Microbial nutrient niches in the gut.
Fátima C. Pereira,David Berry +1 more
TLDR
It is proposed that Freter's nutrient niche theory must be expanded to account for the co‐existence of microorganisms utilizing the same nutrients but in distinct sites or at different times, and that metabolic flexibility and mixed‐substrate utilization are common strategies for survival in the face of ever‐present nutrient fluctuations.Abstract:
The composition and function of the mammalian gut microbiota has been the subject of much research in recent years, but the principles underlying the assembly and structure of this complex community remain incompletely understood. Processes that shape the gut microbiota are thought to be mostly niche-driven, with environmental factors such as the composition of available nutrients largely determining whether or not an organism can establish. The concept that the nutrient landscape dictates which organisms can successfully colonize and persist in the gut was first proposed in Rolf Freter's nutrient niche theory. In a situation where nutrients are perfectly mixed and there is balanced microbial growth, Freter postulated that an organism can only survive if it is able to utilize one or a few limiting nutrients more efficiently than its competitors. Recent experimental work indicates, however, that nutrients in the gut vary in space and time. We propose that in such a scenario, Freter's nutrient niche theory must be expanded to account for the co-existence of microorganisms utilizing the same nutrients but in distinct sites or at different times, and that metabolic flexibility and mixed-substrate utilization are common strategies for survival in the face of ever-present nutrient fluctuations.read more
Citations
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Function and functional redundancy in microbial systems
Stilianos Louca,Martin F. Polz,Florent Mazel,Florent Mazel,Michaeline B. N. Albright,Julie A. Huber,Mary I. O'Connor,Martin Ackermann,Martin Ackermann,Aria S. Hahn,Diane S. Srivastava,Sean A. Crowe,Michael Doebeli,Laura Wegener Parfrey +13 more
TL;DR: Both patterns are unlikely to be the result of ecological drift, but are inevitable emergent properties of open microbial systems resulting mainly from biotic interactions and environmental and spatial processes.
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Enterotypes in the landscape of gut microbial community composition
Paul I. Costea,Falk Hildebrand,Manimozhiyan Arumugam,Fredrik Bäckhed,Fredrik Bäckhed,Martin J. Blaser,Frederic D. Bushman,Willem M. de Vos,Willem M. de Vos,S. Dusko Ehrlich,S. Dusko Ehrlich,Claire M. Fraser,Masahira Hattori,Curtis Huttenhower,Ian B. Jeffery,Dan Knights,James D. Lewis,Ruth E. Ley,Howard Ochman,Paul W. O'Toole,Christopher Quince,David A. Relman,David A. Relman,Fergus Shanahan,Shinichi Sunagawa,Jun Wang,George M. Weinstock,Gary D. Wu,Georg Zeller,Liping Zhao,Jeroen Raes,Jeroen Raes,Rob Knight,Peer Bork,Peer Bork +34 more
TL;DR: The concept of enterotypes and their use to characterize the gut microbiome are debated, a classifier and standardized methodology is provided to aid cross-study comparisons, and a balanced application of the concept is encouraged.
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The Role of Lung and Gut Microbiota in the Pathology of Asthma
TL;DR: This review focuses on recently discovered connections between lung and gut microbiota, including bacteria, fungi, viruses, and archaea, and their influence on asthma.
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Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present and future
Sharon Huws,Christopher J. Creevey,Linda Oyama,Itzhak Mizrahi,Stuart E. Denman,Milka Popova,Rafael Muñoz-Tamayo,Evelyne Forano,Sinead M. Waters,Matthias Hess,Ilma Tapio,Hauke Smidt,Sophie J. Krizsan,David R. Yáñez-Ruiz,Alejandro Belanche,Le Luo Guan,Robert J. Gruninger,Tim A. McAllister,C. Jamie Newbold,Rainer Roehe,Richard J. Dewhurst,Timothy J. Snelling,Mick Watson,Garret Suen,Elizabeth H. Hart,Alison H. Kingston-Smith,Nigel D. Scollan,Rodolpho Martin do Prado,Eduardo Jorge Pilau,Hilário Cuquetto Mantovani,Graeme T. Attwood,Joan E. Edwards,Neil R. McEwan,Steven Morrisson,O. L. Mayorga,Christopher T. Elliott,Diego P. Morgavi +36 more
TL;DR: Advances in computational tools, high-throughput sequencing technologies and cultivation-independent “omics” approaches continue to revolutionize the understanding of the rumen microbiome, which will ultimately provide the knowledge framework needed to solve current and future ruminant livestock challenges.
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