Metataxonomics reveal vultures as a reservoir for Clostridium perfringens

Abstract

The Old World vulture may carry and spread pathogens for emerging infections since they feed on the carcasses of dead animals and participate in the sky burials of humans, some of whom have died from communicable diseases. Therefore, we studied the precise fecal microbiome of the Old World vulture with metataxonomics, integrating the high-throughput sequencing of almost full-length small subunit ribosomal RNA (16S rRNA) gene amplicons in tandem with the operational phylogenetic unit (OPU) analysis strategy. Nine vultures of three species were sampled using rectal swabs on the Qinghai-Tibet Plateau, China. Using the Pacific Biosciences sequencing platform, we obtained 54 135 high-quality reads of 16S rRNA amplicons with an average of 1442±6.9 bp in length and 6015±1058 reads per vulture. Those sequences were classified into 314 OPUs, including 102 known species, 50 yet to be described species and 161 unknown new lineages of uncultured representatives. Forty-five species have been reported to be responsible for human outbreaks or infections, and 23 yet to be described species belong to genera that include pathogenic species. Only six species were common to all vultures. Clostridium perfringens was the most abundant and present in all vultures, accounting for 30.8% of the total reads. Therefore, using the new technology, we found that vultures are an important reservoir for C. perfringens as evidenced by the isolation of 107 strains encoding for virulence genes, representing 45 sequence types. Our study suggests that the soil-related C. perfringens and other pathogens could have a reservoir in vultures and other animals.

Precise Fecal Microbiome of the Herbivorous Tibetan Antelope Inhabiting High-Altitude Alpine Plateau

“…Rarefaction analysis mostly showed saturation ( Supplementary Figures S1B,C ). The error rates generated by PacBio sequencing ranged from 0.09 to 0.13% for each sample ( Supplementary Figure S1A ), which was in accordance with our previous study ( Meng et al, 2017 ). Three OPUs, namely, OPU 726 assigned as uncultured Mogibacterium sp.…”

“…In the current study, we have analyzed the fecal microbiomes of Tibetan antelopes residing in several different locations of the Hoh Xil National Nature Reserve of the Qinghai Province, where besides the high altitude, the climate is extremely fierce and inferior, which is not suitable for human activities. Here, we used the metataxonomics methodology already published using PacBio Technology ( Meng et al, 2017 ) to study the fecal microbiome of Tibetan antelopes. The use of this technology for amplicon diversity studies combined with applying the OPU ( Mora-Ruiz Mdel et al, 2015 ; Vidal et al, 2015 ), has two advantages of (i) using almost full-length 16S rRNA gene sequences to yield higher taxonomic resolution at the genus and species level, and (ii) allowing a de novo tree reconstruction to increase reliability and accuracy.…”

Reverse microbial etiology: A research field for predicting and preventing emerging infectious diseases caused by an unknown microorganism

“…By the method of metataxonomics-integrating high-throughput sequencing of almost full-length small subunit ribosomal RNA (16S rRNA) gene amplicons in tandem with the operational phylogenetic unit (OPU) analysis-we found that there are 50 potential new species and 161 unknown new lineages of uncultured representatives in the feces of only nine vultures sampled in China. 10 We later showed that there are 256 potential new species and 103 potential higher taxa within known lineages, whereas 254 XYZ contain sequences not affiliated with any known family, and all the closest relatives are unclassified lineages of existing orders or classes in the feces of herbivorous Tibetan antelope inhabiting Qinghai-Tibet Plateau in China. Many new species of bacteria have been isolated from wild animals in China and characterized, including new animal pathogens.…”

Landscape of emerging and re-emerging infectious diseases in China: impact of ecology, climate, and behavior

“…Clostridium perfringens is the most abundant in all vultures, and this species accounts for 30.8% of the total reads. Therefore, vultures and other animals can be a reservoir for the soil-related C. perfringens and other pathogens [101]. The possible public health significance of those unknown pathogens residing in the virosphere and microbiome of wild animals warrants extensive evaluation.…”