Reconstruction of ancient microbial genomes from the human gut

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.

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

10.1101/2021.09.02.458484 ◽

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.

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Flavonoid-Modifying Capabilities of the Human Gut Microbiome—An In Silico Study

Nutrients ◽

10.3390/nu13082688 ◽

2021 ◽

Vol 13 (8) ◽

pp. 2688

Author(s):

Tobias Goris ◽

Rafael R. C. Cuadrat ◽

Annett Braune

Keyword(s):

Gut Microbiome ◽

Large Scale ◽

Health Impact ◽

Gut Bacteria ◽

Human Gut ◽

Positive Health ◽

Human Gut Microbiome ◽

Nutritional Recommendations ◽

Genes Encoding ◽

A Minor

Flavonoids are a major group of dietary plant polyphenols and have a positive health impact, but their modification and degradation in the human gut is still widely unknown. Due to the rise of metagenome data of the human gut microbiome and the assembly of hundreds of thousands of bacterial metagenome-assembled genomes (MAGs), large-scale screening for potential flavonoid-modifying enzymes of human gut bacteria is now feasible. With sequences of characterized flavonoid-transforming enzymes as queries, the Unified Human Gastrointestinal Protein catalog was analyzed and genes encoding putative flavonoid-modifying enzymes were quantified. The results revealed that flavonoid-modifying enzymes are often encoded in gut bacteria hitherto not considered to modify flavonoids. The enzymes for the physiologically important daidzein-to-equol conversion, well studied in Slackiaisoflavoniconvertens, were encoded only to a minor extent in Slackia MAGs, but were more abundant in Adlercreutzia equolifaciens and an uncharacterized Eggerthellaceae species. In addition, enzymes with a sequence identity of about 35% were encoded in highly abundant MAGs of uncultivated Collinsella species, which suggests a hitherto uncharacterized daidzein-to-equol potential in these bacteria. Of all potential flavonoid modification steps, O-deglycosylation (including derhamnosylation) was by far the most abundant in this analysis. In contrast, enzymes putatively involved in C-deglycosylation were detected less often in human gut bacteria and mainly found in Agathobacter faecis (formerly Roseburia faecis). Homologs to phloretin hydrolase, flavanonol/flavanone-cleaving reductase and flavone reductase were of intermediate abundance (several hundred MAGs) and mainly prevalent in Flavonifractor plautii. This first comprehensive insight into the black box of flavonoid modification in the human gut highlights many hitherto overlooked and uncultured bacterial genera and species as potential key organisms in flavonoid modification. This could lead to a significant contribution to future biochemical-microbiological investigations on gut bacterial flavonoid transformation. In addition, our results are important for individual nutritional recommendations and for biotechnological applications that rely on novel enzymes catalyzing potentially useful flavonoid modification reactions.

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Large-scale comparative metagenomics of Blastocystis, a common member of the human gut microbiome

The ISME Journal ◽

10.1038/ismej.2017.139 ◽

2017 ◽

Vol 11 (12) ◽

pp. 2848-2863 ◽

Cited By ~ 41

Author(s):

Francesco Beghini ◽

Edoardo Pasolli ◽

Tin Duy Truong ◽

Lorenza Putignani ◽

Simone M Cacciò ◽

...

Keyword(s):

Gut Microbiome ◽

Large Scale ◽

Human Gut ◽

Human Gut Microbiome ◽

Comparative Metagenomics

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Comprehensive Mining and Characterization of CRISPR-Cas Systems in Bifidobacterium

Microorganisms ◽

10.3390/microorganisms8050720 ◽

2020 ◽

Vol 8 (5) ◽

pp. 720 ◽

Cited By ~ 3

Author(s):

Meichen Pan ◽

Matthew A. Nethery ◽

Claudio Hidalgo-Cantabrana ◽

Rodolphe Barrangou

Keyword(s):

Genome Engineering ◽

Rare Variants ◽

Adaptive Immune System ◽

Effector Proteins ◽

Type I ◽

Human Gut ◽

Adaptive Immune ◽

Naturally Occurring ◽

History Of

The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated cas) systems constitute the adaptive immune system in prokaryotes, which provides resistance against bacteriophages and invasive genetic elements. The landscape of applications in bacteria and eukaryotes relies on a few Cas effector proteins that have been characterized in detail. However, there is a lack of comprehensive studies on naturally occurring CRISPR-Cas systems in beneficial bacteria, such as human gut commensal Bifidobacterium species. In this study, we mined 954 publicly available Bifidobacterium genomes and identified CRIPSR-Cas systems in 57% of these strains. A total of five CRISPR-Cas subtypes were identified as follows: Type I-E, I-C, I-G, II-A, and II-C. Among the subtypes, Type I-C was the most abundant (23%). We further characterized the CRISPR RNA (crRNA), tracrRNA, and PAM sequences to provide a molecular basis for the development of new genome editing tools for a variety of applications. Moreover, we investigated the evolutionary history of certain Bifidobacterium strains through visualization of acquired spacer sequences and demonstrated how these hypervariable CRISPR regions can be used as genotyping markers. This extensive characterization will enable the repurposing of endogenous CRISPR-Cas systems in Bifidobacteria for genome engineering, transcriptional regulation, genotyping, and screening of rare variants.

