scholarly journals Manual resolution of virome dark matter uncovers hundreds of viral families in the infant gut

2021 ◽  
Author(s):  
Shiraz A Shah ◽  
Ling Deng ◽  
Jonathan Thorsen ◽  
Anders Gorm Pedersen ◽  
Moïra B Dion ◽  
...  
Keyword(s):  
Dark Matter ◽  
Chronic Diseases ◽  
Gut Microbiome ◽  
Temperate Phage ◽  
Bacterial Populations ◽  
Fecal Samples ◽  
Virulent Phage ◽  
The Family ◽  
Family Level

The gut microbiome (GM) is shaped through infancy and plays a major role in determining susceptibility to chronic diseases later in life. Bacteriophages (phage) are known to modulate bacterial populations in numerous ecosystems, including the gut. However, virome data is difficult to analyse because it mostly consists of unknown viruses, i.e. viral dark matter. Here, we manually resolved the viral dark matter in the largest human virome study published to date. Fecal viromes from a cohort of 647 infants at 1 year of age were deeply sequenced and analysed through successive rounds of clustering and curation. This uncovered more than ten thousand viral species distributed over 248 viral families falling within 17 viral order-level clusters. Most of the defined viral families and orders were novel and belonged to the Caudoviricetes viral class. Bacterial hosts were predicted for 79% of the viral species using CRISPR spacers in metagenomes from the same fecal samples. While Bacteroides-infecting Crassphages were present, novel viral families were more predominant, including phages infecting Clostridiales and Bifidobacterium. Phage lifestyles were determined for more than three thousand caudoviral species. Lifestyles were homogeneous at the family level for 149 caudiviral families. 32 families were found to be virulent, while 117 families were temperate. Virulent phage families were more abundant but temperate phage families were more diverse and widespread. Together, the viral families found in this study represent a major expansion of current bacteriophage taxonomy, and the sequences have been put online for use and validation by the community.

scholarly journals Hundreds of viral families in the healthy infant gut

2021 ◽  
Author(s):  
Dennis Nielsen ◽  
Shiraz Shah ◽  
Ling Deng ◽  
Jonathan Thorsen ◽  
Anders Pedersen ◽  
...  
Keyword(s):  
Dark Matter ◽  
Gut Microbiome ◽  
Inflammatory Diseases ◽  
Healthy Infant ◽  
Bacterial Populations ◽  
Fecal Samples ◽  
Chronic Inflammatory Diseases ◽  
Virulent Phage ◽  
The Family ◽  
Family Level

Abstract The gut microbiome (GM) is shaped through infancy and plays a major role in determining susceptibility to chronic inflammatory diseases later in life. Bacteriophages (phages) are known to modulate bacterial populations in numerous ecosystems, including the gut. However, virome data is difficult to analyse because it mostly consists of unknown viruses, i.e. viral dark matter. Here, we manually resolved the viral dark matter in the largest human virome study published to date. Fecal viromes from a cohort of 647 infants at 1 year of age were deeply sequenced and analysed through successive rounds of clustering and curation. We uncovered more than ten thousand viral species distributed over 248 viral families falling within 17 viral order-level clades. Most of the defined viral families and orders were novel and belonged to the Caudoviricetes viral class. Bacterial hosts were predicted for 79% of the viral species using CRISPR spacers, including those in metagenomes from the same fecal samples. While Bacteroides-infecting Crassphages were present, novel viral families were more predominant, including phages infecting Clostridiales and Bifidobacterium. Phage lifestyles were determined for more than three thousand caudoviral species. Lifestyles were homogeneous at the family level for 149 Caudoviricetes families, including 32 families that were found to be virulent, while 117 were temperate. Virulent phage families were more abundant but temperate ones were more diverse and widespread. Together, the viral families found in this study represent a major expansion of existing bacteriophage taxonomy.

scholarly journals G2S: a new deep learning tool for predicting stool microbiome structure from oral microbiome data

2020 ◽  
Author(s):  
Simone Rampelli ◽  
Marco Candela ◽  
Elena Biagi ◽  
Patrizia Brigidi ◽  
Silvia Turroni
Keyword(s):  
Deep Learning ◽  
Gut Microbiome ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Oral Microbiome ◽  
The Family ◽  
Family Level ◽  
Microbial Metagenomics ◽  
Real Composition ◽  
Microbiome Data

