut relationship: a systematic review of the evaluation of the microbiome and trimethylamine-N-oxide (TMAO) in heart failure.

There is an expanding body of research on the bidirectional relationship of the human gut microbiome and cardiovascular disease, including heart failure (HF). Researchers are examining the microbiome and gut metabolites, primarily trimethylamine-N-oxide (TMAO), to understand clinically observed outcomes. This systematic review explored the current state of the science on the evaluation and testing of the gut biome in persons with HF. Using electronic search methods of Medline, Embase, CINAHL, and Web of Science, until December 2021, we identified 511 HF biome investigations between 2014 and 2021. Of the 30 studies included in the review, six were 16S rRNA and nineteen TMAO, and three both TMAO and 16S rRNA, and two bacterial cultures. A limited range of study designs were represented, the majority involving single cohorts (n = 10) and comparing individuals with HF to controls (n = 15). Patients with HF had less biodiversity in fecal samples compared to controls. TMAO is associated with age, BNP, eGFR, HF severity, and poor outcomes including hospitalizations and mortality. Inconsistent across studies was the ability of TMAO to predict HF development, the independent prognostic value of TMAO when controlling for renal indices, and the relationship of TMAO to LVEF and CRP. Gut microbiome dysbiosis is associated with HF diagnosis, disease severity, and prognostication related to hospitalizations and mortality. Gut microbiome research in patients with HF is developing. Further longitudinal and multi-centered studies are required to inform interventions to promote clinical decision-making and improved patient outcomes.

Stochastic block models reveal a robust nested pattern in healthy human gut microbiomes.

A key question in human gut microbiome research is what are the robust structural patterns underlying its taxonomic composition. Herein, we use whole metagenomic datasets from healthy human guts to show that such robust patterns do exist, albeit not in the conventional enterotype sense. We first introduce the concept of mixed-membership enterotypes using a network inference approach based on stochastic block models. We find that gut microbiomes across a group of people (hosts) display a nested structure, which has been observed in a number of ecological systems. This finding led us to designate distinct ecological roles to both microbes and hosts: generalists and specialists. Specifically, generalist hosts have microbiomes with most microbial species, while specialist hosts only have generalist microbes. Moreover, specialist microbes are only present in generalist hosts. From the nested structure of microbial taxonomies, we show that these ecological roles of microbes are generally conserved across datasets. Our results show that the taxonomic composition of healthy human gut microbiomes is associated with robustly structured combinations of generalist and specialist species.

Standards for Collection, Preservation, and Transportation of Fecal Samples in TCM Clinical Trials.

BackgroundUnlike chemical drugs with a single or a few kinds of active compounds, traditional Chinese medicines (TCMs)uses herbal formulas composed of numerous kinds of chemical constituents. Therefore, TCM clinical trials require unique and stricter standards for collecting, preserving, and transporting fecal samples than those used for chemical drugs. Unfortunately, there are no special standards for processing fecal samples in TCM clinical trials.MethodsWe invited interdisciplinary experts within TCM clinical trials and gut microbiome research to help formulate this standard. After more than a year’s in-depth discussion and amendments, we achieved a standard via expert interviews, literature research, questionnaire surveys, and public opinion solicitation. This standard has been reviewed and approved by the Standards Office of China of the Association of Chinese medicine.ResultsWe established a sample information processing method prior to TCM clinical sample collection, which is adapted to the unique features of TCM. The method formulates detailed processing requirements for TCM information in addition to the factors that may disturb the gut microbiome. We also constructed a set of methods for collecting, preserving, and transporting fecal samples that meet the characteristics of TCM. These methods formulate detailed operating specifications on the collection approaches, storage conditions, transportation requirements, and management of fecal samples.ConclusionsThis standard guides the information processing prior to sample collection and the standard operating procedures for the collection, preservation, and transportation of fecal samples in TCM clinical trials, which also can be used as a reference by clinicians and researchers in modern medicines.