Abstract
Background
The forest musk deer (FMD, Moschus berezovskii) is an threatened species in China. Bacterial pneumonia was found to seriously restrict the development of FMD captive breeding. Historical evidence has demonstrated the relationship between immune system and intestinal Lactobacillus in FMD.
Objective
We sought to elucidate the differences in the gut microbiota of healthy and bacterial pneumonia FMD.
Methods
The bacterial pneumonia FMD was demonstrated by bacterial and pathological diagnosis, and the gut microbiome of healthy and bacterial pneumonia FMD was sequenced and analysed.
Results
There are three pathogens (Pseudomonas aeruginosa, Streptococcus equinus and Trueperella pyogenes) isolated from the bacterial pneumonia FMD individuals. Compared with the healthy group, the abundance of Firmicutes and Proteobacteria in the pneumonia group was changed, and a high level of Proteobacteria was found in the pneumonia group. In addition, a higher abundance of Acinetobacter (p = 0.01) was observed in the population of the pneumonia group compared with the healthy group. Several potentially harmful bacteria and disease-related KEGG subsystems were only found in the gut of the bacterial pneumonia group. Analysis of KEGG revealed that many genes related to type IV secretion system, type IV pilus, lipopolysaccharide export system, HTH-type transcriptional regulator/antitoxin MqsA, and ArsR family transcriptional regulator were significantly enriched in the metagenome of the bacterial pneumonia FMD.
Conclusion
Our results demonstrated that the gut microbiome was significantly altered in the bacterial pneumonia group. Overall, our research improves the understanding of the potential role of the gut microbiota in the FMD bacterial pneumonia.
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References
Amato KR (2013) Co-evolution in context: the importance of studying gut microbiomes in wild animals. Microbiome Sci Med 1:10–29. https://doi.org/10.2478/micsm-2013-0002
Anupriya T, Justine D, David AB, Michael K, Rob K (2018) The gut–liver axis and the intersection with the microbiome. Nat Rev Gastroenterol Hepatol 15:397–411. https://doi.org/10.1038/s41575-018-0011-z
Armstrong D, Tully JG, Yu B, Morton V, Friedman MH, Steger L (1970) Previously uncharacterized mycoplasma isolates from an investigation of canine pneumonia. Infect Immun 1:1–7
Barton MD, Ireland L, Kirschner JL, Forbes C (1985) Isolation of Mycoplasma spumans from polyarthritis in a greyhound. Aust Vet J 62:206–207
Biagi E, Candela M, Fairweather-Tait S, Franceschi C, Brigidi P (2012) Ageing of the human metaorganism: the microbial counterpart. Age 34:247–267. https://doi.org/10.1007/s11357-011-9217-5
Bo-Gie Y, Yeon HK, Myung-Shik L (2017) Alterations in gut microbiota and immunity by dietary fat. Yonsei Med J 58:1083–1091. https://doi.org/10.3349/ymj.2017.58.6.1083
Buchfink B, Xie C, Huson DH (2015) Fast and sensitive protein alignment using DIAMOND. Nat Methods 12:59–60. https://doi.org/10.1038/nmeth.3176
Budden KF, Gellatly SL, Wood DLA, Cooper MA, Morrison M, Hugenholtz P (2017) Emerging pathogenic links between microbiota and the gut–lung axis. Nat Rev Microbiol 15:55–63. https://doi.org/10.1038/nrmicro.2016.142
Burnens AP, Stanley J, Schaad UB, Nicolet J (1993) Novel campylobacter-like organism resembling Helicobacter fennelliae isolated from a boy with gastroenteritis and from dogs. J Clin Microbiol 31:1916–1917
