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Microbiome complexity shapes metabolism | PLOS Biology


Quotation: Litichevskiy L, Thaiss CA (2022) Microbiome complexity shapes metabolism. PLoS Biol 20(9):
e3001793.

https://doi.org/10.1371/journal.pbio.3001793

Printed: September 21, 2022

Copyright: © 2022 Litichevskiy, Thaiss. That is an open entry article distributed below the phrases of the Artistic Commons Attribution License, which allows unrestricted use, distribution, and copy in any medium, offered the unique writer and supply are credited.

Funding: L.L. is supported by NIH Medical Scientist Coaching Program T32-GM-07170 and Coaching Grant in Computational Biology 5-T32-HG-000046–21. C.A.T. is a Pew Biomedical Scholar supported by the NIH Director’s New Innovator Award (DP2-AG-067492). The funders had no position in examine design, information assortment and evaluation, resolution to publish, or preparation of the manuscript.

Competing pursuits: The authors have declared that no competing pursuits exist.

Abbreviations:
GF,
germ-free; RER,
respiratory trade ratio; SCFA,
short-chain fatty acid; SPF,
specific-pathogen-free

The intestine microbiome impacts how its host makes use of vitality [1]. Analysis into this matter usually compares germ-free (GF) mice—mice which can be born in a sterile surroundings and are by no means uncovered to micro organism—to conventionally colonized, or specific-pathogen-free (SPF), mice. Nonetheless, SPF mice might have very totally different intestine microbiomes relying on the ability through which they’re born and raised. Because of this, investigators are more and more utilizing gnotobiotic mice, i.e., mice with easy however well-defined microbial communities that may be replicated throughout amenities. An instance of such a gnotobiotic mannequin is the OligoMM12 mouse, whose microbiome consists of 12 cultivable bacterial strains representing 5 main bacterial phyla of the mouse intestine microbiome [2]. Whereas the impact of outlined microbial communities on immune system improvement, irritation, and host protection have been extensively characterised [35], their affect on host metabolism stays poorly understood. In a brand new examine in PLOS Biology, Hoces and colleagues [6] completely in contrast OligoMM12, GF, and SPF mice to find out the methods through which colonization with OligoMM12 does or doesn’t recapitulate the properties of a standard microbiome (Fig 1). A key technological innovation on this examine was the usage of an isolator-housed metabolic cage system. Utilizing this setup, the authors have been in a position to constantly monitor meals consumption, water consumption, temperature, and the degrees of carbon dioxide, oxygen, and hydrogen gases below situations of outlined microbial colonization.

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Fig 1. Abstract of key metabolic parameters in mice harboring microbiomes of various complexity.

(High) GF mice are heavier than OligoMM12 mice and traditional mice, however after subtracting the burden of the cecum, all 3 teams have roughly the identical weight. OligoMM12 have larger fats mass than the opposite 2 teams. (Center) GF mice have larger meals consumption, elevated fecal output, and decrease fecal vitality density than the opposite 2 teams. The result’s that GF mice extract as a lot complete vitality from meals as the opposite 2 teams. All 3 teams even have roughly equal vitality expenditure, resulting in impartial vitality stability. (Backside) In the course of the mild section, GF and OligoMM12 mice have decrease RER than typical mice, however in the course of the darkish section, OligoMM12 and traditional mice each have larger RER than GF mice. GF mice don’t produce SCFAs, whereas OligoMM12 mice produce fewer SCFAs than typical mice. Pictures have been created with BioRender.com. GF, germ-free; RER, respiratory trade ratio, SCFA, short-chain fatty acid.


https://doi.org/10.1371/journal.pbio.3001793.g001

The authors made a number of attention-grabbing discoveries associated to systemic metabolism. At first look, GF mice weighed greater than OligoMM12 and SPF mice, however this distinction disappeared after subtracting the burden of the cecum, a piece of the gastrointestinal tract between the small and enormous gut, from complete physique mass. Cecum measurement dramatically expands in GF mice, in all probability as a consequence of intestinal osmosis and decreased intestinal motility [7,8]. Subtracting the burden of the cecum considerably modifications the conclusion about physique weight variations between the three teams; this highlights the significance of correctly accounting for the massively enlarged cecum in microbiome-depleted mice.

