PMID- 34428120
OWN - NLM
STAT- MEDLINE
DCOM- 20220111
LR  - 20220111
IS  - 1949-0984 (Electronic)
IS  - 1949-0976 (Print)
IS  - 1949-0976 (Linking)
VI  - 13
IP  - 1
DP  - 2021 Jan-Dec
TI  - Imaging the in vivo growth patterns of bacteria in human gut Microbiota.
PG  - 1960134
LID - 10.1080/19490976.2021.1960134 [doi]
LID - 1960134
AB  - How to study the unculturable bacteria in the laboratory is one of the major 
      challenges in human gut microbiota research. The resulting lack of microbiology 
      knowledge of this "dark matter" greatly hinders further understanding of our gut 
      microbiota. Here, to characterize the in vivo growth and division of human gut 
      bacteria, we report the integrative use of STAMP (sequential tagging with D-amino 
      acid-based metabolic probes) and fluorescence in situ hybridization (FISH) in a 
      human microbiota-associated mouse model. After stable colonization of the human 
      fecal microbiotas in germ-free mice, two fluorescent D-amino acid probes were 
      sequentially administered by gavage, and the dually labeled peptidoglycan of the 
      bacteria provided a chronological recording of their cell wall syntheses. 
      Following taxonomic identification with FISH staining, the growth patterns of 32 
      species, including 5 currently unculturables, were identified. Surprisingly, we 
      found that many bacterial species in the human microbiota were significantly 
      shorter than those in the mouse gut microbiota. An imaging database for gut 
      bacteria ̶ Microbiome Atlas was built for summarizing STAMP imaging of bacteria 
      from different microbiotas, which can be contributed by the microbiota research 
      community worldwide. This integrative imaging strategy and the database will 
      promote our understanding of the bacterial cytology in gut microbiotas and 
      facilitate communications among cellular microbiologists.
FAU - Lin, Liyuan
AU  - Lin L
AUID- ORCID: 0000-0002-9202-0652
AD  - Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University 
      School of Medicine, Shanghai, China.
FAU - Song, Jia
AU  - Song J
AD  - Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University 
      School of Medicine, Shanghai, China.
FAU - Li, Jian
AU  - Li J
AD  - Institute of Immunology, PLA, Third Military Medical University, Chongqing, 
      China.
FAU - Zuo, Xiaolei
AU  - Zuo X
AD  - Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University 
      School of Medicine, Shanghai, China.
FAU - Wei, Hong
AU  - Wei H
AD  - Central Laboratory, Clinical Medicine Scientific and Technical Innovation Park, 
      Shanghai Tenth People's Hospital, Tongji University, Shanghai, China.
AD  - State Key Laboratory of Agricultural Microbiology, College of Animal Sciences and 
      Technology, Huazhong Agricultural University, Wuhan, P. R. China.
FAU - Yang, Chaoyong
AU  - Yang C
AUID- ORCID: 0000-0002-2374-5342
AD  - Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University 
      School of Medicine, Shanghai, China.
AD  - The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Key 
      Laboratory for Chemical Biology of Fujian Province State Key Laboratory of 
      Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of 
      Chemistry and Chemical Engineering, Xiamen University, Xiamen, China.
FAU - Wang, Wei
AU  - Wang W
AUID- ORCID: 0000-0002-5539-4532
AD  - Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University 
      School of Medicine, Shanghai, China.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - United States
TA  - Gut Microbes
JT  - Gut microbes
JID - 101495343
RN  - 0 (Fluorescent Dyes)
SB  - IM
MH  - Animals
MH  - Bacteria/*classification/*growth & development
MH  - Cecum/microbiology
MH  - Fluorescent Dyes
MH  - Gastrointestinal Microbiome/*physiology
MH  - Germ-Free Life
MH  - Humans
MH  - In Situ Hybridization, Fluorescence/*methods
MH  - Mice
MH  - Mice, Inbred BALB C
MH  - Optical Imaging/*methods
MH  - Staining and Labeling
PMC - PMC8386752
OTO - NOTNLM
OT  - D-amino acids
OT  - FISH
OT  - Human gut microbiota
OT  - Microbiome Atlas
OT  - STAMP
OT  - bacterial division patterns
OT  - fluorescence imaging
OT  - metabolic labeling
OT  - peptidoglycan
COIS- The authors declare no competing interests.
EDAT- 2021/08/25 06:00
MHDA- 2022/01/12 06:00
PMCR- 2021/08/24
CRDT- 2021/08/24 17:15
PHST- 2021/08/24 17:15 [entrez]
PHST- 2021/08/25 06:00 [pubmed]
PHST- 2022/01/12 06:00 [medline]
PHST- 2021/08/24 00:00 [pmc-release]
AID - 1960134 [pii]
AID - 10.1080/19490976.2021.1960134 [doi]
PST - ppublish
SO  - Gut Microbes. 2021 Jan-Dec;13(1):1960134. doi: 10.1080/19490976.2021.1960134.