Byrd AL, Segre JA (2016) Infectious disease. Adapting Koch’s postulates. Science 351:224–226. https://doi.org/10.1126/science.aad6753
Chen Y, Liao K, Ai L, Guo P, Liu M (2017) Bacteremia caused by Bergeyella zoohelcum in an infective endocarditis patient: case report and review of literature. BMC Infect Dis 17:271. https://doi.org/10.1186/s12879-017-2391-z
Chen C, Chen H, Zhang Y, Thomas HR, Frank MH, He Y, Xia R (2020) TBtools: an integrative toolkit developed for interactive analyses of big biological data. Mol Plant 13:1194–1202. https://doi.org/10.1016/j.molp.2020.06.009
Craig L, Pique ME, Tainer JA (2004) Type IV pilus structure and bacterial pathogenicity. Nat Rev Microbiol 21:363–378
Delgado ML, Singh P, Funk JA, Moore JA, Cannell EM, Kanesfsky J, Manning SD, Scribner KT (2017) Intestinal microbial community dynamics of white-tailed deer (Odocoileus virginianus) in an agroecosystem. Microb Ecol 74:496–506. https://doi.org/10.1007/s00248-017-0961-7
den Hartigh AB, Rolán HG, de Jong MF, Tsolis RM (2008) VirB3 to VirB6 and VirB8 to VirB11, but not VirB7, are essential for mediating persistence of Brucella in the reticuloendothelial system. J Bacteriol 190:4427–4436. https://doi.org/10.1128/JB.00406-08
Dong X, Song J, Chen J, Bi D, Wang W, Ren Y, Wang H, Wang G, Tang KFJ, Wang X, Huang J (2019) Conjugative transfer of the pVA1-Type plasmid carrying the pirABvp genes results in the formation of new AHPND-causing Vibrio. Front Cell Infect Microbiol 9:195. https://doi.org/10.3389/fcimb.2019.00195
Earing JE, Durig AC, Gellin GL, Lawrence LM, Flythe MD (2012) Bacterial colonization of the equine gut; comparison of mare and foal pairs by PCR-DGGE. Adv Microbiol 2:79–86
El AS, Kunze W, Bienenstock J, Kleerebezem M (2012) The microbiota and the gut–brain axis: insights from the temporal and spatial mucosal alterations during colonisation of the germfree mouse intestine. Benef Microbes 3:251–259. https://doi.org/10.3920/BM2012.0042
Enaud R, Prevel R, Ciarlo E, Beaufils F, Wieërs G, Guery B, Delhaes L (2020) The gut–lung axis in health and respiratory diseases: a place for inter-organ and inter-kingdom crosstalks. Front Cell Infect Microbiol 10:9. https://doi.org/10.3389/fcimb.2020.00009
Francesca P, Sandra SC, Iñaki E, Manuel MV, Francesca G, Maurizio B (2016) Role of gut microbiota and nutrients in amyloid formation and pathogenesis of alzheimer disease. Nutr Rev 74:624–634. https://doi.org/10.1093/nutrit/nuw023
Fredrik B, Hao D (2011) Programming of host metabolism by the gut microbiota. Ann Nutr Metab 58:44–52. https://doi.org/10.1159/000328042
Fujiya Y, Nagamatsu M, Tomida J, Kawamura Y, Yamamoto K, Mawatari M, Kutsuna S, Takeshita N, Hayakawa K, Kanagawa S, Mezaki K, Hashimoto M, Ishii S, Ohmagari N (2016) Successful treatment of recurrent Helicobacter fennelliae bacteraemia by selective digestive decontamination with Kanamycin in a lung cancer patient receiving chemotherapy. JMM Case Rep 3:e005069. https://doi.org/10.1099/jmmcr.0.005069
Gemmell MR, Berry S, Mukhopadhya I, Hansen R, Nielsen HL, Bajaj-Elliott M, Nielsen H, Hold GL (2018) Comparative genomics of Campylobacter concisus: analysis of clinical strains reveals genome diversity and pathogenic potential. Emerg Microbes Infect 7:116. https://doi.org/10.1038/s41426-018-0118-x
