scholarly journals Characterization of Metagenome-Assembled Genomes and Carbohydrate-Degrading Genes in the Gut Microbiota of Tibetan Pig

2020 ◽  
Vol 11 ◽  
Author(s):  
Saisai Zhou ◽  
Runbo Luo ◽  
Ga Gong ◽  
Yifei Wang ◽  
Zhuoma Gesang ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
De Novo ◽  
Sequence Data ◽  
Fecal Microbiota ◽  
Tibet Plateau ◽  
Future Application ◽  
Metagenomic Sequence ◽  
Bacterial Phyla ◽  
Tibetan Pig ◽  
Tibetan Pigs

Tibetan pig is an important domestic mammal, providing products of high nutritional value for millions of people living in the Qinghai-Tibet Plateau. The genomes of mammalian gut microbiota encode a large number of carbohydrate-active enzymes, which are essential for the digestion of complex polysaccharides through fermentation. However, the current understanding of microbial degradation of dietary carbohydrates in the Tibetan pig gut is limited. In this study, we produced approximately 145 gigabases of metagenomic sequence data for the fecal samples from 11 Tibetan pigs. De novo assembly and binning recovered 322 metagenome-assembled genomes taxonomically assigned to 11 bacterial phyla and two archaeal phyla. Of these genomes, 191 represented the uncultivated microbes derived from novel prokaryotic taxa. Twenty-three genomes were identified as metagenomic biomarkers that were significantly abundant in the gut ecosystem of Tibetan pigs compared to the other low-altitude relatives. Further, over 13,000 carbohydrate-degrading genes were identified, and these genes were more abundant in some of the genomes within the five principal phyla: Firmicutes, Bacteroidetes, Spirochaetota, Verrucomicrobiota, and Fibrobacterota. Particularly, three genomes representing the uncultivated Verrucomicrobiota encode the most abundant degradative enzymes in the fecal microbiota of Tibetan pigs. These findings should substantially increase the phylogenetic diversity of specific taxonomic clades in the microbial tree of life and provide an expanded repertoire of biomass-degrading genes for future application to microbial production of industrial enzymes.

scholarly journals Gut Microbiome Changes in Captive Plateau Zokors (Eospalax baileyi)

2021 ◽  
Vol 17 ◽  
pp. 117693432199635
Author(s):  
Daoxin Liu ◽  
Pengfei Song ◽  
Jingyan Yan ◽  
Haijing Wang ◽  
Zhenyuan Cai ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
High Throughput Sequencing ◽  
Tibet Plateau ◽  
Rrna Gene ◽  
Diversity Analysis ◽  
Bacterial Phyla ◽  
In Captivity ◽  
Relative Abundances ◽  
Plateau Zokor

Wild-caught animals must cope with drastic lifestyle and dietary changes after being induced to captivity. How the gut microbiome structure of these animals will change in response receives increasing attention. The plateau zokor ( Eospalax baileyi), a typic subterranean rodent endemic to the Qinghai-Tibet plateau, spends almost the whole life underground and is well adapted to the environmental pressures of both plateau and underground. However, how the gut microbiome of the plateau zokor will change in response to captivity has not been reported to date. This study compared the microbial community structure and functions of 22 plateau zokors before (the WS group) and after being kept in captivity for 15 days (the LS group, fed on carrots) using the 16S rRNA gene via high-throughput sequencing technology. The results showed that the LS group retained 973 of the 977 operational taxonomic units (OTUs) in the WS group, and no new OTUs were found in the LS group. The dominant bacterial phyla were Bacteroides and Firmicutes in both groups. In alpha diversity analysis, the Shannon, Sobs, and ACE indexes of the LS group were significantly lower than those of the WS group. A remarkable difference ( P < 0.01) between groups was also detected in beta diversity analysis. The UPGMA clustering, NMDS, PCoA, and Anosim results all showed that the intergroup difference was significantly greater than the intragroup difference. And compared with the WS group, the intragroup difference of the gut microbiota in the LS group was much larger, which failed to support the assumption that similar diets should drive convergence of gut microbial communities. PICRUSt revealed that although some functional categories displayed significant differences between groups, the relative abundances of these categories were very close in both groups. Based on all the results, we conclude that as plateau zokors enter captivity for a short time, although the relative abundances of different gut microbiota categories shifted significantly, they can maintain almost all the OTUs and the functions of the gut microbiota in the wild. So, the use of wild-caught plateau zokors in gut microbial studies is acceptable if the time in captivity is short.

scholarly journals Gut microbiota and fecal metabolites in captive and wild North China leopard (Panthera pardus japonensis) by comparsion using 16 s rRNA gene sequencing and LC/MS-based metabolomics

