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A Comparative Analysis of the Stomach, Gut, and Lung Microbiomes in Rattus norvegicus

Urban rats serve as reservoirs for several zoonotic pathogens that seriously endanger public health, destroy stored food, and damage infrastructure due to their close interaction with humans and domestic animals. Here, we characterize the core microbiomes of R. norvegicus’s stomach, gut, and lung us...

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Autores principales: Shah, Taif, Wang, Yuhan, Wang, Yixuan, Li, Qian, Zhou, Jiuxuan, Hou, Yutong, Wang, Binghui, Xia, Xueshan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10534326/
https://www.ncbi.nlm.nih.gov/pubmed/37764203
http://dx.doi.org/10.3390/microorganisms11092359
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author Shah, Taif
Wang, Yuhan
Wang, Yixuan
Li, Qian
Zhou, Jiuxuan
Hou, Yutong
Wang, Binghui
Xia, Xueshan
author_facet Shah, Taif
Wang, Yuhan
Wang, Yixuan
Li, Qian
Zhou, Jiuxuan
Hou, Yutong
Wang, Binghui
Xia, Xueshan
author_sort Shah, Taif
collection PubMed
description Urban rats serve as reservoirs for several zoonotic pathogens that seriously endanger public health, destroy stored food, and damage infrastructure due to their close interaction with humans and domestic animals. Here, we characterize the core microbiomes of R. norvegicus’s stomach, gut, and lung using 16S rRNA next-generation Illumina HiSeq sequencing. The USEARCH software (v11) assigned the dataset to operational taxonomic units (OTUs). The alpha diversity index was calculated using QIIME1, while the beta diversity index was determined using the Bray–Curtis and Euclidean distances between groups. Principal component analyses visualized variation across samples based on the OTU information using the R package. Linear discriminant analysis, effect sizes (LEfSe), and phylogenetic investigation were used to identify differentially abundant taxa among groups. We reported an abundance of microbiota in the stomach, and they shared some of them with the gut and lung microbiota. A close look at the microbial family level reveals abundant Lactobacillaceae and Bifidobacteriaceae in the stomach, whereas Lactobacillaceae and Erysipelotrichaceae were more abundant in the gut; in contrast, Alcaligenaceae were abundant in the lungs. At the species level, some beneficial bacteria, particularly Lactobacillus reuteri and Lactobacillus johnsonii, and some potential pathogens, such as Bordetella hinzii, Streptococcus parauberis, Porphyromonas pogonae, Clostridium perfringens, etc., were identified in stomach, gut, and lung samples. Moreover, the alpha and beta diversity indexes revealed significant differences between the groups. Further analysis revealed abundant differential taxonomic biomarkers, i.e., increased Prevotellaceae and Clostridia in the lungs, whereas Campylobacteria and Lachnospirales were richest in the stomachs. In conclusion, we identified many beneficial, opportunistic, and highly pathogenic bacteria, confirming the importance of urban rats for public health. This study recommends a routine survey program to monitor rodent distribution and the pathogens they carry and transmit to humans and other domestic mammals.
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spelling pubmed-105343262023-09-29 A Comparative Analysis of the Stomach, Gut, and Lung Microbiomes in Rattus norvegicus Shah, Taif Wang, Yuhan Wang, Yixuan Li, Qian Zhou, Jiuxuan Hou, Yutong Wang, Binghui Xia, Xueshan Microorganisms Article Urban rats serve as reservoirs for several zoonotic pathogens that seriously endanger public health, destroy stored food, and damage infrastructure due to their close interaction with humans and domestic animals. Here, we characterize the core microbiomes of R. norvegicus’s stomach, gut, and lung using 16S rRNA next-generation Illumina HiSeq sequencing. The USEARCH software (v11) assigned the dataset to operational taxonomic units (OTUs). The alpha diversity index was calculated using QIIME1, while the beta diversity index was determined using the Bray–Curtis and Euclidean distances between groups. Principal component analyses visualized variation across samples based on the OTU information using the R package. Linear discriminant analysis, effect sizes (LEfSe), and phylogenetic investigation were used to identify differentially abundant taxa among groups. We reported an abundance of microbiota in the stomach, and they shared some of them with the gut and lung microbiota. A close look at the microbial family level reveals abundant Lactobacillaceae and Bifidobacteriaceae in the stomach, whereas Lactobacillaceae and Erysipelotrichaceae were more abundant in the gut; in contrast, Alcaligenaceae were abundant in the lungs. At the species level, some beneficial bacteria, particularly Lactobacillus reuteri and Lactobacillus johnsonii, and some potential pathogens, such as Bordetella hinzii, Streptococcus parauberis, Porphyromonas pogonae, Clostridium perfringens, etc., were identified in stomach, gut, and lung samples. Moreover, the alpha and beta diversity indexes revealed significant differences between the groups. Further analysis revealed abundant differential taxonomic biomarkers, i.e., increased Prevotellaceae and Clostridia in the lungs, whereas Campylobacteria and Lachnospirales were richest in the stomachs. In conclusion, we identified many beneficial, opportunistic, and highly pathogenic bacteria, confirming the importance of urban rats for public health. This study recommends a routine survey program to monitor rodent distribution and the pathogens they carry and transmit to humans and other domestic mammals. MDPI 2023-09-21 /pmc/articles/PMC10534326/ /pubmed/37764203 http://dx.doi.org/10.3390/microorganisms11092359 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Shah, Taif
Wang, Yuhan
Wang, Yixuan
Li, Qian
Zhou, Jiuxuan
Hou, Yutong
Wang, Binghui
Xia, Xueshan
A Comparative Analysis of the Stomach, Gut, and Lung Microbiomes in Rattus norvegicus
title A Comparative Analysis of the Stomach, Gut, and Lung Microbiomes in Rattus norvegicus
title_full A Comparative Analysis of the Stomach, Gut, and Lung Microbiomes in Rattus norvegicus
title_fullStr A Comparative Analysis of the Stomach, Gut, and Lung Microbiomes in Rattus norvegicus
title_full_unstemmed A Comparative Analysis of the Stomach, Gut, and Lung Microbiomes in Rattus norvegicus
title_short A Comparative Analysis of the Stomach, Gut, and Lung Microbiomes in Rattus norvegicus
title_sort comparative analysis of the stomach, gut, and lung microbiomes in rattus norvegicus
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10534326/
https://www.ncbi.nlm.nih.gov/pubmed/37764203
http://dx.doi.org/10.3390/microorganisms11092359
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