Stable-Isotope Probing of Human and Animal Microbiome Function

被引：66

作者：

Berry, David ^{[1
]}

Loy, Alexander ^{[1
]}

机构：

[1] Univ Vienna, Res Network Chem Meets Microbiol, Dept Microbiol & Ecosyst Sci, Div Microbial Ecol, Althanstr 14, Vienna, Austria

来源：

TRENDS IN MICROBIOLOGY | 2018年 / 26卷 / 12期

基金：

奥地利科学基金会; 欧洲研究理事会;

关键词：

BACTERIA; MODEL; HYDROGEN; NUTRIENT; OLIGOSACCHARIDES; ECOPHYSIOLOGY; COLONIZATION; INFLAMMATION; COMMUNITIES; METABOLISM;

D O I：

10.1016/j.tim.2018.06.004

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Humans and animals host diverse communities of microorganisms important to their physiology and health. Despite extensive sequencing-based characterization of host-associated microbiomes, there remains a dramatic lack of understanding of microbial functions. Stable-isotope probing (SIP) is a powerful strategy to elucidate the ecophysiology of microorganisms in complex host-associated microbiotas. Here, we suggest that SIP methodologies should be more frequently exploited as part of a holistic functional microbiomics approach. We provide examples of how SIP has been used to study host-associated microbes in vivo and ex vivo. We highlight recent developments in SIP technologies and discuss future directions that will facilitate deeper insights into the function of human and animal microbiomes.

引用

页码：999 / 1007

页数：9

共 63 条

[1] Metatranscriptome of human faecal microbial communities in a cohort of adult men [J].

Abu-Ali, Galeb S. ;

Mehta, Raaj S. ;

Lloyd-Price, Jason ;

Mallick, Himel ;

Branck, Tobyn ;

Ivey, Kerry L. ;

Drew, David A. ;

DuLong, Casey ;

Rimm, Eric ;

Izard, Jacques ;

Chan, Andrew T. ;

Huttenhower, Curtis .

NATURE MICROBIOLOGY, 2018, 3 (03) :356-366

[2]

Antoniewicz Maciek R, 2013, Methods Mol Biol, V985, P353, DOI 10.1007/978-1-62703-299-5_17

[3] Hydrogen Sulfide: Redox Metabolism and Signaling [J].

Banerjee, Ruma .

ANTIOXIDANTS & REDOX SIGNALING, 2011, 15 (02) :339-341

[4] ENERGY CONTRIBUTIONS OF VOLATILE FATTY-ACIDS FROM THE GASTROINTESTINAL-TRACT IN VARIOUS SPECIES [J].

BERGMAN, EN .

PHYSIOLOGICAL REVIEWS, 1990, 70 (02) :567-590

[5] Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells [J].

Berry, David ;

Mader, Esther ;

Lee, Tae Kwon ;

Woebken, Dagmar ;

Wang, Yun ;

Zhu, Di ;

Palatinszky, Marton ;

Schintimeister, Arno ;

Schmid, Markus C. ;

Hanson, Buck T. ;

Shterzer, Naama ;

Mizrahi, Itzhak ;

Rauch, Isabella ;

Decker, Thomas ;

Bocklitz, Thomas ;

Popp, Jurgen ;

Gibson, Christopher M. ;

Fowler, Patrick W. ;

Huang, Wei E. ;

Wagner, Michael .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2015, 112 (02) :E194-E203

[6] Host-compound foraging by intestinal microbiota revealed by single-cell stable isotope probing [J].

Berry, David ;

Stecher, Baerbel ;

Schintlmeister, Arno ;

Reichert, Jochen ;

Brugiroux, Sandrine ;

Wild, Birgit ;

Wanek, Wolfgang ;

Richter, Andreas ;

Rauch, Isabella ;

Decker, Thomas ;

Loy, Alexander ;

Wagner, Michael .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2013, 110 (12) :4720-4725

[7] Stable Isotope Techniques for the Assessment of Host and Microbiota Response During Gastrointestinal Dysfunction [J].

Butler, Ross N. ;

Kosek, Tmargaret ;

Krebs, Nancy F. ;

Loechl, Cornelia U. ;

Loy, Alexander ;

Owino, Victor O. ;

Zimmermann, Michael B. ;

Morrison, Douglas J. .

JOURNAL OF PEDIATRIC GASTROENTEROLOGY AND NUTRITION, 2017, 64 (01) :8-14

[8] Targeted metagenomics of active microbial populations with stable-isotope probing [J].

Coyotzi, Sara ;

Pratscher, Jennifer ;

Murrell, J. Colin ;

Neufeld, Josh D. .

CURRENT OPINION IN BIOTECHNOLOGY, 2016, 41 :1-8

[9] Microbial conversion of choline to trimethylamine requires a glycyl radical enzyme [J].

Craciun, Smaranda ;

Balskus, Emily P. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2012, 109 (52) :21307-21312

[10] Gaining insight into microbial physiology in the large intestine: A special role for stable isotopes [J].

de Graaf', Albert A. ;

Venema, Koen .

ADVANCES IN MICROBIAL PHYSIOLOGY, VOL 53, 2008, 53 :73-+

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