2020 ◽  
Vol 16 (1) ◽  
Author(s):  
Yan Hua ◽  
Heqin Cao ◽  
Jiao Wang ◽  
Fengping He ◽  
Guangshun Jiang
Keyword(s):  
Gut Microbiota ◽  
North China ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Panthera Pardus ◽  
Bacterial Phyla ◽  
Metabolic Phenotypes ◽  
Rrna Gene Sequencing ◽  
First Time ◽  
16 S Rrna

Abstract Background Gut microbes significantly contribute to nutrient digestion and absorption, intestinal health and immunity, and are essential for the survival and environmental adaptation of wild animals. However, there are few studies on the gut microbiota of captive and wild North China leopard (Panthera pardus japonensis). Results A total of 10 mainly bacterial phyla were identified in the fecal microbiota of North China leopard, Lachnoclostridium (p = 0.003), Peptoclostridium (p = 0.005), Bacteroides (p = 0.008), Fusobacterium (p = 0.017) and Collinsella (p = 0.019) were significantly higher than those of wild North China leopard. Distinct differences in the fecal metabolic phenotypes of captive and wild North China leopard were found, such as content of l-methionine, n-acetyl-l-tyrosine, pentadecanoic acid and oleic acid. Differentially abundant gut microbes were associated with fecal metabolites, especially the bacteria in Firmicutes and Bacteroidetes, involved in the metabolism of N-acetyl-L-alanine and D-quinovose. Conclusion This study reports for the first time the differences in gut microbiota abundance between captive and wild North China leopard, as well as significant differences in fecal metabolic phenotypes between two groups.

scholarly journals Microbial Strain Engraftment, Persistence and Replacement after Fecal Microbiota Transplantation

2020 ◽  
Author(s):  
Daniel Podlesny ◽  
W. Florian Fricke
Keyword(s):  
Fecal Microbiota Transplantation ◽  
Sequence Data ◽  
Fecal Microbiota ◽  
Functional Restoration ◽  
Donor Strain ◽  
Metagenomic Sequence ◽  
Clostridioides Difficile ◽  
Clostridioides Difficile Infection ◽  
Species Specific ◽  
Microbial Strain

Fecal Microbiota Transplantation (FMT) has been clinically validated as a treatment for recurrent Clostridioides difficile infection (rCDI) and associated with the compositional and functional restoration of the patient gut microbiota. To characterize the underlying microbiota dynamics of patient and donor strain engraftment, persistence and replacement during FMT, we combined new and existing metagenomic sequence data and developed the bioinformatic SameStr program for the species-specific detection of shared subspecies lineages, including non-dominant strains. We show that personal gut strain profiles are identifiable and detect engraftment after successful and failed FMT in rCDI recipients, specifically of those donor strains that are abundant and stable in healthy individuals. We identify microbiota parameters in statistical models to predict donor species and strain engraftment, as well as recipient strain persistence and replacement. Our findings raise concerns over FMT consequences from questionable donors and suggest that personalized FMT strategies are feasible for targeted microbiota modulation.

scholarly journals The Chaperonin-60 Universal Target Is a Barcode for Bacteria That Enables De Novo Assembly of Metagenomic Sequence Data

PLoS ONE ◽  
2012 ◽  
Vol 7 (11) ◽  
pp. e49755 ◽  
Author(s):  
Matthew G. Links ◽  
Tim J. Dumonceaux ◽  
Sean M. Hemmingsen ◽  
Janet E. Hill
Keyword(s):  
De Novo Assembly ◽  
De Novo ◽  
Sequence Data ◽  
Metagenomic Sequence ◽  
Chaperonin 60 ◽  
Metagenomic Sequence Data

scholarly journals Rapid profiling of the preterm infant gut microbiota using nanopore sequencing aids pathogen diagnostics

2017 ◽  
Author(s):  
Richard M. Leggett ◽  
Cristina Alcon-Giner ◽  
Darren Heavens ◽  
Shabhonam Caim ◽  
Thomas C. Brook ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Real Time ◽  
Time Course ◽  
Sequence Data ◽  
Clinical Samples ◽  
Metagenomic Sequencing ◽  
Time Analysis ◽  
Metagenomic Sequence ◽  
Real Time Analysis ◽  
Increased Risk

