| Intestinal microorganism is closely related to host health,which could enter the environment through feces,spreading with the movement of animals.So intestinal microorganism has potential impact for natural environment.Metagenomics as a method of studying the intestinal microbiome of animals,take a great helpful to understand the relationship between animal intestinal microbiome and host and external environment.Birds and livestock are mobile reservoirs of zoonoses and resistance genes,which could bring great pollution to the environment.Intestinal microbiome of migrating whooper swan(Cygnus cygnus),ornamental black swan(Cygnus atratus)and beef calves was analyzed in platform of metagenomics set up in this study,to reveal the importance of intestinal microbiota for the health and survival of the animals;and screen endemic and common resistance genes and opportunistic pathogens in the animals to provide data support for the studies of distribution of drug resistance genes and opportunistic pathogens in nature.1.A total of 21 fresh fecal samples were collected from migratory whooper swan in early(October to November),mid-term(December to January)and late(February to March)wintering period in Sanmenxia and 7 ornamental black swan fresh fecal samples collected from Zhengzhou to take metagenomic sequencing.The results shows that intestinal microorganisms of whooper swan and black swan were mainly composed by Firmicutes,Bacteroidetes and Proteobacteria,and has abundant metabolism-related genes,which is important for food fermentation in hindgut of whooper swan and black swan.There were significant differences in the relative abundance of some intestinal microbes between whooper swans and black swans.Bacteroidetes and Verrucomicrobia were significantly enriched in whooper swans,while Actinobacteria were significantly enriched in black swans;Bacteroides and Prevotella were significantly enriched in whooper swans.724 and 525 resistance genes were detected in whooper swans and black swans,respectively,and them resistant to almost all types of antibiotics.Tetracycline and fluoroquinolone resistance genes accounted for the highest proportion,and polymyxin-resistant gene mcr-5 was widely prevalent in whooping swans and black swans.A total of 116 resistance genes were significantly different between the two birds.276 and 299 opportunistic pathogens and 2 avian viruses(Avian myeloblastoma virus and Avian leukaemia virus)were detected in whooper swans and black swans,respectively.The abundance of Fusobacterium mortiferum,Escherichia coli and Acinetobacter baumannii was the highest in the two bird species.There were 33 genus of intestinal microorganisms changed significantly during the wintering whooper swan,accounting for about 1.4% of all microbial species in this order.Firmicutes and Romboutsia were significantly enriched in the late wintering period,which contributed to intestinal cellulose decomposition and fat accumulation in whooper swans.During the wintering,the abundance of resistance genes in whooper swans decreased,while the species of resistance genes increased.2.A total of 15 fresh fecal samples were collected from bloody diarrheal(4 samples),watery diarrheal(4 samples)and healthy calves(7 samples).Diarrhea calves show intestinal microbiome disorders,and intestinal microbiome disorder seriously in bloody diarrheal calves,which intestinal microbial richness and diversity decreased significantly,and the functional richness and diversity of intestinal microorganisms decreased significantly.The intestinal microbial richness of watery diarrhea calves was significantly higher than bloody diarrhea calves and lower than healthy calves,and the diversity was higher than bloody diarrhea calves and lower than that of healthy calves.The diarrhea of calves may be caused by pathogen infection: 147,275 and 320 pathogenic bacteria were detected from bloody diarrheal,watery diarrheal and healthy calves respectively;Fusobacterium mortiferum,Escherichia coli and Streptococcus suis have a highest relative abundance in bloody diarrhea calves,meanwhile,Escherichia fergussiae,Escherichia coli,Streptococcus gallolyticus and Anaplasma phagocytophilum enriched significantly;Chlamydia trachomatis,Bacteroides fragilis and Bacteroides vulgatus have a highest relative abundance in watery diarrhea calves,meanwhile,Chlamydia trachomatis enriched significantly.Resistance gene changes in diarrhea calves: A total of 199 resistance genes were detected in bloody diarrheal calves,and β-lactam resistance gene TEM-1 had the highest abundance;354 and 557 resistance genes were detected in watery diarrheal and healthy calves and tet Q had the highest abundance.β-lactam resistance gene was significantly enriched in bloody diarrheal calves,and the tetracycline resistance gene tet Q andβ-lactam resistance gene Cfx A5 were significantly enriched in watery diarrheal calves,and tetracycline resistance gene tet W/N/W was significantly enriched in healthy calves.3.Drug resistance genes and opportunistic pathogens in whooper swan,black swan and beef cattle in this study were screened.A total of 309 resistant genes and 234 opportunistic pathogens were simultaneously detected in whooper swans,black swans and beef cattle.Types of aminoglycosides and tetracycline resistance genes have a high number in common species,and cephalosporin-penicillane resistance genes have a high number in endemic species.The abundance of Clostridium mortality and Escherichia coli was the highest among common opportunistic pathogens.In this study,whooper swans,black swans and beef cattle had strong geographical isolation,however,multiple resistant genes and opportunistic pathogens were detected in them at the same time,which may indicate that these resistant genes and opportunistic pathogens widely distributed in the nature.Some resistant genes and opportunistic pathogens in whooper swans,black swans and beef cattle specifically,which may indicate the resistant genes and opportunistic pathogens spread in a limited range,however,them may widely distribute in the future.In this study,metagenomic sequencing was performed on fecal samples of 21 migrating whooper swans,7 ornamental black swans,4 bloody diarrhea calves,4 watery diarrhea calves and 7 healthy calves.Results showed that intestinal microorganisms are important for hindgut fermentation of whooper swans and black swans.The enrichment of Firmicutes and Romboutsia take great significance to the northward migration of whooper swans in late winter.Diarrhea of calves is associated with intestinal microbiome.Diarrhea Intestinal microbiome disorder and diarrhea of calves may be related to the proliferation of pathogenic bacteria.724,525 and 599 drug-resistant genes and 276,299 and 331 opportunistic pathogens were detected in whooper swans,black swans and beef cattle,respectively.Two avian viruses and one zoonotic virus were detected.Avian myeloblastosis virus was found in whooper swans commonly,avian leukaemia virus was found in black swans commonly,and orf virus was widely distributed in beef calves.724,525 and 599 drug-resistant genes and 276,299 and 331 opportunistic pathogens were detected in whooper swans,black swans and beef cattle,respectively.And a total of 309 resistant genes and 234 opportunistic pathogens were common among the three animals.This study revealed the importance of intestinal microbiota to the health and survival of the animals,and causes of diarrhea in calves were screened.At the same time,the potential impact of whooper swan,black swan and beef cattle on public health safety was described,and the distribution of drug resistance genes and opportunistic pathogens in animals was evaluated.This study is innovative and provides reference for swan population management,beef cattle production and public health security. |
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