Dataset Information

Comparing the taxonomic and functional profiles of gut microbiota from three pig breeds by metagenomic sequencing.

ABSTRACT: To investigate the difference of microbial communities among Diannan small-ear (DNSE), Dahe black (DHB) and Yorkshire (YS) pigs, we compared the microbial taxonomic and functional composition using a metagenomic approach. A total of 1,002,362 non-redundant microbial genes were identified, DHB and YS pigs had more similar genetic makeup compared with DNSE pigs. Bacteroidetes, Firmicutes and Spirochetes were the three most abundant phyla for all pig breeds, and DNSE pigs had a higher abundance of Prevotella genus than DHB and YS pigs. The functional profiles varied among the three pig breeds, DNSE pigs had more active carbohydrate metabolism and more abundant antibiotic resistance genes than the other two pig breeds. Moreover, we found that peptide and macrolide resistances genes in DNSE pigs were more abundant than that in DHB pigs (p < 0.05). This study will help to provide a theoretical basis for the development of native pig breeds in Yunnan Province, China.

SUBMITTER: Xu T

PROVIDER: S-EPMC9614230 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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Comparing the taxonomic and functional profiles of gut microbiota from three pig breeds by metagenomic sequencing.

Xu Taojie T Sun Haichao H Yi Lanlan L Yang Minghua M Zhu Junhong J Huang Ying Y Pan Hongbin H Li Honghui H Li Weizhen W Zhao Hongye H Wei Hongjiang H Zhao Sumei S

Frontiers in genetics 20221014

To investigate the difference of microbial communities among Diannan small-ear (DNSE), Dahe black (DHB) and Yorkshire (YS) pigs, we compared the microbial taxonomic and functional composition using a metagenomic approach. A total of 1,002,362 non-redundant microbial genes were identified, DHB and YS pigs had more similar genetic makeup compared with DNSE pigs. Bacteroidetes, Firmicutes and Spirochetes were the three most abundant phyla for all pig breeds, and DNSE pigs had a ...[more]

PMID: 36313418

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Project description:Porcine enteric diseases including swine dysentery involves a wide range of possible aetiologies and seriously damages the intestine of pigs of all ages. Metagenomic next-generation sequencing is commonly used in research for detecting and analyzing pathogens. In this study, the feces of pigs from a commercial swine farm with dysentery-like diarrhea was collected and used for microbiota analysis by next-generation sequencing. While Brachyspira spp. was not detected in diarrheal pig fecal samples, indicating that the disease was not swine dysentery. The quantity of microbial population was extremely lowered, and the bacterial composition was altered with a reduction in the relative abundance of the probiotics organisms, Firmicutes and Bacteroidetes, with an increase in pathogens like Fusobacterium and Proteobacteria, in which the specific bacteria were identified at species-level. Viral pathogens, porcine circovirus type 2, porcine lymphotropic herpesviruses 1, and porcine mastadenovirus A were also detected at pretty low levels. Carbohydrate-active enzymes (CAZy) analysis indicated that the constitute of Firmicutes and Bacteroidete were also changed. Further, the Kyoto Encyclopedia of Genes and Genomes (KEGG) alignment analysis indicated that the microbiota of diarrheal pigs had a lower ability in utilizing energy sources but were enriched in multi-drug resistance pathways. Comprehensive Antibiotic Resistance Database (CARD) and Virulence Factors of Pathogenic Bacteria (VFDB) analysis indicated that genes for elfamycin and sulfonamide resistance and the iron uptake system were enriched in diarrheal pigs. This revealed potential bacterial infection and can guide antibiotic selection for treating dysentery. Overall, our data suggested that alterations in both the population and functional attributes of microbiota in diarrheal pigs with decreased probiotic and increased pathogenic microorganisms. These results will help elucidate the mechanism of dysentery-like diarrhea and the development of approaches to control the disease.

Project description:BackgroundNurse researchers are well poised to study the connection of the microbiome to health and disease. Evaluating published microbiome results can assist with study design and hypothesis generation.ObjectivesThis article aims to present and define important analysis considerations in microbiome study planning and to identify genera shared across studies despite methodological differences. This methods article will highlight a workflow that the nurse scientist can use to combine and evaluate taxonomy tables for microbiome study or research proposal planning.MethodsWe compiled taxonomy tables from 13 published gut microbiome studies that had used Ion Torrent sequencing technology. We searched for studies that had amplified multiple hypervariable (V) regions of the 16S rRNA gene when sequencing the bacteria from healthy gut samples.ResultsWe obtained 15 taxonomy tables from the 13 studies, comprised of samples from four continents and eight V regions. Methodology among studies was highly variable, including differences in V regions amplified, geographic location, and population demographics. Nevertheless, of the 354 total genera identified from the 15 data sets, 25 were shared in all V regions and the four continents. When relative abundance differences across the V regions were compared, Dorea and Roseburia were statistically different. Taxonomy tables from Asian subjects had increased average abundances of Prevotella and lowered abundances of Bacteroides compared with the European, North American, and South American study subjects.DiscussionEvaluating taxonomy tables from previously published literature is essential for study planning. The genera found from different V regions and continents highlight geography and V region as important variables to consider in microbiome study design. The 25 shared genera across the various studies may represent genera commonly found in healthy gut microbiomes. Understanding the factors that may affect the results from a variety of microbiome studies will allow nurse scientists to plan research proposals in an informed manner. This work presents a valuable framework for future cross-study comparisons conducted across the globe.

Dataset Information

Comparing the taxonomic and functional profiles of gut microbiota from three pig breeds by metagenomic sequencing.

Publications

Comparing the taxonomic and functional profiles of gut microbiota from three pig breeds by metagenomic sequencing.

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