Gorrie CL, Mirceta M, Wick RR, Edwards DJ, Thomson NR, Strugnell RA, Pratt NF, Garlick JS, Watson KM, Pilcher DV, McGloughlin SA, Spelman DW, Jenney AWJ, Holt KE (2017) Gastrointestinal carriage is a major reservoir of Klebsiella pneumoniae infection in intensive care patients. Clin Infect Dis 65:208–215. https://doi.org/10.1093/cid/cix270
Hu X, Liu G, Shafer A, Wei Y, Zhou J, Lin S, Wu H, Zhou M, Hu D, Liu S (2017) Comparative analysis of the gut microbial communities in forest and alpine musk deer using high-throughput sequencing. Front Microbiol 8:572. https://doi.org/10.3389/fmicb.2017.00572
Hu X, Liu G, Li Y, Wei Y, Lin S, Liu S, Zhang Y, Hu D (2018) High-throughput analysis reveals seasonal variation of the gut microbiota composition within forest musk deer (Moschus berezovskii). Front Microbiol 9:1674. https://doi.org/10.3389/fmicb.2018.01674
Jiang JQ, Cheng JG, Zhao W, Luo Y, Wang WY, Tian Q (2017) Isolation, identification and bioinformatics analysis of Streptococcus gallolyticus. Chin J Vet Med 53:20–23
Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K (2017) KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res 45:353–361. https://doi.org/10.1093/nar/gkw1092
Karlsson FH, Fåk F, Nookaew I, Tremaroli V, Fagerberg B, Petranovic D, Bäckhed F, Nielsen J (2012) Symptomatic atherosclerosis is associated with an altered gut metagenome. Nat Commun 3:1245. https://doi.org/10.1038/ncomms2266
Kim Y, Wang X, Zhang XS, Grigoriu S, Page R, Peti W, Wood TK (2010) Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD. Environ Microbiol 12:1105–1121. https://doi.org/10.1111/j.1462-2920.2009.02147.x
Kwan BW, Lord DM, Peti W, Page R, Benedik MJ, Wood TK (2015) The MqsR/MqsA toxin/antitoxin system protects Escherichia coli during bile acid stress. Environ Microbiol 17:3168–3181. https://doi.org/10.1111/1462-2920.12749
Lamousé-Smith ES, Alice T, Starnbach MN, Stefan B (2011) The intestinal flora is required to support antibody responses to systemic immunization in infant and germ free mice. PLoS ONE 6:e27662. https://doi.org/10.1371/journal.pone.0027662
Li Y, Hu X, Yang S, Zhou J, Zhang T, Qi L, Sun X, Fan M, Xu S, Cha M, Zhang M, Lin S, Liu S, Hu D (2017) Comparative analysis of the gut microbiota composition between captive and wild forest musk deer. Front Microbiol 8:1705. https://doi.org/10.3389/fmicb.2017.01705
Li Y, Hu X, Yang S, Zhou J, Qi L, Sun X, Fan M, Xu S, Cha M, Zhang M, Lin S, Liu S, Hu D (2018) Comparison between the fecal bacterial microbiota of healthy and diarrheic captive musk deer. Front Microbiol 9:300. https://doi.org/10.3389/fmicb.2018.00300
Lin WR, Chen YS, Liu YC (2007) Cellulitis and bacteremia caused by Bergeyella zoohelcum. J Formos Med Assoc 106:570–576
Liu H, He H, Cheng C, Liu J, Shu M, Jiao Y, Tao F, Zhong W (2015) Diversity analysis of the bacterial community in tobacco waste extract during reconstituted tobacco process. Appl Microbiol Biotechnol 99:469–476. https://doi.org/10.1007/s00253-014-5960-8
Liu X, Zhao W, Yu D, Cheng JG, Luo Y, Wang Y, Yang ZX, Yao XP, Wu SS, Wang WY, Yang W, Li DQ, Wu YM (2019) Effects of compound probiotics on the weight, immunity performance and fecal microbiota of forest musk deer. Sci Rep 9:19146. https://doi.org/10.1038/s41598-019-55731-5
Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y et al (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 27:18. https://doi.org/10.1186/2047-217X-1-18