Abstract Background Deep learning methodologies have revolutionized prediction in many fields and show the potential to do the same in microbial metagenomics. However, deep learning is still unexplored in the field of microbiology, with only a few software designed to work with microbiome data. In the frame of meta-community theory, we foresee new perspectives for the development and application of deep learning algorithms in microbiology, with a great potential in the field of human microbiome. Results G2S is a bioinformatic tool for the taxonomic prediction of the human stool microbiome directly from oral microbiome data of the same individual. The tool uses a deep convolutional neural network trained on data of the Human Microbiome Project, allowing to infer the stool microbiome at the family level more accurately than other approaches. G2S was validated on already characterized oral and fecal sample pairs, and then applied to ancient microbiome data from dental calculi, to derive putative intestinal components in medieval subjects. Conclusions G2S infers the family-level taxonomic configuration of the stool microbiome mirroring the real composition with exceptional performance. G2S can be used with modern samples, allowing to predict the eubiotic/dysbiotic state of the gut microbiome when fecal sampling is missing, and especially with ancient samples, as a unique opportunity in the field of paleomicrobiology to recover data related to ancient gut microbiome configurations.

scholarly journals Bacterial community structure alterations within the colorectal cancer gut microbiome

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Mark Loftus ◽  
Sayf Al-Deen Hassouneh ◽  
Shibu Yooseph
Keyword(s):  
Colorectal Cancer ◽  
Community Structure ◽  
Bacterial Community ◽  
Gut Microbiome ◽  
Late Stage ◽  
Bacterial Community Structure ◽  
Whole Genome ◽  
Human Gut ◽  
Fecal Samples ◽  
Human Gut Microbiome

Abstract Background Colorectal cancer is a leading cause of cancer-related deaths worldwide. The human gut microbiome has become an active area of research for understanding the initiation, progression, and treatment of colorectal cancer. Despite multiple studies having found significant alterations in the carriage of specific bacteria within the gut microbiome of colorectal cancer patients, no single bacterium has been unequivocally connected to all cases. Whether alterations in species carriages are the cause or outcome of cancer formation is still unclear, but what is clear is that focus should be placed on understanding changes to the bacterial community structure within the cancer-associated gut microbiome. Results By applying a novel set of analyses on 252 previously published whole-genome shotgun sequenced fecal samples from healthy and late-stage colorectal cancer subjects, we identify taxonomic, functional, and structural changes within the cancer-associated human gut microbiome. Bacterial association networks constructed from these data exhibited widespread differences in the underlying bacterial community structure between healthy and colorectal cancer associated gut microbiomes. Within the cancer-associated ecosystem, bacterial species were found to form associations with other species that are taxonomically and functionally dissimilar to themselves, as well as form modules functionally geared towards potential changes in the tumor-associated ecosystem. Bacterial community profiling of these samples revealed a significant increase in species diversity within the cancer-associated gut microbiome, and an elevated relative abundance of species classified as originating from the oral microbiome including, but not limited to, Fusobacterium nucleatum, Peptostreptococcus stomatis, Gemella morbillorum, and Parvimonas micra. Differential abundance analyses of community functional capabilities revealed an elevation in functions linked to virulence factors and peptide degradation, and a reduction in functions involved in amino-acid biosynthesis within the colorectal cancer gut microbiome. Conclusions We utilize whole-genome shotgun sequenced fecal samples provided from a large cohort of late-stage colorectal cancer and healthy subjects to identify a number of potentially important taxonomic, functional, and structural alterations occurring within the colorectal cancer associated gut microbiome. Our analyses indicate that the cancer-associated ecosystem influences bacterial partner selection in the native microbiota, and we highlight specific oral bacteria and their associations as potentially relevant towards aiding tumor progression.

scholarly journals A Metabolic Model of Intestinal Secretions: The Link between Human Microbiota and Colorectal Cancer Progression

Metabolites ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 456
Author(s):  
Pejman Salahshouri ◽  
Modjtaba Emadi-Baygi ◽  
Mahdi Jalili ◽  
Faiz M. Khan ◽  
Olaf Wolkenhauer ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Cancer Progression ◽  
Gut Microbiome ◽  
Metabolic Model ◽  
System Level ◽  
Mathematical Framework ◽  
Bacterial Populations ◽  
Colorectal Cancer Progression ◽  
Genome Scale ◽  
High Throughput Data Analysis

