scholarly journals Characterisation of novel functionality within the Blastocystis tryptophanase gene

2021 ◽  
Vol 15 (9) ◽  
pp. e0009730
Author(s):  
Steven Santino Leonardi ◽  
Feng-Jun Li ◽  
Melissa Su-Juan Chee ◽  
John Anthony Yason ◽  
Hui Yi Tay ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Phylogenetic Reconstruction ◽  
Bioinformatic Analysis ◽  
Complex Relationship ◽  
High Homology ◽  
Pathogenic Role ◽  
Human Gut ◽  
Functional Variation ◽  
Gastrointestinal Conditions

In recent years, the human gut microbiome has been recognised to play a pivotal role in the health of the host. Intestinal homeostasis relies on this intricate and complex relationship between the gut microbiota and the human host. While much effort and attention has been placed on the characterization of the organisms that inhabit the gut microbiome, the complex molecular cross-talk between the microbiota could also exert an effect on gastrointestinal conditions. Blastocystis is a single-cell eukaryotic parasite of emerging interest, as its beneficial or pathogenic role in the microbiota has been a subject of contention even to-date. In this study, we assessed the function of the Blastocystis tryptophanase gene (BhTnaA), which was acquired by horizontal gene transfer and likely to be of bacterial origin within Blastocystis. Bioinformatic analysis and phylogenetic reconstruction revealed distinct divergence of BhTnaA versus known bacterial homologs. Despite sharing high homology with the E. coli tryptophanase gene, we show that Blastocystis does not readily convert tryptophan into indole. Instead, BhTnaA preferentially catalyzes the conversion of indole to tryptophan. We also show a direct link between E. coli and Blastocystis tryptophan metabolism: In the presence of E. coli, Blastocystis ST7 is less able to metabolise indole to tryptophan. This study examines the potential for functional variation in horizontally-acquired genes relative to their canonical counterparts, and identifies Blastocystis as a possible producer of tryptophan within the gut.

scholarly journals Systematic characterization of human gut microbiome-secreted molecules by integrated multi-omics

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Bianca De Saedeleer ◽  
Antoine Malabirade ◽  
Javier Ramiro-Garcia ◽  
Janine Habier ◽  
Jean-Pierre Trezzi ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Complex Mixture ◽  
Host Cells ◽  
Methodological Framework ◽  
Secretion Systems ◽  
Human Gut ◽  
Healthy Human ◽  
Human Gut Microbiome ◽  
Health And Disease

AbstractThe human gut microbiome produces a complex mixture of biomolecules that interact with human physiology and play essential roles in health and disease. Crosstalk between micro-organisms and host cells is enabled by different direct contacts, but also by the export of molecules through secretion systems and extracellular vesicles. The resulting molecular network, comprised of various biomolecular moieties, has so far eluded systematic study. Here we present a methodological framework, optimized for the extraction of the microbiome-derived, extracellular biomolecular complement, including nucleic acids, (poly)peptides, and metabolites, from flash-frozen stool samples of healthy human individuals. Our method allows simultaneous isolation of individual biomolecular fractions from the same original stool sample, followed by specialized omic analyses. The resulting multi-omics data enable coherent data integration for the systematic characterization of this molecular complex. Our results demonstrate the distinctiveness of the different extracellular biomolecular fractions, both in terms of their taxonomic and functional composition. This highlights the challenge of inferring the extracellular biomolecular complement of the gut microbiome based on single-omic data. The developed methodological framework provides the foundation for systematically investigating mechanistic links between microbiome-secreted molecules, including those that are typically vesicle-associated, and their impact on host physiology in health and disease.

scholarly journals Characterization of the SOS meta-regulon in the human gut microbiome

2014 ◽  
Vol 30 (9) ◽  
pp. 1193-1197 ◽  
Author(s):  
Joseph P. Cornish ◽  
Neus Sanchez-Alberola ◽  
Patrick K. O’Neill ◽  
Ronald O'Keefe ◽  
Jameel Gheba ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Human Gut ◽  
Human Gut Microbiome

scholarly journals Reconstruction of ancient microbial genomes from the human gut

Nature ◽  
2021 ◽  
Author(s):  
Marsha C. Wibowo ◽  
Zhen Yang ◽  
Maxime Borry ◽  
Alexander Hübner ◽  
Kun D. Huang ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Large Scale ◽  
De Novo ◽  
Human Gut ◽  
Microbial Genomes ◽  
Functional Profiling ◽  
History Of ◽  
Southwestern Usa ◽  
Gut Microorganisms

AbstractLoss of gut microbial diversity1–6 in industrial populations is associated with chronic diseases7, underscoring the importance of studying our ancestral gut microbiome. However, relatively little is known about the composition of pre-industrial gut microbiomes. Here we performed a large-scale de novo assembly of microbial genomes from palaeofaeces. From eight authenticated human palaeofaeces samples (1,000–2,000 years old) with well-preserved DNA from southwestern USA and Mexico, we reconstructed 498 medium- and high-quality microbial genomes. Among the 181 genomes with the strongest evidence of being ancient and of human gut origin, 39% represent previously undescribed species-level genome bins. Tip dating suggests an approximate diversification timeline for the key human symbiont Methanobrevibacter smithii. In comparison to 789 present-day human gut microbiome samples from eight countries, the palaeofaeces samples are more similar to non-industrialized than industrialized human gut microbiomes. Functional profiling of the palaeofaeces samples reveals a markedly lower abundance of antibiotic-resistance and mucin-degrading genes, as well as enrichment of mobile genetic elements relative to industrial gut microbiomes. This study facilitates the discovery and characterization of previously undescribed gut microorganisms from ancient microbiomes and the investigation of the evolutionary history of the human gut microbiota through genome reconstruction from palaeofaeces.