Luo X, Wang P, Cheng JG, Luo Y, Dai L, Zhou X, Zou LK, Li B, Xiao JJ (2016) Characterization of virulence genes and antimicrobial resistance of lung pathogenic Escherichia coli isolates in forest musk deer (Moschus berezovskii). J Zoo Wildl Med 47:540–550. https://doi.org/10.1638/2014-0167.1
Motiani KK, Collado MC, Eskelinen JJ, Virtanen KA, Löyttyniemi E, Salminen P, Nuutila P, Kalliokoski KK, Hannukainen JC (2020) Exercise training modulates gut microbiota profile and improves endotoxemia. Med Sci Sports Exerc 52:94–104. https://doi.org/10.1249/MSS.0000000000002112
Nagy-Szakal D, Williams BL, Mishra N, Che X, Lee B, Bateman L, Klimas NG, Komaroff AL, Levine S, Montoya JG et al (2017) Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome. Microbiome 5:44. https://doi.org/10.1186/s40168-017-0261-y
Navaneetharaja N, Griffiths V, Wileman T, Carding SR (2016) A role for the intestinal microbiota and virome in myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). J Clin Med 5:1–22. https://doi.org/10.3390/jcm5060055
Negi S, Pahari S, Bashir H, Agrewala JN (2019) Gut microbiota regulates Mincle mediated activation of lung dendritic cells to protect against Mycobacterium tuberculosis. Front Immunol 10:1142. https://doi.org/10.3389/fimmu.2019.01142
Nielsen HB, Almeida M, Juncker AS, Rasmussen S, Li J, Sunagawa S, Plichta DR, Gautier L, Pedersen AG, Le CE et al (2014) Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nat Biotechnol 32:822–828. https://doi.org/10.1038/nbt.2939
Norman JM, Handley SA, Baldridge MT, Droit L, Liu CY, Keller BC, Kambal A, Monaco CL, Zhao G, Fleshner P, Stappenbeck TS, McGovern DPB et al (2015) Disease-specific alterations in the enteric virome in inflammatory bowel disease. Cell 160:447–460. https://doi.org/10.1016/j.cell.2015.01.002
Pan D, Zhong TY (2014) Intestinal microbiome of poultry and its interaction with host and diet. Gut Microbes 5:108–119. https://doi.org/10.4161/gmic.26945
Park CH, Lee AR, Lee YR, Eun CS, Lee SK, Han DS (2019) Evaluation of gastric microbiome and metagenomic function in patients with intestinal metaplasia using 16S rRNA gene sequencing. Helicobacter 24:e12547. https://doi.org/10.1111/hel.12547
Preston GM, Studholme DJ, Caldelari I (2005) Profiling the secretomes of plant pathogenic Proteobacteria. FEMS Microbiol Rev 29:331–360
Rimbara E, Mori S, Kim H, Matsui M, Suzuki S, Takahashi S, Yamamoto S, Mukai M, Shibayama K (2013) Helicobacter cinaedi and Helicobacter fennelliae transmission in a hospital from 2008 to 2012. J Clin Microbiol 51:2439–2442. https://doi.org/10.1128/JCM.01035-13
Schuijt TJ, Lankelma JM, Scicluna BP, Felipe DSEM, Roelofs JJ, De Boer JD, Hoogendijk AJ, de Beer R, de Vos A, Belzer C et al (2016) The gut microbiota plays a protective role in the host defence against pneumococcal pneumonia. Gut 65:575–583. https://doi.org/10.1136/gutjnl-2015-309728
Seong CN, Kang JW, Lee JH, Seo SY, Woo JJ, Park C, Bae KS, Kim MS (2018) Taxonomic hierarchy of the phylum Firmicutes and novel Firmicutes species originated from various environments in Korea. J Microbiol 56:1–10. https://doi.org/10.1007/s12275-018-7318-x
Tan Y, Zhou K, Tang X, Kudinha T, Wang L, Guo Z, Akova M, Zhuo C (2017) Bacteremic and non-bacteremic pneumonia caused by Acinetobacterbaumannii in icus of south china: a clinical and microbiological study. Sci Rep 7:5279. https://doi.org/10.1038/s41598-017-13148-y
Tian Q, Zhou X, Cheng JG, Luo Y, Dai L, Zhao W (2017) Genome sequence of lung pathogenic Escherichia coli O78, a chimeric strain isolated from pneumonia forest musk deer. Genes Genomics 39:805–815