The human gut microbiota plays a dual key role in maintaining human health or inducing disorders, for example, obesity, type 2 diabetes, and cancers such as colorectal cancer (CRC). High-throughput data analysis, such as metagenomics and metabolomics, have shown the diverse effects of alterations in dynamic bacterial populations on the initiation and progression of colorectal cancer. However, it is well established that microbiome and human cells constantly influence each other, so it is not appropriate to study them independently. Genome-scale metabolic modeling is a well-established mathematical framework that describes the dynamic behavior of these two axes at the system level. In this study, we created community microbiome models of three conditions during colorectal cancer progression, including carcinoma, adenoma and health status, and showed how changes in the microbial population influence intestinal secretions. Conclusively, our findings showed that alterations in the gut microbiome might provoke mutations and transform adenomas into carcinomas. These alterations include the secretion of mutagenic metabolites such as H2S, NO compounds, spermidine and TMA, as well as the reduction of butyrate. Furthermore, we found that the colorectal cancer microbiome can promote inflammation, cancer progression (e.g., angiogenesis) and cancer prevention (e.g., apoptosis) by increasing and decreasing certain metabolites such as histamine, glutamine and pyruvate. Thus, modulating the gut microbiome could be a promising strategy for the prevention and treatment of CRC.

scholarly journals Unearthing LTR retrotransposon gag genes co-opted in the deep evolution of eukaryotes

2021 ◽  
Author(s):  
Jianhua Wang ◽  
Guan-Zhu Han
Keyword(s):  
Gene Expression ◽  
Selective Pressure ◽  
Ltr Retrotransposon ◽  
Ltr Retrotransposons ◽  
Cellular Functions ◽  
The Family ◽  
Family Level ◽  
Gene Expression Analyses ◽  
Comprehensive Picture ◽  
Gypsy Retrotransposons

Abstract LTR retrotransposons comprise a major component of the genomes of eukaryotes. On occasion, retrotransposon genes can be recruited by their hosts for diverse functions, a process formally referred to as co-option. However, a comprehensive picture of LTR retrotransposon gag gene co-option in eukaryotes is still lacking, with several documented cases exclusively involving Ty3/Gypsy retrotransposons in animals. Here we use a phylogenomic approach to systemically unearth co-option of retrotransposon gag genes above the family level of taxonomy in 2,011 eukaryotes, namely co-option occurring during the deep evolution of eukaryotes. We identify a total of 14 independent gag gene co-option events across more than 740 eukaryote families, eight of which have not been reported previously. Among these retrotransposon gag gene co-option events, nine, four, and one involve gag genes of Ty3/Gypsy, Ty1/Copia, and Bel-Pao retrotransposons, respectively. Seven, four, and three co-option events occurred in animals, plants, and fungi, respectively. Interestingly, two co-option events took place in the early evolution of angiosperms. Both selective pressure and gene expression analyses further support that these co-opted gag genes might perform diverse cellular functions in their hosts, and several co-opted gag genes might be subject to positive selection. Taken together, our results provide a comprehensive picture of LTR retrotransposon gag gene co-option events that occurred during the deep evolution of eukaryotes, and suggest paucity of LTR retrotransposon gag gene co-option during the deep evolution of eukaryotes.

scholarly journals The Role of Botanical Families in Medicinal Ethnobotany: A Phylogenetic Perspective

Plants ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 163
Author(s):  
Airy Gras ◽  
Oriane Hidalgo ◽  
Ugo D’Ambrosio ◽  
Montse Parada ◽  
Teresa Garnatje ◽  
...  
Keyword(s):  
Diversity Indices ◽  
Specific Level ◽  
Medicinal Uses ◽  
The Family ◽  
Family Level ◽  
Phylogenetic Level ◽  
Molecular Phylogenetic ◽  
Quantitative Analyses ◽  
Medicinal Flora

Studies suggesting that medicinal plants are not chosen at random are becoming more common. The goal of this work is to shed light on the role of botanical families in ethnobotany, depicting in a molecular phylogenetic frame the relationships between families and medicinal uses of vascular plants in several Catalan-speaking territories. The simple quantitative analyses for ailments categories and the construction of families and disorders matrix were carried out in this study. A Bayesian approach was used to estimate the over- and underused families in the medicinal flora. Phylogenetically informed analyses were carried out to identify lineages in which there is an overrepresentation of families in a given category of use, i.e., hot nodes. The ethnobotanicity index, at a specific level, was calculated and also adapted to the family level. Two diversity indices to measure the richness of reported taxa within each family were calculated. A total of 47,630 use reports were analysed. These uses are grouped in 120 botanical families. The ethnobotanicity index for this area is 14.44% and the ethnobotanicity index at the family level is 68.21%. The most-reported families are Lamiaceae and Asteraceae and the most reported troubles are disorders of the digestive and nutritional system. Based on the meta-analytic results, indicating hot nodes of useful plants at the phylogenetic level, specific ethnopharmacological research may be suggested, including a phytochemical approach of particularly interesting taxa.

