Influence of H7N9 virus infection and associated treatment on human gut microbiota.
Between March and June, 2013, forty H7N9 patients were hospitalized in our hospital. Next-generation sequencing technologies have been used to sequence the fecal DNA samples of the patient, the within sample diversity analysis, enterotyping, functional gene and metagenomic species analysis have been carried on both the patients and healthy controls. The influence of associated treatment in H7N9 infected patients is dramatic and was firstly revealed in species level due to deep sequencing technology. We found that most of the MetaGenomic Species (MGS) enriched in the control samples were Roseburia inulinivorans DSM 16841, butyrate producing bacterium SS3/4 and most of MGS enriched in the H7N9 patients were Clostridium sp. 7 2 43FAA and Enterococcus faecium. It was concluded that H7N9 viral infection and antibiotic administration have a significant effect on the microbiota community with decreased diversity and overgrowth of the bacteria such as Escherichia coli and Enterococcus faecium. Enterotype analysis showed that the communities were unstable. Treatment including antivirals, probiotics and antibiotics helps to improve the microbiota diversity and the abundance of beneficial bacteria in the gut.
State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated College of Medicine, Zhejiang University, 310003 Hangzhou, China.|Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China.
Nan
N
Qin
State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated College of Medicine, Zhejiang University, 310003 Hangzhou, China.|Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China.
Beiwen
B
Zheng
State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated College of Medicine, Zhejiang University, 310003 Hangzhou, China.|Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China.
Jian
J
Yao
State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated College of Medicine, Zhejiang University, 310003 Hangzhou, China.
Lihua
L
Guo
State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated College of Medicine, Zhejiang University, 310003 Hangzhou, China.
Jian
J
Zuo
State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated College of Medicine, Zhejiang University, 310003 Hangzhou, China.
Lingjiao
L
Wu
State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated College of Medicine, Zhejiang University, 310003 Hangzhou, China.|Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China.
Jiawei
J
Zhou
State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated College of Medicine, Zhejiang University, 310003 Hangzhou, China.|Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China.
Lin
L
Liu
State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated College of Medicine, Zhejiang University, 310003 Hangzhou, China.
Jing
J
Guo
State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated College of Medicine, Zhejiang University, 310003 Hangzhou, China.
Shujun
S
Ni
State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated College of Medicine, Zhejiang University, 310003 Hangzhou, China.
Ang
A
Li
State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated College of Medicine, Zhejiang University, 310003 Hangzhou, China.|Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China.
Yixin
Y
Zhu
State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated College of Medicine, Zhejiang University, 310003 Hangzhou, China.|Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China.
Weifeng
W
Liang
State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated College of Medicine, Zhejiang University, 310003 Hangzhou, China.|Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China.
Yonghong
Y
Xiao
Metagenopolis, Institut National de la Recherche Agronomique, 78350, Jouy en Josas, France.|King's College London, Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy's Hospital, London Bridge, London SE1 9RT, UK.
S Dusko
SD
Ehrlich
State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated College of Medicine, Zhejiang University, 310003 Hangzhou, China.|Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China.
Lanjuan
L
Li
D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D003013:Clostridium / Q000235:genetics / Q000472:pathogenicity; D016984:Enterococcus faecium / Q000235:genetics / Q000472:pathogenicity; D004926:Escherichia coli / Q000235:genetics / Q000472:pathogenicity; D005260:Female; D000069196:Gastrointestinal Microbiome / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D064766:Influenza A Virus, H7N9 Subtype / Q000235:genetics* / Q000472:pathogenicity; D007251:Influenza, Human / Q000235:genetics* / Q000382:microbiology / Q000821:virology; D008297:Male; D056186:Metagenomics; D008875:Middle Aged