ABSTRACTThe Oxford Nanopore MinION sequencing platform offers near real time analysis of DNA reads as they are generated, which makes the device attractive for in-field or clinical deployment, e.g. rapid diagnostics. We used the MinION platform for shotgun metagenomic sequencing and analysis of gut-associated microbial communities; firstly, we used a 20-species human microbiota mock community to demonstrate how Nanopore metagenomic sequence data can be reliably and rapidly classified. Secondly, we profiled faecal microbiomes from preterm infants at increased risk of necrotising enterocolitis and sepsis. In single patient time course, we captured the diversity of the immature gut microbiota and observed how its complexity changes over time in response to interventions, i.e. probiotic, antibiotics and episodes of suspected sepsis. Finally, we performed ‘real-time’ runs from sample to analysis using faecal samples of critically ill infants and of healthy infants receiving probiotic supplementation. Real-time analysis was facilitated by our new NanoOK RT software package which analysed sequences as they were generated. We reliably identified potentially pathogenic taxa (i.e. Klebsiella pneumoniae and Enterobacter cloacae) and their corresponding antimicrobial resistance (AMR) gene profiles within as little as one hour of sequencing. Antibiotic treatment decisions may be rapidly modified in response to these AMR profiles, which we validated using pathogen isolation, whole genome sequencing and antibiotic susceptibility testing. Our results demonstrate that our pipeline can process clinical samples to a rich dataset able to inform tailored patient antimicrobial treatment in less than 5 hours.

scholarly journals Gut microbiota and fecal metabolites in captive and wild North China leopard (Panthera pardus japonensis) by comparsion using 16s rRNA gene sequencing and LC/MS-based metabolomics

2020 ◽  
Author(s):  
Yan Hua ◽  
Heqin cao ◽  
Jiao Wang ◽  
Fengping He ◽  
Guangshun Jiang
Keyword(s):  
Gut Microbiota ◽  
North China ◽  
16S Rrna Gene Sequencing ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Panthera Pardus ◽  
Bacterial Phyla ◽  
Metabolic Phenotypes ◽  
Rrna Gene Sequencing ◽  
First Time

Abstract Background: Gut microbes significantly contribute to nutrient digestion and absorption, intestinal health and immunity, and are essential for the survival and environmental adaptation of wild animals. However, there are few studies on the gut microbiota of captive and wild North China leopard (Panthera pardus japonensis). Results: A total of 10 mainly bacterial phyla were identified in the fecal microbiota of North China leopard, Lachnoclostridium (p = 0.003), Peptoclostridium (p = 0.005), Bacteroides (p =0.008), Fusobacterium (p = 0.017) and Collinsella (p = 0.019) were significantly higher than those of wild North China leopard. Distinct differences in the fecal metabolic phenotypes of captive and wild North China leopard were found, such as content of l-methionine, n-acetyl-l-tyrosine, pentadecanoic acid and oleic acid. Differentially abundant gut microbes were associated with fecal metabolites, especially the bacteria in Firmicutes and Bacteroidetes, involved in the metabolism of N-acetyl-L-alanine and D-quinovose.Conclusion: This study reports for the first time the differences in gut microbiota abundance between captive and wild North China leopard, as well as significant differences in fecal metabolic phenotypes between two groups.

scholarly journals Gut microbiota and fecal metabolites in captive and wild North China leopard (Panthera pardus japonensis) by comparsion using 16s rRNA gene sequencing and LC/MS-based metabolomics

2020 ◽  
Author(s):  
Yan Hua ◽  
Heqin cao ◽  
Jiao Wang ◽  
Fengping He ◽  
Guangshun Jiang
Keyword(s):  
Gut Microbiota ◽  
North China ◽  
16S Rrna Gene Sequencing ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Panthera Pardus ◽  
Gut Microbes ◽  
Bacterial Phyla ◽  
Metabolic Phenotypes ◽  
Rrna Gene Sequencing

Abstract Background: Gut microbes significantly contribute to nutrient digestion and absorption, intestinal health and immunity, and are essential for the survival and environmental adaptation of wild animals. However, there are few studies on the gut microbiota of captive and wild North China leopard (Panthera pardus japonensis). Results: A total of 10 mainly bacterial phyla were identified in the fecal microbiota of North China leopard, Lachnoclostridium (p = 0.003), Peptoclostridium (p = 0.005), Bacteroides (p =0.008), Fusobacterium (p = 0.017) and Collinsella (p = 0.019) were significantly higher than those of wild North China leopard. Distinct differences in the fecal metabolic phenotypes of captive and wild North China leopard were found, such as content of l-methionine, n-acetyl-l-tyrosine, pentadecanoic acid and oleic acid. Differentially abundant gut microbes were associated with fecal metabolites, especially the bacteria in Firmicutes and Bacteroidetes, involved in the metabolism of N-acetyl-L-alanine and D-quinovose.Conclusion: This study reports for the first time the differences in gut microbiota abundance between captive and wild North China leopard, as well as significant differences in fecal metabolic phenotypes between two groups.

scholarly journals Gut microbiota and fecal metabolites in captive and wild North China leopard (Panthera pardus japonensis) by comparsion using 16s rRNA gene sequencing and LC/MS-based metabolomics

2020 ◽  
Author(s):  
Yan Hua ◽  
Heqin cao ◽  
Jiao Wang ◽  
Fengping He ◽  
Guangshun Jiang
Keyword(s):  
Gut Microbiota ◽  
North China ◽  
16S Rrna Gene Sequencing ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Panthera Pardus ◽  
Bacterial Phyla ◽  
Metabolic Phenotypes ◽  
Rrna Gene Sequencing ◽  
First Time