scholarly journals Inuit plant use in the eastern Subarctic: comparative ethnobotany in Kangiqsualujjuaq, Nunavik, and in Nain, Nunatsiavut

Botany ◽  
2019 ◽  
Vol 97 (5) ◽  
pp. 271-282
Author(s):  
Alain Cuerrier ◽  
Courtenay Clark ◽  
Christian H. Norton
Keyword(s):  
Lifestyle Changes ◽  
Ethnobotanical Knowledge ◽  
Structured Interviews ◽  
Medicinal Species ◽  
Medicinal Uses ◽  
Plant Uses ◽  
The Family ◽  
Plant Names ◽  
Family Level ◽  
Comparative Ethnobotany

Plants are important in traditional Inuit life. They are used for food, tea, medicine, etc. Based on semi-structured interviews with 35 informants, we documented and compared plant names and uses in Kangiqsualujjuaq, Nunavik, and in Nain, Nunatsiavut. Plant names and uses were expected to be similar between communities owing to common boreal–subarctic environments and cultural ties. Both communities reported the same number of taxa, with equivalent proportions of vascular and nonvascular plants, growth forms, use categories, and medicinal uses. Forty-three species were used in each community, for a total of 78 species from 39 families. Despite a high overlap in species distributions, only 35% of nonvascular and 56% of vascular species were used in both communities. Correspondence was higher at the family level (64% of nonvascular and 75% of vascular families shared). The Ericaceae family was the most used, followed by Rosaceae. Thirteen of 30 medicinal species were shared between communities. There was a low correspondence regarding the conditions for which the medicinal species were used. Edible taxa were shared the most (52%). Plant uses unique to either Nain or Kangiqsualujjuaq may reveal separate bodies of traditional knowledge, or may reflect an overall loss of ethnobotanical knowledge in the Subarctic due to recent lifestyle changes.

scholarly journals Effect of Environmental Factors and Influence of Rumen and Hindgut Biogeography on Bacterial Communities in Steers

2010 ◽  
Vol 77 (1) ◽  
pp. 258-268 ◽  
Author(s):  
Gustavo A. Romero-Pérez ◽  
Kim H. Ominski ◽  
Tim A. McAllister ◽  
Denis O. Krause
Keyword(s):  
Ambient Temperature ◽  
Bacterial Communities ◽  
Volatile Fatty Acids ◽  
Principal Component ◽  
Population Diversity ◽  
Access Time ◽  
Sample Type ◽  
Bacterial Populations ◽  
Fecal Samples ◽  
Alfalfa Silage

ABSTRACTFeces from cattle production are considered important sources of bacterial contamination of food and the environment. Little is known about the combined effects of arctic temperatures and fodder tannins on rumen and hindgut bacterial populations. Individual rumen liquor and rectal fecal samples from donor steers fed either alfalfa silage or sainfoin (Onobrychis viciifoliaScop.) silage and waterad libitumwere collected weekly on the first three sampling days and fortnightly afterwards. The daily ambient temperatures were registered and averaged to weekly mean temperatures. Steers fed sainfoin silage had lower (P< 0.05) concentrations of branched-chain volatile fatty acids (VFA) than those fed alfalfa silage. All VFA concentrations were higher (P< 0.001) in rumen liquor samples than in fecal samples. The interaction of sample type and diet showed a significant effect (P< 0.05) on the proportions of the bacterial community that were from the phylaProteobacteriaandVerrucomicrobia.Ambient temperature had an indirect effect (P< 0.05) on the phylumFirmicutes, as it affected its proportional balance. The bacterial population diversity in samples appeared to decrease concurrently with the ambient temperature. The phylumFirmicutesexplained the first principal component at 64.83 and 42.58% of the total variance in rumen liquor and fecal samples, respectively. The sample type had a larger effect on bacterial communities than diet and temperature. Certain bacterial populations seemed to be better adapted than others to environmentally adverse conditions, such as less access time to nutrients due to higher motility and rate of passage of digesta caused by extreme temperatures, or antimicrobials such as tannins, possibly due to an influence of their biogeographical location within the gut.

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