Ticinesi A, Milani C, Guerra A, Allegri F, Lauretani F, Nouvenne A (2018) Understanding the gut–kidney axis in nephrolithiasis: an analysis of the gut microbiota composition and functionality of stone formers. Gut 67:2097–2106. https://doi.org/10.1136/gutjnl-2017-315734
Tran AX, Dong C, Whitfield C (2010) Structure and functional analysis of LptC, a conserved membrane protein involved in the lipopolysaccharide export pathway in Escherichia coli. J Biol Chem 285:33529–33539. https://doi.org/10.1074/jbc.M110.144709
Van der Kolk JH, Endimiani A, Graubner C, Gerber V, Perreten V (2019) Acinetobacter in veterinary medicine, with an emphasis onAcinetobacter baumannii. J Glob Antimicrob Resist 16:59–71. https://doi.org/10.1016/j.jgar.2018.08.011
Von KE, Ekmekciu I, Bereswill S, Heimesaat MM (2017) Intestinal and systemic immune responses upon multi-drug resistant Pseudomonas aeruginosa colonization of mice harboring a human gut microbiota. Front Microbiol 22:2590. https://doi.org/10.3389/fmicb.2017.02590
Wagner J, Maksimovic J, Farries G, Sim WH, Bishop RF, Cameron DJ, Catto-Smith AG, Kirkwood CD (2013) Bacteriophages in gut samples from pediatric Crohn’s disease patients: metagenomic analysis using 454 pyrosequencing. Inflamm Bowel Dis 19:1598–1608. https://doi.org/10.1097/MIB.0b013e318292477c
Wang JH, Lu J, Zhang YX, Wu J, Luo Y, Liu H (2018a) Metagenomic analysis of antibiotic resistance genes in coastal industrial mariculture systems. Bioresour Technol 189:235–243. https://doi.org/10.1016/j.biortech.2018.01.035
Wang AR, Ran C, Ringø E, Zhou ZG (2018b) Progress in fish gastrointestinal microbiota research. Rev Aquacult 10:626–640
Wang H, Lian P, Niu X, Zhao L, Mu X, Feng B, Li J, Liang Z, Qiao J (2018c) TLR4 deficiency reduces pulmonary resistance to Streptococcus pneumoniae in gut microbiota-disrupted mice. PLoS ONE 13:e0209183. https://doi.org/10.1371/journal.pone.0209183
Wang WY, Tian Q, Cheng JG, Zhao W, Deng L, Luo Y (2018d) Establishment and evaluation of BALB/c mice challenge model with lung pathogenic Escherichia coli O78 of forest musk deer origin. Microbiol China 45:1333–1341
Wen XH, He PW, Yu LW, Wen KD, Yue JZ (2016) High-throughput sequencing reveals the change of gut microbiota in infants with pneumonia following antibiotic treatment. Chin J Microecol 28:497–500
Williams SG, Attridge SR, Manning PA (1993) The transcriptional activator HlyU of Vibrio cholerae: nucleotide sequence and role in virulence gene expression. Mol Microbiol 9:751–760. https://doi.org/10.1111/j.1365-2958.1993.tb01735.x
Wong S, Rawls JF (2012) Intestinal microbiota composition in fishes is influenced by host ecology and environment. Mol Ecol 21:3100–3112
Wong D, Nielsen TB, Bonomo RA, Pantapalangkoor P, Luna B, Spellberg B (2017) Clinical and pathophysiological overview of acinetobacter infections: a century of challenges. Clin Microbiol Rev 30:409–447
Ximenez C, Torres J (2017) Development of microbiota in infants and its role in maturation of gut mucosa and immune system. Arch Med Res 48:666–680. https://doi.org/10.1016/j.arcmed.2017.11.007
Yan M, Yan QG, Yang GY (2016) The mass diseases of captive musk deer. J Econ Anim 2:112–117. https://doi.org/10.13326/j.jea.2016.1126
Yao G, Wu S, Zeng X, Zhao H, Wang G, Chen M, Qian N (2019) Different gut microbiome composition in obese Guizhou minipigs between female and castrated male. Folia Microbiol 64:889–898. https://doi.org/10.1007/s12223-019-00704-4