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Shedding new light on opsin evolution

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2011.1819 ◽

2011 ◽

Vol 279 (1726) ◽

pp. 3-14 ◽

Cited By ~ 140

Author(s):

Megan L. Porter ◽

Joseph R. Blasic ◽

Michael J. Bok ◽

Evan G. Cameron ◽

Thomas Pringle ◽

...

Keyword(s):

Evolutionary History ◽

Large Scale ◽

Current Model ◽

Expression Patterns ◽

Model Organisms ◽

Biological Functions ◽

Site Specific ◽

History Of ◽

Functional Features

Opsin proteins are essential molecules in mediating the ability of animals to detect and use light for diverse biological functions. Therefore, understanding the evolutionary history of opsins is key to understanding the evolution of light detection and photoreception in animals. As genomic data have appeared and rapidly expanded in quantity, it has become possible to analyse opsins that functionally and histologically are less well characterized, and thus to examine opsin evolution strictly from a genetic perspective. We have incorporated these new data into a large-scale, genome-based analysis of opsin evolution. We use an extensive phylogeny of currently known opsin sequence diversity as a foundation for examining the evolutionary distributions of key functional features within the opsin clade. This new analysis illustrates the lability of opsin protein-expression patterns, site-specific functionality (i.e. counterion position) and G-protein binding interactions. Further, it demonstrates the limitations of current model organisms, and highlights the need for further characterization of many of the opsin sequence groups with unknown function.

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Complementation of Cobalamin Auxotrophy in Synechococcus sp. Strain PCC 7002 and Validation of a Putative Cobalamin RiboswitchIn Vivo

Journal of Bacteriology ◽

10.1128/jb.00475-16 ◽

2016 ◽

Vol 198 (19) ◽

pp. 2743-2752 ◽

Cited By ~ 17

Author(s):

Adam A. Pérez ◽

Zhenfeng Liu ◽

Dmitry A. Rodionov ◽

Zhongkui Li ◽

Donald A. Bryant

Keyword(s):

Large Scale ◽

De Novo ◽

Expression System ◽

Industrial Applications ◽

Methionine Synthase ◽

Methionine Biosynthesis ◽

Content Type ◽

Methyl Donor ◽

Synechococcus Sp

ABSTRACTThe euryhaline cyanobacteriumSynechococcussp. strain PCC 7002 has an obligate requirement for exogenous vitamin B12(cobalamin), but little is known about the roles of this compound in cyanobacteria. Bioinformatic analyses suggest that only the terminal enzyme in methionine biosynthesis, methionine synthase, requires cobalamin as a coenzyme inSynechococcussp. strain PCC 7002. Methionine synthase (MetH) catalyzes the transfer of a methyl group fromN5-methyl-5,6,7,8-tetrahydrofolate tol-homocysteine duringl-methionine synthesis and uses methylcobalamin as an intermediate methyl donor. Numerous bacteria and plants alternatively employ a cobalamin-independent methionine synthase isozyme, MetE, that catalyzes the same methyl transfer reaction as MetH but usesN5-methyl-5,6,7,8-tetrahydrofolate directly as the methyl donor. The cobalamin auxotrophy ofSynechococcussp. strain PCC 7002 was complemented by using themetEgene from the closely related cyanobacteriumSynechococcussp. strain PCC 73109, which possesses genes for both methionine synthases. This result suggests that methionine biosynthesis is probably the sole use of cobalamin inSynechococcussp. strain PCC 7002. Furthermore, a cobalamin-repressible gene expression system was developed inSynechococcussp. strain PCC 7002 that was used to validate the presence of a cobalamin riboswitch in the promoter region ofmetEfromSynechococcussp. strain PCC 73109. This riboswitch acts as a cobalamin-dependent transcriptional attenuator formetEin that organism.IMPORTANCESynechococcussp. strain PCC 7002 is a cobalamin auxotroph because, like eukaryotic marine algae, it uses a cobalamin-dependent methionine synthase (MetH) for the final step ofl-methionine biosynthesis but cannot synthesize cobalaminde novo. Heterologous expression ofmetE, encoding cobalamin-independent methionine synthase, fromSynechococcussp. strain PCC 73109, relieved this auxotrophy and enabled the construction of a truly autotrophicSynechococcussp. strain PCC 7002 more suitable for large-scale industrial applications. Characterization of a cobalamin riboswitch expands the genetic toolbox forSynechococcussp. strain PCC 7002 by providing a cobalamin-repressible expression system.

