Animals · 2020 · 19 citations · 45 references
Life SciencesAnimal SciencesMicrobiologyBacteriologyMicrobial EcologyMicrobiome Research16S Ribosomal Ribonucleic Acid AnalysisAnimal Microbial EcologyGut MicrobiomeGut MicrobiotaMicrobiome CompositionMicrobiome Function16S Ribosomal Ribonucleic Acid (Rrna) SequencingAnimal MicrobiomeGut Microbiome DiversityIntestinal Microbial DiversityLivestock MicrobiomesMicrobial Community CompositionMicrobial Diversity AnalysisMicrobial Functional Diversity
The gut microbiome plays an important role in the health and disease status of the host. Research on the effect of sex on animal intestinal microorganisms is still limited; and the effect of castration on the gut microbiome of male pigs has not been fully investigated. In this study, 30 Hainan special wild boars at the same growth stage were divided into three groups (10 entire males, 10 females, and 10 castrated males). High-throughput 16S rRNA sequencing was used to investigate the fecal microbiota of the Hainan special wild boar. Firmicutes, Bacteroidetes, Actinobacteria, Spirochaetes, and Proteobacteria were the five dominant phyla found in the specimens. The relative abundance of Bacteroidetes was higher in the microbiota of female pigs than in male pigs, while Firmicutes was on the contrary. The percentage of Streptococcus and Lactobacillus was higher in males than females. The microbial diversity of females was significantly higher compared to males; castration increased the intestinal microbial diversity of males. Functional prediction showed that male fecal microorganisms were rich in membrane transport and carbohydrate metabolism; energy metabolism, glycan biosynthesis, and metabolism of cofactors and vitamins were rich in the female group; the fecal microorganisms of castrated males had higher membrane transport abundance.
45
Trimmomatic: a flexible trimmer for Illumina sequence data
Anthony Bolger, Marc Lohse, Björn Usadel · Bioinformatics · 2014 · 69.7K citations · Full text
Patrick D. Schloss, Sarah L. Westcott, Thomas Ryabin et al. · Applied and Environmental Microbiology · 2009 · 21.8K citations · Full text
UPARSE: highly accurate OTU sequences from microbial amplicon reads
R. C. Edgar · Nature Methods · 2013 · 17.3K citations
Metagenomic biomarker discovery and explanation
Nicola Segata, Jacques Izard, Levi Waldron et al. · Genome biology · 2011 · 16.7K citations · Full text