One other notable distinction in physique composition is that OligoMM12 mice have larger fats mass than both GF or SPF mice. To additional examine this relationship between microbiome standing and fats storage, the authors leveraged their isolator-housed metabolic cage system. By way of oblique calorimetry (which depends on measuring carbon dioxide and oxygen ranges), the authors discovered that each one 3 teams had equal vitality expenditure. GF mice had larger vitality consumption than the opposite 2 teams (they ate extra meals), however in addition they had larger vitality loss (they produced extra feces with decrease fecal vitality density), such that their enhance in vitality consumption was completely compensated by elevated fecal vitality loss (Fig 1). In all 3 teams, vitality extraction was roughly equal to vitality expenditure, main the authors to conclude that the rise in fats mass in OligoMM12 mice is probably going not defined by an extra of energy being transformed to fats.

Quite, the authors hypothesized that the elevated fats mass is perhaps as a consequence of totally different utilization of energy. In help of this speculation, all 3 teams had totally different patterns of their respiratory trade ratio (RER)—a metric that quantifies whether or not fats or carbohydrates are getting used for vitality manufacturing—over the course of the day. There have been additionally variations over the course of the day in ranges of hepatic glycogen shops, hydrogen fuel manufacturing, and ranges of short-chain fatty acids (SCFAs) (the latter 2 being indicators of microbial metabolism), additional supporting the concept that the three teams make the most of the identical caloric consumption in numerous methods.

The authors continued their investigation of time-of-day variations in host metabolism by performing metabolomics of the liver and blood collected in the course of the day and in the course of the night time. They discovered that each in the course of the mild and darkish phases, the metabolomes of OligoMM12 mice have been constantly extra much like these of GF mice than SPF mice. This discovering means that this minimal microbiome is unable to completely reproduce the consequences of a standard microbiome on the host metabolome.

The examine highlights a number of observations with broader implications for the investigation of microbiome results on systemic metabolism. As an example, the authors found that EchoMRI shouldn’t be dependable for measuring fats mass in GF mice. EchoMRI is an instrument that makes use of nuclear magnetic resonance to measure the proportion of physique mass that’s fats mass, lean mass, or water mass. The EchoMRI inaccuracy is expounded to GF mice having very giant ceca. The authors found that, in GF mice solely, estimates of fats mass earlier than and after removing of the cecum have been poorly correlated. They speculated that this was as a consequence of inconsistent project of cecal content material as fats or water mass. In lieu of EchoMRI, the authors as a substitute dissected and weighed numerous fats depots so as to estimate general fats mass. This discovering serves as a phrase of warning towards utilizing EchoMRI to quantify fats mass in animals with totally different microbiome standing.

One other stunning discovering was that GF mice had decrease fecal vitality density than the opposite 2 teams. Intuitively, one would count on GF mice to have larger fecal vitality density as a result of they lack microbes to assist extract energy from meals. Nonetheless, the authors speculated that the decrease fecal vitality density is as a result of microbial biomass itself incorporates energy. In help of this speculation, the authors calculated that the vitality content material of microbes in stool is roughly equal to the distinction in fecal vitality density between GF mice and the opposite 2 teams.

Together with a earlier report [9], this examine demonstrates the feasibility of multiday metabolic monitoring below gnotobiotic situations. As a result of the monitoring was steady, the authors have been in a position to detect attention-grabbing time-of-day variations between teams. Such observations promote continued investigation into how microbiome complexity influences circadian biology [10]. One particular extension of this work is asking how the circadian system of OligoMM12 mice compares to mice with different reduced-complexity microbiomes, comparable to monocolonized mice or mice colonized with the altered Schaedler flora. The examine additionally paves the way in which for the systematic investigation of commensal species that regulate the extraction and utilization of energy from meals.

In abstract, Hoces and colleagues have added to our understanding of the methods through which the metabolism of mice with a minimal microbiome does and doesn’t resemble that of mice with a standard microbiome. Though the exact mechanism regulating variations in vitality storage between mice harboring the OligoMM12 neighborhood and a fancy microbiota stays to be additional elucidated, considerate research comparable to this can pave the way in which towards elevated reproducibility in microbiome experiments.

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