Amplicon pyrosequencing and ion torrent sequencing of wild duck eubacterial microbiome from fecal samples reveals numerous species linked to human and animal diseases

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Abstract

Our investigation into the composition of the wild duck, Aythya americana, eubacterial microbiome from a fecal sample using amplicon pyrosequencing revealed that the representative bacterial species were quite distinct from a pond water sample, and we were able to classify the major operational taxonomic units with Fusobacterium mortiferum, Streptobacillus moniliformis, Lactobacillus intermedius, Actinomyces suimastitidis, Campylobacter Canadensis, Enterococcus cecorum, Lactobacillus aviarus, Actimomyces spp., Pseudobutyrivibrio spp. and Helicobacter brantae representing the majority of the eubacterial fecal microbiome. Bacterial species present in the analysis revealed numerous organisms linked to human and animal diseases including septicemia, rat bite fever, pig mastitis, endocarditis, malar masses, genital infections, skin lesions, peritonitis, wound infections, septic arthritis, urocystitis, gastroenteritis and drinking water diseases. In addition, to being known carriers of viral pathogens wild ducks should also be recognized as a potential source of a range of bacterial diseases.

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The ongoing revolution in high-throughput sequencing continues to democratize the ability of small groups of investigators to map the microbial component of the biosphere. In particular, the coevolution of new sequencing platforms and new software tools allows data acquisition and analysis on an unprecedented scale. Here we report the next stage in this coevolutionary arms race, using the Illumina GAIIx platform to sequence a diverse array of 25 environmental samples and three known "mock communities" at a depth averaging 3.1 million reads per sample. We demonstrate excellent consistency in taxonomic recovery and recapture diversity patterns that were previously reported on the basis of metaanalysis of many studies from the literature (notably, the saline/nonsaline split in environmental samples and the split between host-associated and free-living communities). We also demonstrate that 2,000 Illumina single-end reads are sufficient to recapture the same relationships among samples that we observe with the full dataset. The results thus open up the possibility of conducting large-scale studies analyzing thousands of samples simultaneously to survey microbial communities at an unprecedented spatial and temporal resolution.

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Only type A influenza viruses are known to cause natural infections in birds, but viruses of all 15 haemagglutinin and all nine neuraminidase influenza A subtypes in the majority of possible combinations have been isolated from avian species. Influenza A viruses infecting poultry can be divided into two distinct groups on the basis of their ability to cause disease. The very virulent viruses cause highly pathogenic avian influenza (HPAI), in which mortality may be as high as 100%. These viruses have been restricted to subtypes H5 and H7, although not all viruses of these subtypes cause HPAI. All other viruses cause a much milder, primarily respiratory disease, which may be exacerbated by other infections or environmental conditions. Since 1959, primary outbreaks of HPAI in poultry have been reported 17 times (eight since 1990), five in turkeys and 12 in chickens. HPAI viruses are rarely isolated from wild birds, but extremely high isolation rates of viruses of low virulence for poultry have been recorded in surveillance studies, giving overall figures of about 15% for ducks and geese and around 2% for all other species. Influenza viruses have been shown to affect all types of domestic or captive birds in all areas of the world, but the frequency with which primary infections occur in any type of bird depends on the degree of contact there is with feral birds. Secondary spread is usually associated with human involvement, probably by transferring infective faeces from infected to susceptible birds.

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Streptococcus suis is a major porcine pathogen worldwide, and can be transmitted to human beings by close contact with sick or carrier pigs. S suis causes meningitis, septicaemia, endocarditis, arthritis, and septic shock in both pigs and human beings, and mortality is high. Human infection with S suis occurs mainly among certain risk groups that have frequent exposure to pigs or pork. Outbreaks of human S suis infection are uncommon, although several outbreaks have occurred in China in recent years. In July, 2005, the largest outbreak of human S suis infection occurred in Sichuan province, China, where 204 people were infected and 38 of them died. There have been 409 cases of human S suis infection worldwide, most of which have occurred in China, Thailand, and the Netherlands, and these infections have led to 73 deaths. This review provides background information on the biology and molecular characteristics of this Gram-positive bacterium, and describes the clinical signs, pathology, epidemiology, diagnosis, and treatment of human infection with S suis.