Metagenomics analysis of the gut microbiome in healthy and bacterial pneumonia forest musk deer

Zhao, Wei; Ren, Ziwei; Luo, Yan; Cheng, Jin; Wang, Jie; Wang, Yin; Yang, Zexiao; Yao, Xueping; Zhong, Zhijun; Yang, Weng Lang; Wu, Xi

doi:10.1007/s13258-020-01029-0

Cited by 17 publications

(21 citation statements)

References 73 publications

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“…The gut microbiota, which refers to all microorganisms present in the gastrointestinal tract ( Kim et al, 2020 ), has important roles in the digestion ( Rowland et al, 2018 ), metabolism ( Nicholson et al, 2012 ), immunity ( Round & Mazmanian, 2009 ; Thaiss et al, 2016 ), and entro-endocrine function ( Rastelli, Cani & Knauf, 2019 ) of the host. However, in a state of dysbiosis, the gut microbiota can cause many diseases, such as diarrhea ( Wang et al, 2018 ; Xi et al, 2021 ), follicular cysts ( Feng et al, 2021 ), and bacterial pneumonia ( Zhao et al, 2021 ). Thus, the gut microbiota can affect the health of the host either positively or negatively.…”

Section: Introductionmentioning

confidence: 99%

Seasonal variations in the composition and diversity of gut microbiota in white-lipped deer (Cervus albirostris)

You

Deng

Liu

et al. 2022

PeerJ

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The gut microbiota has key physiological functions in host adaptation, although little is known about the seasonal changes in the composition and diversity of the gut microbiota in deer. In this study, seasonal variations (grassy and withering season) in the gut microbiota of white-lipped deer (Cervus albirostris), which lives in alpine environments, were explored through 16S rRNA high-throughput sequencing based on sixteen fecal samples collected from Gansu Qilian Mountain National Nature Reserve in China. At the phylum level, Firmicutes, Bacteroidota, and Actinobacteriota dominated the grassy season, while Firmicutes, Proteobacteria, and Actinobacteriota dominated the withering season. At the genus level, Carnobacterium dominated the grassy season, while Arthrobacter and Acinetobacter dominated the withering season. Alpha diversity results (Shannon: P = 0.01, ACE: P = 0.00, Chao1: P = 0.00) indicated that there was a difference in the diversity and richness of the gut microbiota between the two seasons, with higher diversity in the grassy season than in the withering season. Beta diversity results further indicated that there was a significant difference in the community structure between the two seasons (P = 0.001). In summary, the composition, diversity, and community structure of the gut microbiota showed significant seasonal variations, which could be explained by variations in the seasonal food availability, composition, diversity, and nutrition due to phenological alternations. The results of this study indicate that the gut microbiota can adapt to changes in the environment and provide the scientific basis for health assessment of white-lipped deer.

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Section: Introductionmentioning

confidence: 99%

Seasonal variations in the composition and diversity of gut microbiota in white-lipped deer (Cervus albirostris)

You

Deng

Liu

et al. 2022

PeerJ

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“…However, respiratory diseases have restricted the development of FMD captive breeding. K. pneumoniae is an important pathogen which causes respiratory sickness in FMD ( Zhao et al, 2021 ). K. pneumoniae belongs to the genus Klebsiella Trevisan in the Enterobacteriaceae family, and it is an essentially conditional pathogen that exists widely in nature ( Zhao et al, 2017 ).…”

Section: Introductionmentioning

confidence: 99%

Isolation of Klebsiella pneumoniae Phage vB_KpnS_MK54 and Pathological Assessment of Endolysin in the Treatment of Pneumonia Mice Model

Yao

Han

et al. 2022

Front. Microbiol.

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With the improper use of antibiotics, an increasing number of multidrug-resistant bacteria have been reported worldwide, posing challenges for disease treatment. Klebsiella pneumoniae is an important zoonotic pathogen that colonises the respiratory tract. Endolysin therapy has emerged with the development of phages. In this study, a lytic phage vB_KpnS_MK54 was isolated from the drinking water of a forest musk deer (FMD) farm in Sichuan Province. It was the first reported phage obtained from FMD. The primary biological characteristics were determined, and whole-genome sequencing analysis was performed. The phage which belongs to the family Siphoviridae is highly specific for lytic host bacteria and is moderately adaptable to different environments. Whole-genome sequencing results showed that the phage genome size was 46,218 bp. There were 80 coding DNA sequences (CDSs) in total, 32 of which had known functions. The last CDS is the phage endolysin LysG24. A new peptide-modified endolysin (LysCA) was constituted by connecting the cecropin A peptide residues with LysG24 to investigate the antibacterial activities of both LysG24 and LysCA. The results showed that the lytic profile of LysG24 and LysCA was wider than that of phage MK54. For in vitro tests, both endolysins destroyed 99% of the host bacteria within 6 h. The lysing ability and environmental adaptability of LysCA were significantly stronger than those of LysG24. For in vivo tests, LysG24 and LysCA exhibited therapeutic effects in a mouse model of pneumonia wherewith the mice were infected with K. pneumoniae (LPKP), wherein both LysG24 and LysCA can effectively reduce the pulmonary inflammatory response. The LPKP bacterial load in the treatment group was significantly lower than that in the bacterial group, among which LysCA displayed a more obvious therapeutic effect. Furthermore, the safety test showed that the endolysins had no toxic effects on mice. In general, both LysG24 and LysCA showed excellent antibacterial activity in vivo and in vitro, with high safety and strong adaptability to the environment, manifesting their latent potential as new antimicrobial agents.