scholarly journals Metaproteomics as a tool for studying the protein landscape of human-gut bacterial species

2021 ◽  
Author(s):  
Moses Stamboulian ◽  
Jamie Canderan ◽  
Yuzhen Ye
Keyword(s):  
Human Health ◽  
Gut Microbiome ◽  
De Novo ◽  
Bacterial Species ◽  
Individual Species ◽  
Human Gut ◽  
Human Gut Microbiome ◽  
Microbial Species ◽  
Microbial Organisms

AbstractHost-microbiome interactions and the microbial community have broad impact in human health and diseases. Most microbiome based studies are performed at the genome level based on next-generation sequencing techniques, but metaproteomics is emerging as a powerful technique to study microbiome functional activity by characterizing the complex and dynamic composition of microbial proteins. We conducted a large-scale survey of human gut microbiome metaproteomic data to identify generalist species that are ubiquitously expressed across all samples and specialists that are highly expressed in a small subset of samples associated with a certain phenotype. We were able to utilize the metaproteomic mass spectrometry data to reveal the protein landscapes of these species, which enables the characterization of the expression levels of proteins of different functions and underlying regulatory mechanisms, such as operons. Finally, we were able to recover a large number of open reading frames (ORFs) with spectral support, which were missed by de novo protein-coding gene predictors. We showed that a majority of the rescued ORFs overlapped with de novo predicted proteincoding genes, but on opposite strands or on different frames. Together, these demonstrate applications of metaproteomics for the characterization of important gut bacterial species. Results are available for public access at https://omics.informatics.indiana.edu/GutBac.Author summaryMany reference genomes for studying human gut microbiome are available, but knowledge about how microbial organisms work is limited. Identification of proteins at individual species or community level provides direct insight into the functionality of microbial organisms. By analyzing more than a thousand metaproteomics datasets, we examined protein landscapes of more than two thousands of microbial species that may be important to human health and diseases. This work demonstrated new applications of metaproteomic datasets for studying individual genomes. We made the analysis results available through the GutBac website, which we believe will become a resource for studying microbial species important for human health and diseases.

scholarly journals Discovery and Characterization of FMN-Binding β-Glucuronidases in the Human Gut Microbiome

2019 ◽  
Vol 431 (5) ◽  
pp. 970-980 ◽  
Author(s):  
Samuel J. Pellock ◽  
William G. Walton ◽  
Samantha M. Ervin ◽  
Dariana Torres-Rivera ◽  
Benjamin C. Creekmore ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Human Gut ◽  
Human Gut Microbiome

scholarly journals The Application of High-Throughput Technologies for the Study of Microbiome and Cancer

2021 ◽  
Vol 12 ◽  
Author(s):  
Lu Qi Wei ◽  
Io Hong Cheong ◽  
Guang Huan Yang ◽  
Xiao Guang Li ◽  
Zisis Kozlakidis ◽  
...  
Keyword(s):  
High Throughput ◽  
Gut Microbiome ◽  
Technological Advancement ◽  
Human Gut ◽  
Current Review ◽  
Microbiome Diversity ◽  
Microbiome Research ◽  
Cancer Types ◽  
Functional Analyses

Human gut microbiome research, especially gut microbiome, has been developing at a considerable pace over the last decades, driven by a rapid technological advancement. The emergence of high-throughput technologies, such as genomics, transcriptomics, and others, has afforded the generation of large volumes of data, and in relation to specific pathologies such as different cancer types. The current review identifies high-throughput technologies as they have been implemented in the study of microbiome and cancer. Four main thematic areas have emerged: the characterization of microbial diversity and composition, microbial functional analyses, biomarker prediction, and, lastly, potential therapeutic applications. The majority of studies identified focus on the microbiome diversity characterization, which is reaching technological maturity, while the remaining three thematic areas could be described as emerging.

scholarly journals Characterization of the human gut microbiome during travelers' diarrhea

Gut Microbes ◽  
2015 ◽  
Vol 6 (2) ◽  
pp. 110-119 ◽  
Author(s):  
Bonnie P Youmans ◽  
Nadim J Ajami ◽  
Zhi-Dong Jiang ◽  
Frederick Campbell ◽  
W Duncan Wadsworth ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Human Gut ◽  
Human Gut Microbiome

scholarly journals Predictability and persistence of prebiotic dietary supplementation in a healthy human cohort

2017 ◽  
Author(s):  
Thomas Gurry ◽  
Sean M Gibbons ◽  
Le Thanh Tu Nguyen ◽  
Sean M Kearney ◽  
Ashwin Ananthakrishnan ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Dietary Supplementation ◽  
Low Complexity ◽  
Dietary Interventions ◽  
Human Gut ◽  
Healthy Human ◽  
Induced Stress ◽  
Quantitative Impact ◽  
Functional Strain

AbstractDietary interventions to manipulate the human gut microbiome for improved health have received increasing attention. However, their design has been limited by a lack of understanding of the quantitative impact of diet on a host’s microbiota. We present a highly controlled diet perturbation experiment in a healthy, human cohort in which individual micronutrients are spiked in against a standardized background. We identify strong and predictable responses of specific microbes across participants consuming prebiotic spike-ins, at the level of both strains and functional genes, suggesting fine-scale resource partitioning in the human gut. No predictable responses to non-prebiotic micronutrients were found. Surprisingly, we did not observe decreases in day-to-day variability of the microbiota compared to a complex, varying diet, and instead found evidence of diet-induced stress and an associated loss of biodiversity. Our data offer insights into the effect of a low complexity diet on the gut microbiome, and suggest that effective personalized dietary interventions will rely on functional, strain-level characterization of a patient’s microbiota.

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