scholarly journals Metagenomic analysis of gut microbiome and resistome of diarrheal fecal samples from Kolkata, India, reveals the core and variable microbiota including signatures of microbial dark matter

Gut Pathogens ◽  
2020 ◽  
Vol 12 (1) ◽  
Author(s):  
Rituparna De ◽  
Asish Kumar Mukhopadhyay ◽  
Shanta Dutta
Keyword(s):  
Dark Matter ◽  
Gut Microbiome ◽  
Metagenomic Analysis ◽  
Fecal Samples ◽  
The Core

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 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 Comparative metagenomic analysis of small ruminants' fecal microbiota

2020 ◽  
Author(s):  
Iman Shabana ◽  
N A Bouqellah ◽  
N N Albakri
Keyword(s):  
Small Ruminants ◽  
Fecal Microbiota ◽  
16S Rrna Genes ◽  
Metagenomic Analysis ◽  
Rrna Genes ◽  
Bacterial Composition ◽  
Fecal Samples ◽  
Sheep And Goats ◽  
The Core ◽  
Genus Level

Abstract Background Ruminant's gastrointestinal tract inhabits complex microbial communities that influence several aspects of their development and health. Due to the limited knowledge of the fecal microbial population of sheep and goats, the current study aimed to determine the core fecal microbiota of sheep and goats at different ages. Metagenomic analysis was performed by Illumina MiSeq targeting the V3-V4 region of the 16S rRNA genes. Fecal samples were collected from sheep and goats aged 6 months and 12 months, obtained from a single farm. The fecal bacterial composition of both species was investigated at the phylum, class, order, family, and genus levels. Observed Species, Chao1, and Shannon indices were calculated to measure the microbial diversity.Results The core phyla of sheep and goats were Firmicutes (>93.01% in sheep, >95.37% in goat), followed by Proteobacteria (>26.83%in sheep, >62.03% in goat). At the genus level, a total of 36 genera were identified. Of these, 10 genera were identified in both sheep and goats including Escherichia (>40.12%), Clostridium (19.38%), Enterococcus (>5.03%), Lysinibacillus (>76.95%) Streptococcus (>2.83%), Anaerocolumna (>1.63%), Anaerotignum (>35.95%), Muricomes (>0.99%), Tissierella (>0.91%) and Bifidobacterium (>0.51%). Alpha diversity indices indicated that the highest level for the complexity of species diversity was detected in sheep fecal samples at 12 months of age.Conclusion Fecal bacterial metagenomic analysis of sheep and goats showed no significant differences in the microbiota composition on the phyla level. There was an increase in microbiota diversity with age at the genus level. Although analyzing the bacterial composition and diversity is important, further studies on their poten­tial functionality are required.

Genetic Risk for Type 1 Diabetes Profoundly Influences the Core Gut Microbiome in Children

Diabetes ◽  
2018 ◽  
Vol 67 (Supplement 1) ◽  
pp. 209-LB ◽  
Author(s):  
JORDAN RUSSELL ◽  
LUIZ ROESCH ◽  
MARK A. ATKINSON ◽  
DESMOND SCHATZ ◽  
ERIC W. TRIPLETT ◽  
...  
Keyword(s):  
Type 1 Diabetes ◽  
Gut Microbiome ◽  
Genetic Risk ◽  
The Core

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 Compartmentalization of bacterial and fungal microbiomes in the gut of adult honeybees

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Matteo Callegari ◽  
Elena Crotti ◽  
Marco Fusi ◽  
Ramona Marasco ◽  
Elena Gonella ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Bacterial Phylotypes ◽  
Specific Variable ◽  
The Core ◽  
Physico Chemical ◽  
Metabolic Conditions ◽  
Chemical Conditions ◽  
And Behavior

AbstractThe core gut microbiome of adult honeybee comprises a set of recurring bacterial phylotypes, accompanied by lineage-specific, variable, and less abundant environmental bacterial phylotypes. Several mutual interactions and functional services to the host, including the support provided for growth, hormonal signaling, and behavior, are attributed to the core and lineage-specific taxa. By contrast, the diversity and distribution of the minor environmental phylotypes and fungal members in the gut remain overlooked. In the present study, we hypothesized that the microbial components of forager honeybees (i.e., core bacteria, minor environmental phylotypes, and fungal members) are compartmentalized along the gut portions. The diversity and distribution of such three microbial components were investigated in the context of the physico-chemical conditions of different gut compartments. We observed that changes in the distribution and abundance of microbial components in the gut are consistently compartment-specific for all the three microbial components, indicating that the ecological and physiological interactions among the host and microbiome vary with changing physico-chemical and metabolic conditions of the gut.

scholarly journals On the formation and stability of fermionic dark matter halos in a cosmological framework

2020 ◽  
Author(s):  
Carlos R Argüelles ◽  
Manuel I Díaz ◽  
Andreas Krut ◽  
Rafael Yunis
Keyword(s):  
Black Hole ◽  
Dark Matter ◽  
Space Distribution ◽  
Coarse Grained ◽  
Dark Matter Halos ◽  
The Core ◽  
The Galaxy ◽  
Gravitating Systems ◽  
The Given ◽  
First Time

Abstract The formation and stability of collisionless self-gravitating systems is a long standing problem, which dates back to the work of D. Lynden-Bell on violent relaxation, and extends to the issue of virialization of dark matter (DM) halos. An important prediction of such a relaxation process is that spherical equilibrium states can be described by a Fermi-Dirac phase-space distribution, when the extremization of a coarse-grained entropy is reached. In the case of DM fermions, the most general solution develops a degenerate compact core surrounded by a diluted halo. As shown recently, the latter is able to explain the galaxy rotation curves while the DM core can mimic the central black hole. A yet open problem is whether this kind of astrophysical core-halo configurations can form at all, and if they remain stable within cosmological timescales. We assess these issues by performing a thermodynamic stability analysis in the microcanonical ensemble for solutions with given particle number at halo virialization in a cosmological framework. For the first time we demonstrate that the above core-halo DM profiles are stable (i.e. maxima of entropy) and extremely long lived. We find the existence of a critical point at the onset of instability of the core-halo solutions, where the fermion-core collapses towards a supermassive black hole. For particle masses in the keV range, the core-collapse can only occur for Mvir ≳ E9M⊙ starting at zvir ≈ 10 in the given cosmological framework. Our results prove that DM halos with a core-halo morphology are a very plausible outcome within nonlinear stages of structure formation.

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