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“…Therefore, in this study, BIPF model in rat was established by FMD origin pathogens, including Klebsiella pneumoniae , Pseudomonas aeruginosa and Streptococcus equinus . These pathogens are isolated from the FMD lung and have been shown to cause the death of mice ( Zhao et al, 2020 ; Zhao et al, 2021 ). HE, Picrosirius red and Masson’s trichrome staining showed increased inflammatory cells, fibrin and collagen in the lung of test group rats, demonstrating that these lung tissues are fibrosis.…”

Section: Discussionmentioning

confidence: 99%

“…In order to establish BIPF model, we carried out a pilot study and found that the pathogenic bacteria isolated from FMD lung, including Klebsiella pneumoniae strain DJY-1, Pseudomonas aeruginosa strain YW1 and Streptococcus equinus strain FMD1, which could cause bacterial pneumonia in rodents ( Zhao et al, 2021 ). A total of 20 adult female Wistar rats (8-week-old; specific-pathogen-free) (Chengdu Dossy Experimental Animals Co, Ltd, Chengdu, 610000, China) were randomly divided into four groups, which received sterile physiologic saline as control group (CG group, n = 5), Klebsiella pneumoniae (KG group, n = 5), Pseudomonas aeruginosa (PG group, n = 5) and Streptococcus equinus (SG group, n = 5) by nasal drip under anesthesia as described in Chen et al (2017) .…”

Section: Methodsmentioning

confidence: 99%

MicroRNA let-7f-5p regulates PI3K/AKT/COX2 signaling pathway in bacteria-induced pulmonary fibrosis via targeting of PIK3CA in forest musk deer

Zhao

Cheng²,

Luo

et al. 2022

PeerJ

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Background Recent studies have characterized that microRNA (miRNA) is a suitable candidate for the study of bleomycin/LPS-induced pulmonary fibrosis, but the knowledge on miRNA in bacteria-induced pulmonary fibrosis (BIPF) is limited. Forest musk deer (Moschus berezovskii, FMD) is an important endangered species that has been seriously affected by BIPF. We sought to determine whether miRNA exist that modulates the pathogenesis of BIPF in FMD. Methods High-throughput sequencing and RT-qPCR were used to determine the differentially expressed miRNAs (DEmiRNAs) in the blood of BIPF FMD. The DEmiRNAs were further detected in the blood and lung of BIPF model rat by RT-qPCR, and the targeting relationship between candidate miRNA and its potential target gene was verified by dual-luciferase reporter activity assay. Furthermore, the function of the candidate miRNA was verified in the FMD lung fibroblast cells (FMD-C1). Results Here we found that five dead FMD were suffered from BIPF, and six circulating miRNAs (miR-30g, let-7f-5p, miR-27-3p, miR-25-3p, miR-9-5p and miR-652) were differentially expressed in the blood of the BIPF FMD. Of these, let-7f-5p showed reproducibly lower level in the blood and lung of the BIPF model rat, and the expression levels of PI3K/AKT/COX2 signaling pathway genes (PIK3CA, PDK1, Akt1, IKBKA, NF-κB1 and COX2) were increased in the lung of BIPF model rats, suggesting that there is a potential correlation between BIPF and the PI3K/AKT/COX2 signaling pathway. Notably, using bioinformatic prediction and experimental verification, we demonstrated that let-7f-5p is conserved across mammals, and the seed sequence of let-7f-5p displays perfect complementarity with the 3’ UTR of PIK3CA gene and the expression of the PIK3CA gene was regulated by let-7f-5p. In order to determine the regulatory relationship between let-7f-5p and the PI3K/AKT/COX2 signaling pathway in FMD, we successfully cultured FMD-C1, and found that let-7f-5p could act as a negative regulator for the PI3K/Akt/COX2 signaling pathway in FMD-C1. Collectively, this study not only provided a study strategy for non-invasive research in pulmonary disease in rare animals, but also laid a foundation for further research in BIPF.

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Metagenomics analysis of the gut microbiome in healthy and bacterial pneumonia forest musk deer

Cited by 17 publications

References 73 publications

Seasonal variations in the composition and diversity of gut microbiota in white-lipped deer (Cervus albirostris)

Seasonal variations in the composition and diversity of gut microbiota in white-lipped deer (Cervus albirostris)

Isolation of Klebsiella pneumoniae Phage vB_KpnS_MK54 and Pathological Assessment of Endolysin in the Treatment of Pneumonia Mice Model

MicroRNA let-7f-5p regulates PI3K/AKT/COX2 signaling pathway in bacteria-induced pulmonary fibrosis via targeting of PIK3CA in forest musk deer

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