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Virulence Characterization of Puccinia striiformis f. sp. tritici Using a New Set of Yr Single-Gene Line Differentials in the United States in 2010

Plant Disease ◽

10.1094/pdis-01-14-0071-re ◽

2014 ◽

Vol 98 (11) ◽

pp. 1534-1542 ◽

Cited By ~ 89

Author(s):

Anmin Wan ◽

Xianming Chen

Keyword(s):

United States ◽

Stripe Rust ◽

Large Scale ◽

Puccinia Striiformis ◽

Yellow Rust ◽

Single Gene ◽

The United States ◽

The Past ◽

History Of

Puccinia striiformis f. sp. tritici causes stripe rust (yellow rust) of wheat and is highly variable in virulence toward wheat with race-specific resistance. During 2010, wheat stripe rust was the most widespread in the recorded history of the United States, resulting in large-scale application of fungicides and substantial yield loss. A new differential set with 18 yellow rust (Yr) single-gene lines was established and used to differentiate races of P. striiformis f. sp. tritici, which were named as race PSTv in distinction from the PST races identified in the past. An octal system was used to describe the virulence and avirulence patterns of the PSTv races. From 348 viable P. striiformis f. sp. tritici isolates recovered from a total of 381 wheat and grass stripe rust samples collected in 24 states, 41 races, named PSTv-1 to PSTv-41, were identified using the new set of 18 Yr single-gene differentials, and their equivalent PST race names were determined on the previous set of 20 wheat cultivar differentials. The frequencies and distributions of the races and their virulences were determined. The five most predominant races were PSTv-37 (34.5%), PSTv-11 (17.5%), PSTv-14 (7.2%), PSTv-36 (5.2%), and PSTv-34 (4.9%). PSTv-37 was distributed throughout the country while PSTv-11 and PSTv-14 were almost restricted to states west of the Rocky Mountains. The races had virulence to 0 to 13 of the 18 Yr genes. Frequencies of virulences toward resistance genes Yr6, Yr7, Yr8, Yr9, Yr17, Yr27, Yr43, Yr44, YrTr1, and YrExp2 were high (67.0 to 93.7%); those to Yr1 (32.8%) and YrTye (31.3%) were moderate; and those to Yr10, Yr24, Yr32, and YrSP were low (3.4 to 5.7%). All of the isolates were avirulent to Yr5 and Yr15.

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Altered Bacteria-Fungi Inter-Kingdom Network in Gut of Ankylosing Spondylitis Patients

10.1101/396812 ◽

2018 ◽

Author(s):

Ming Li ◽

Bingbing Dai ◽

Yawei Tang ◽

Lei Lei ◽

Ningning Li ◽

...

Keyword(s):

Ankylosing Spondylitis ◽

Disease Activity ◽

Large Scale ◽

Human Gut ◽

Radiographic Damage ◽

Fungal Microbiota ◽

Bacteria And Fungi ◽

The Relationship ◽

Disease Specific

ABSTRACTIntestinal bacterial dysbiosis has been increasingly linked to Ankylosing Spondylitis (AS), which is a prototypic and best studied subtype of Spondyloarthritis (SpA). Fungi and bacteria coexist in human gut and interact with each other, although they have been shown to contribute actively to health or diseases, no studies have investigated whether fungal microbiota in AS patients is perturbed. In this study, fecal samples of 22 AS patients, with clinical and radiographic assessments, and 16 healthy controls (HCs) were collected to systematically characterize the gut microbiota and mycobiota in AS patients by 16S rDNA and ITS2-based DNA sequencing. The relationships between therapeutic regimens, disease activity, radiographic damage of AS and gut micro/mycobiome were investigated. Our results showed a distinct mycobiota pattern in AS in addition to microbiota dysbiosis. The gut mycobiome of AS patients was characterized by higher taxonomic levels of Ascomycota, especially the class of Dothideomycetes, and decreased abundance of Basidiomycota, which was mainly contributed by the decease of Agaricales. Compared to HCs, changing of the ITS2/16S biodiversity ratio, and bacteria-fungi interkingdom network were observed in AS patients. Alteration of gut mycobiota was associated with different therapeutic regimens, disease activity, as well as different degrees of radiographic damage. Moreover, we unraveled a disease-specific interkingdom network alteration in AS. Finally, we also identified some trends suggesting that different therapeutic regimens may induce changing of both bacterial and fungal microbiota in AS.IMPORTANCEHuman gut is colonized by diverse fungi (mycobiome), and they have long been suspected in the pathogenesis of Spondyloarthritis (SpA). Our study unraveled a disease-specific interkingdom network alteration in AS, suggesting that fungi, or the interkingdom interactions between bacteria and fungi, may play an essential role in AS development. However, limited by sample size and indeep mechanism studies, further large scale investigations on the characterization of gut mycobiome in AS patients are needed to form a foundation for research into the relationship between mycobiota dysbiosis and AS development.