Abstract Background: Gut microbes significantly contribute to nutrient digestion and absorption, intestinal health and immunity, and are essential for the survival and environmental adaptation of wild animals. However, there are few studies on the gut microbiota of captive and wild North China leopard (Panthera pardus japonensis). Results: A total of 10 mainly bacterial phyla were identified in the fecal microbiota of North China leopard, Lachnoclostridium (p = 0.003), Peptoclostridium (p = 0.005), Bacteroides (p =0.008), Fusobacterium (p = 0.017) and Collinsella (p = 0.019) were significantly higher than those of wild North China leopard. Distinct differences in the fecal metabolic phenotypes of captive and wild North China leopard were found, such as content of l-methionine, n-acetyl-l-tyrosine, pentadecanoic acid and oleic acid. Differentially abundant gut microbes were associated with fecal metabolites, especially the bacteria in Firmicutes and Bacteroidetes, involved in the metabolism of N-acetyl-L-alanine and D-quinovose.Conclusion: This study reports for the first time the differences in gut microbiota abundance between captive and wild North China leopard, as well as significant differences in fecal metabolic phenotypes between two groups.

scholarly journals Fecal Microbiota Transplantation Modulates Renal Phenotype in the Humanized Mouse Model of IgA Nephropathy

2021 ◽  
Vol 12 ◽  
Author(s):  
Gabriella Lauriero ◽  
Lilia Abbad ◽  
Mirco Vacca ◽  
Giuseppe Celano ◽  
Jonathan M. Chemouny ◽  
...  
Keyword(s):  
Cell Surface ◽  
Gut Microbiota ◽  
Fecal Microbiota Transplantation ◽  
Immunoglobulin A ◽  
Surface Expression ◽  
Fecal Microbiota ◽  
Cell Surface Expression ◽  
Humanized Mouse Model ◽  
Bacterial Phyla ◽  
Renal Phenotype

Immunoglobulin A nephropathy (IgAN) is the most common primary glomerulonephritis. Several observations suggest that gut microbiota could be implicated in IgAN pathophysiology. Aiming at exploring whether microbiota modulation is able to influence disease outcome, we performed fecal microbiota transplantation (FMT) from healthy controls (HC-sbjs), non-progressor (NP-pts) and progressor (P-pts) IgAN patients to antibiotic-treated humanized IgAN mice (α1KI-CD89Tg), by oral gavage. FMT was able to modulate renal phenotype and inflammation. On one hand, the microbiota from P-pts was able to induce an increase of serum BAFF and galactose deficient-IgA1 levels and a decrease of CD89 cell surface expression on blood CD11b+ cells which was associated with soluble CD89 and IgA1 mesangial deposits. On the other hand, the microbiota from HC-sbjs was able to induce a reduction of albuminuria immediately after gavage, an increased cell surface expression of CD89 on blood CD11b+ cells and a decreased expression of KC chemokine in kidney. Higher serum BAFF levels were found in mice subjected to FMT from IgAN patients. The main bacterial phyla composition and volatile organic compounds profile significantly differed in mouse gut microbiota. Microbiota modulation by FMT influences IgAN phenotype opening new avenues for therapeutic approaches in IgAN.

scholarly journals MetaCRAST: Reference-guided extraction of CRISPR spacers from unassembled metagenomes

2016 ◽  
Author(s):  
Abraham G Moller ◽  
Chun Liang
Keyword(s):  
De Novo ◽  
Sequence Data ◽  
Direct Repeat ◽  
Detection Methods ◽  
Direct Repeats ◽  
Metagenomic Sequence ◽  
Adaptive Immune ◽  
Adaptive Immune Systems ◽  
Metagenomic Sequence Data ◽  
Better Than

Summary: Clustered regularly interspaced palindromic repeat (CRISPR) systems are prokaryotic adaptive immune systems against phage infection. CRISPR spacer sequences can provide valuable ecological insights by linking environmental viruses to their microbial hosts. Despite this importance, metagenomic CRISPR detection remains a major challenge. Here we present a reference-guided CRISPR detection tool (Metagenomic CRISPR Reference-Aided Search Tool - MetaCRAST) that constrains searches based on user-specified direct repeats. These DRs could be expected from assembly or taxonomic profiles of metagenomic sequence data. Our evaluation shows MetaCRAST improves CRISPR spacer detection in real metagenomes compared to de novo detection methods. Simulations show it performs better than comparable tools when analyzing Illumina metagenomes. Availability and implementation: MetaCRAST is implemented in Perl and takes metagenomic sequence reads and direct repeat queries in FASTA format as input. It is freely available for download at https://github.com/molleraj/MetaCRAST .

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