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Microbiome complexity shapes metabolism | PLOS Biology

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

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

Revealed: September 21, 2022

Copyright: © 2022 Litichevskiy, Thaiss. That is an open entry article distributed underneath the phrases of the Inventive Commons Attribution License, which allows unrestricted use, distribution, and copy in any medium, supplied 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 alternate 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 subject usually compares germ-free (GF) mice—mice which might be born in a sterile surroundings and are by no means uncovered to micro organism—to conventionally colonized, or specific-pathogen-free (SPF), mice. Nevertheless, SPF mice could have very totally different intestine microbiomes relying on the power wherein 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 services. 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 [3–5], their impression on host metabolism stays poorly understood. In a brand new examine in PLOS Biology, Hoces and colleagues [6] totally in contrast OligoMM12, GF, and SPF mice to find out the methods wherein colonization with OligoMM12 does or doesn’t recapitulate the properties of a standard microbiome (Fig 1). A key technological innovation on this examine was using an isolator-housed metabolic cage system. Utilizing this setup, the authors had been capable of repeatedly monitor meals consumption, water consumption, temperature, and the degrees of carbon dioxide, oxygen, and hydrogen gases underneath circumstances 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 whole 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 standard 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 standard mice. Photographs had been created with BioRender.com. GF, germ-free; RER, respiratory alternate 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 whole physique mass. Cecum dimension dramatically expands in GF mice, most likely as a result 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 every 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.

Relatively, the authors hypothesized that the elevated fats mass may be as a result of totally different utilization of energy. In help of this speculation, all 3 teams had totally different patterns of their respiratory alternate 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 gasoline manufacturing, and ranges of short-chain fatty acids (SCFAs) (the latter 2 being indicators of microbial metabolism), additional supporting the concept the three teams make the most of the identical caloric consumption in several 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 evening. They discovered that each in the course of the mild and darkish phases, the metabolomes of OligoMM12 mice had been persistently extra just like these of GF mice than SPF mice. This discovering means that this minimal microbiome is unable to totally reproduce the results 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 illustration, the authors found that EchoMRI just isn’t dependable for measuring fats mass in GF mice. EchoMRI is an instrument that makes use of nuclear magnetic resonance to measure the share of physique mass that’s fats mass, lean mass, or water mass. The EchoMRI inaccuracy is said to GF mice having very massive ceca. The authors found that, in GF mice solely, estimates of fats mass earlier than and after removing of the cecum had been poorly correlated. They speculated that this was as a result of inconsistent project of cecal content material as fats or water mass. In lieu of EchoMRI, the authors as an alternative dissected and weighed numerous fats depots with a purpose to estimate total fats mass. This discovering serves as a phrase of warning in opposition to 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 anticipate GF mice to have larger fecal vitality density as a result of they lack microbes to assist extract energy from meals. Nevertheless, the authors speculated that the decrease fecal vitality density is as a result of microbial biomass itself comprises 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 underneath gnotobiotic circumstances. As a result of the monitoring was steady, the authors had been capable of 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, akin 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 wherein 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 group and a fancy microbiota stays to be additional elucidated, considerate research akin to it will pave the way in which towards elevated reproducibility in microbiome experiments.

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