91Ӱ

Journal News

Our internal ecology

Ecosystem models help explain the diversity of the gut microbiome
Laurel Oldach
Sept. 29, 2020

According to a , if you sample enough humans’ intestines, almost 40,000 types of microbe can be found. Any individual individual micro-organisms in one or two thousand taxonomic groups. How does the microbiome maintain such diversity?

One model to explain the enormous variety borrows from studies of larger ecosystems. A well-known theory in ecology, nonequilibrium coexistence of competitors, suggests that as an environment fluctuates, different species gain an edge over neighbors — but their ascendance rarely lasts long.

Cover-890x496.jpg
Leyuan Li
Macro- and microecosystems may have more in common than we might think.

Intestinal nutrients fluctuate as the human host eats and excretes, in time with the physiology of sleep–wake cycles, and along the length of the gut. A layer of mucus that protects host cells from commensal microbes introduces new oligosaccharides as a fuel source and also separates microbial communities into mucosal and luminal niches. As conditions change, species in the microbiome shift in abundance and jockey for survival, and the constantly changing competitive edge keeps the ecosystem diverse.

According to University of Ottawa postdoctoral fellow Leyuan Li, the time is ripe for microbiome studies to apply population modeling and systems dynamics from macroecology to this more intimate ecosystem.

“Most of the time we study the gut microbiome as a whole: We sequence one sample as if it were representative of our whole gut,” said Li. “The gut is actually a heterogeneous system … so we need to start thinking about the gut microbiome like a rainforest.”

Li, who conducted her Ph.D. studies building artificial ecosystems, now studies gut microbiome dynamics in health and diseases such as inflammatory bowel disease in the lab of Ottawa professor Daniel Figeys. In a in the journal Molecular & Cellular Proteomics, the pair offer an introduction to microbiome ecology.

The review highlights the potential for metaproteomics, which characterizes the proteins of whole communities of microbes, to describe microbial function. Most microbiome studies use metagenomics, ribosomal RNA sequencing of the mixed population of a microbial community, to identify the bacteria, fungi and archaea that are present. Li thinks metaproteomics also may help researchers road-test increasingly popular ex vivo experimental models of the microbiome to make sure they match up to the real thing.

“Using metagenomics, you know who are there and what they can do,” Li said. “With metaproteomics you know who are there and what they are doing.”

Enjoy reading 91ӰToday?

Become a member to receive the print edition four times a year and the digital edition monthly.

Learn more
Laurel Oldach

Laurel Oldach is a former science writer for the ASBMB.

Get the latest from 91ӰToday

Enter your email address, and we’ll send you a weekly email with recent articles, interviews and more.

Latest in Science

Science highlights or most popular articles

Hope for a cure hangs on research
Essay

Hope for a cure hangs on research

July 17, 2025

Amid drastic proposed cuts to biomedical research, rare disease families like Hailey Adkisson’s fight for survival and hope. Without funding, science can’t “catch up” to help the patients who need it most.

Before we’ve lost what we can’t rebuild: Hope for prion disease
Feature

Before we’ve lost what we can’t rebuild: Hope for prion disease

July 15, 2025

Sonia Vallabh and Eric Minikel, a husband-and-wife team racing to cure prion disease, helped develop ION717, an antisense oligonucleotide treatment now in clinical trials. Their mission is personal — and just getting started.

Defeating deletions and duplications
News

Defeating deletions and duplications

July 11, 2025

Promising therapeutics for chromosome 15 rare neurodevelopmental disorders, including Angelman syndrome, Dup15q syndrome and Prader–Willi syndrome.

Using 'nature’s mistakes' as a window into Lafora disease
Feature

Using 'nature’s mistakes' as a window into Lafora disease

July 10, 2025

After years of heartbreak, Lafora disease families are fueling glycogen storage research breakthroughs, helping develop therapies that may treat not only Lafora but other related neurological disorders.

Cracking cancer’s code through functional connections
News

Cracking cancer’s code through functional connections

July 2, 2025

A machine learning–derived protein cofunction network is transforming how scientists understand and uncover relationships between proteins in cancer.

Gaze into the proteomics crystal ball
In-person Conference

Gaze into the proteomics crystal ball

July 1, 2025

The 15th International Symposium on Proteomics in the Life Sciences symposium will be held August 17–21 in Cambridge, Massachusetts.