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The human gut virome is highly diverse, stable and individual-specific

10.1101/657528 ◽

2019 ◽

Cited By ~ 1

Author(s):

Andrey N. Shkoporov ◽

Adam G. Clooney ◽

Thomas D.S. Sutton ◽

Feargal J. Ryan ◽

Karen M. Daly ◽

...

Keyword(s):

Gut Microbiome ◽

De Novo ◽

Temporal Stability ◽

Human Gut ◽

Vast Array ◽

Bacterial Microbiome ◽

Viral Communities ◽

Metagenomic Study ◽

Individual Specificity ◽

Taxonomic Annotation

SummaryThe human gut contains a vast array of viruses, mostly bacteriophages. The majority remain uncharacterised and their roles in shaping the gut microbiome and in impacting on human health remain poorly understood. Here we performed a longitudinal focused metagenomic study of faecal bacteriophage populations in healthy adults. Our results reveal high temporal stability and individual specificity of bacteriophage consortia which correlates with the bacterial microbiome. We report the existence of a stable, numerically predominant individual-specific persistent personal virome. Clustering of bacteriophage genomes and de novo taxonomic annotation identified several groups of crAss-like and Microviridae bacteriophages as the most stable colonizers of the human gut. CRISPR-based host prediction highlighted connections between these stable viral communities and highly predominant gut bacterial taxa such as Bacteroides, Prevotella and Faecalibacterium. This study provides insights into the structure of the human gut virome and serves as an important baseline for hypothesis-driven research.

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Alterations in human gut microbiome composition and metabolism after exposure to glyphosate and Roundup and/or a spore-based formulation using the SHIME® technology

10.1101/2021.12.16.472928 ◽

2021 ◽

Author(s):

Robin Mesnage ◽

Marta Calatayud ◽

Cindy Duysburgh ◽

Massimo Marzorati ◽

Michael Antoniou

Keyword(s):

Gut Microbiota ◽

Gut Microbiome ◽

Large Scale ◽

Epidemiological Studies ◽

Human Gut ◽

Microbiome Composition ◽

Human Gut Microbiome ◽

Ammonium Production ◽

Profiling Techniques ◽

Microbial Environment

Despite extensive research into the toxicology of the herbicide glyphosate, there are still major unknowns regarding its effects on the human gut microbiome. As a step in addressing this knowledge gap, we describe for the first time the effects of glyphosate and a Roundup glyphosate-based herbicide on infant gut microbiota using SHIME technology, which mimics the entire gastrointestinal tract. SHIME microbiota culture was undertaken in the presence of a concentration of 100 mg/L (corresponding to a dose of 1.6 mg/kg/day) glyphosate and the same glyphosate equivalent concentration of Roundup, which is in the range of the US chronic reference dose, and subjected to molecular profiling techniques to assess outcomes. Roundup and to a lesser extent glyphosate caused an increase in fermentation activity, resulting in acidification of the microbial environment. This was also reflected by an increase in lactate and acetate production concomitant to a decrease in the levels of propionate, valerate, caproate and butyrate. Ammonium production reflecting proteolytic activities was increased by Roundup exposure. Global metabolomics revealed large scale disturbances in metabolite profiles, including an increased abundance of long chain polyunsaturated fatty acids (n3 and n6). Although changes in bacterial composition measured by qPCR and 16S rRNA sequencing were less clear, our results suggested that lactobacilli had their growth stimulated as a result of microenvironment acidification. Co-treatment with the spore-based probiotic formulation MegaSporeBiotic reverted some of the changes in short-chain fatty acid levels. Altogether, our results suggest that glyphosate can exert effects on human gut microbiota at permitted regulatory levels of exposure, highlighting the need for epidemiological studies aimed at evaluating the effects of glyphosate herbicides on human gut microbiome function.

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