Zhao KL, Liu Y, Zhang XY, Palahati P, Wang HN, Yue BS (2011) Detection and characterization of antibiotic-resistance genes in Arcanobacteriumpyogenes strains from abscesses of forest musk deer. J Med Microbiol 60:1820–1826. https://doi.org/10.1099/jmm.0.033332-0
Zhao K, Tian Y, Yue BS, Hong NW (2013) Virulence determinants and biofilm production among Trueperella pyogenes recovered from abscesses of captive forest musk deer. Arch Microbiol 195:203–209. https://doi.org/10.1007/s00203-013-0869-7
Zhao W, Tian Q, Luo Y, Wang Y, Yang ZX, Yao XP, Cheng JG, Zhou X, Wang WY (2017) Isolation, identification, and genome analysis of lung pathogenic Klebsiella pneumoniae (LPKP) in forest musk deer. J Zoo Wildl Med 48:1039–1048. https://doi.org/10.1638/2016-0241.1
Zhao K, Ma J, Wang X, Guo Y, Yue BS, Chu Y (2019) Population divergence of Pseudomonas aeruginosa can lead to the coexistence with Escherichia coli in animal suppurative lesions. Vet Microbiol 231:169–176. https://doi.org/10.1016/j.vetmic.2019.03.014
Zhao W, Yu D, Cheng JG, Wang Y, Yang ZX, Yao XP, Luo Y (2020) Identification and pathogenicity analysis of Streptococcus equinus FMD1, a beta-hemolytic strain isolated from forest musk deer lung. J Vet Med Sci 82:172–176. https://doi.org/10.1292/jvms.19-0566
Zhou L, Vorhölter FJ, He YQ, Jing BL, Tang JL, Xu YQ, Pühler A, He YW (2011) Gene discovery by genome-wide CDS re-prediction and microarray-based transcriptional analysis in phytopathogen Xanthomonas campestris. BMC Genomics 12:359. https://doi.org/10.1186/1471-2164-12-359
Zi Y, Ni Z, Chun YW, Xin YZ, Qing FW, Xin YH, Du LP, Cao QF, Tang JH, Zhou GJ et al (2018) A metagenomic study of the gut microbiome in Behcet’s disease. Microbiome 6:135. https://doi.org/10.1186/s40168-018-0520-6
Zuo T, Ng SC (2018) The gut Microbiota in the pathogenesis and therapeutics of inflammatory bowel disease. Front Microbiol 9:2247. https://doi.org/10.3389/fmicb.2018.02247
Acknowledgements
The authors are grateful to Novogene Bioinformatics Technology, Co., Ltd. (Beijing, China) for their skillful support in metagenomic sequencing
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This work was funded by the Science and Technology Achievements Transfer Project in 2020 from Scientific Research Institutions of Science and Technology Department of Sichuan Province, Sichuan, China (No. 2020JDZH0024).
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All authors contributed to the study conception and design. Material preparation, data collection and analysis were performed by WZ, ZR, YL and JC. The first draft of the manuscript was written by WZ and ZR, and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript. WZ and RW contributed equally to this work.
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The process of FMD and mouse specimens collected was accorded with animal protection law of the People’s Republic of China and approved by the National Institute of Animal Health Animal Care and Use Committee at Sichuan Agricultural University (No. SYXK2014-187).
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Zhao, W., Ren, Z., Luo, Y. et al. Metagenomics analysis of the gut microbiome in healthy and bacterial pneumonia forest musk deer. Genes Genom 43, 43–53 (2021). https://doi.org/10.1007/s13258-020-01029-0
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DOI: https://doi.org/10.1007/s13258-020-01029-0