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<p>Rodents serve as important reservoirs and vectors of zoonotic pathogens that can affect both human and animal health, especially in ecologically complex areas like Tanzania’s Ngorongoro District, where humans, domestic animals, and wildlife frequently interact. These interactions increase the risk of disease transmission across species. This study investigated the bacterial communities shared among rodents, domestic dogs, and humans using a comparative metagenomic approach. Blood samples from 230 rodents, 100 dogs, and 200 humans (a total of 530 samples) were analyzed using next-generation sequencing on Oxford Nanopore and Illumina platforms. In total, 91,436 high-quality reads were analyzed, and Shannon diversity indices indicated higher diversity in rodents and dogs compared to humans. Taxonomic classification through the Kraken2 pipeline identified 239 bacterial species across 158 genera. The genera <i>Enterococcus</i>, <i>Streptococcus</i>, and <i>Proteus</i> were most prevalent in humans (detected in 72%, 59%, and 27.3%), rodents (87.5%, 93.8%, and 31.3%), and dogs (70%, 80%, and 40%) of the pools respectively. Other genera such as <i>Campylobacter</i>, <i>Francisella</i>, <i>Haemophilus</i>, and <i>Klebsiella</i> appeared more frequently in rodents and dogs but were rare or absent in humans, indicating host-specific bacterial distributions. Rodents carried a variety of zoonotic and opportunistic bacteria including <i>Helicobacter</i>, <i>Campylobacter</i>, <i>Francisella</i>, <i>Listeria</i>, and <i>Klebsiella</i>. Dogs commonly harbored <i>Mycoplasmopsis</i>, <i>Staphylococcus</i>, <i>Capnocytophaga</i>, and <i>Streptococcus</i>, while human samples were dominated by <i>Klebsiella pneumoniae</i>, <i>Cronobacter sakazakii</i>, <i>Staphylococcus</i>, and <i>Enterococcus</i> species. Several genera, including <i>Klebsiella pneumoniae</i>, <i>Proteus rettgeri</i>, <i>Francisella hispaniensis</i>, and <i>Staphylococcus cohnii</i>, were found across multiple hosts, highlighting the overlap in bacterial communities. These findings underscore the interconnectedness of humans, animals, and their environment in this region. Understanding these shared bacterial communities is crucial for informing health strategies that protect both human and animal populations. The study supports the importance of a One Health approach that fosters hygiene, responsible animal care, and ongoing monitoring to maintain healthy ecosystems and reduce disease risks.</p>

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Comparative metagenomic analysis of bacterial communities across rodents, dogs, and humans in Ngorongoro district, Tanzania

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年8月22日

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  • Amina Ramadhani Issae,
  • Emma Peter Njau,
  • Augustino Alfred Chengula

摘要

Rodents serve as important reservoirs and vectors of zoonotic pathogens that can affect both human and animal health, especially in ecologically complex areas like Tanzania’s Ngorongoro District, where humans, domestic animals, and wildlife frequently interact. These interactions increase the risk of disease transmission across species. This study investigated the bacterial communities shared among rodents, domestic dogs, and humans using a comparative metagenomic approach. Blood samples from 230 rodents, 100 dogs, and 200 humans (a total of 530 samples) were analyzed using next-generation sequencing on Oxford Nanopore and Illumina platforms. In total, 91,436 high-quality reads were analyzed, and Shannon diversity indices indicated higher diversity in rodents and dogs compared to humans. Taxonomic classification through the Kraken2 pipeline identified 239 bacterial species across 158 genera. The genera Enterococcus, Streptococcus, and Proteus were most prevalent in humans (detected in 72%, 59%, and 27.3%), rodents (87.5%, 93.8%, and 31.3%), and dogs (70%, 80%, and 40%) of the pools respectively. Other genera such as Campylobacter, Francisella, Haemophilus, and Klebsiella appeared more frequently in rodents and dogs but were rare or absent in humans, indicating host-specific bacterial distributions. Rodents carried a variety of zoonotic and opportunistic bacteria including Helicobacter, Campylobacter, Francisella, Listeria, and Klebsiella. Dogs commonly harbored Mycoplasmopsis, Staphylococcus, Capnocytophaga, and Streptococcus, while human samples were dominated by Klebsiella pneumoniae, Cronobacter sakazakii, Staphylococcus, and Enterococcus species. Several genera, including Klebsiella pneumoniae, Proteus rettgeri, Francisella hispaniensis, and Staphylococcus cohnii, were found across multiple hosts, highlighting the overlap in bacterial communities. These findings underscore the interconnectedness of humans, animals, and their environment in this region. Understanding these shared bacterial communities is crucial for informing health strategies that protect both human and animal populations. The study supports the importance of a One Health approach that fosters hygiene, responsible animal care, and ongoing monitoring to maintain healthy ecosystems and reduce disease risks.