Abstract. The intestinal epithelium is protected from direct contact with gut microbes by a mucus layer. This mucus layer consists of secreted mucin glycop

The human gut outer mucus layer hosts specific microbes. Using a synthetic mucin glycan-degrading microbial community to mimic this mucosal microbiome, we show that mucin type affects microbial commu...

Abstract. Elucidating interaction mechanisms and substrate specialization is central to understanding bacterial adaptation across ecological niches. Specia

The human gut outer mucus layer hosts specific microbes. Using a synthetic mucin glycan-degrading microbial community to mimic this mucosal microbiome, we show that mucin type affects microbial commu...

Nature Microbiology, Published online: 24 April 2026; doi:10.1038/s41564-026-02318-2Cayman enables computational analysis of carbohydrate-active enzymes (CAZymes) in microbial community data. It revealed novel mucus-foraging gut microorganisms and differences in gut microbial CAZyme repertoires associated with lifestyle and disease.

Equal contribution designations (co-first and co-last authorship) is on the rise, yet this information is routinely lost, creating inequity in recognition and crediting. This Perspective calls for…

Abstract. In addition to the specific causes of infertility, two components of the vaginal ecosystem, the vaginal microbiota and the cervicovaginal mucus (

In this phase 1 randomized trial of women with bacterial vaginosis in South Africa and the United States, Potloane et al. show that a multi-strain vaginal Lactobacillus crispatus live biotherapeutic administered for just 3–7 days following antibiotics can achieve vaginal colonization lasting up to 12 weeks.

Clostridium perfringens lacking perfringolysin O toxin isolated from preterm infants metabolizes human milk oligosaccharide disialyllacto-N-tetraose to produce metabolites that promote the growth of c...

Aging is frequently accompanied by inflammaging—a chronic, low-grade inflammatory state that contributes to functional decline and disease risk. Disruption of the intestinal barrier is increasingly...

A metagenomic survey of babies attending the first year of nursery detected extensive baby-to-baby microbial strain transmission, pointing to social interactions in infancy as crucial drivers of infan...

Abstract. Intestinal mucin glycan-degrading bacteria are important for mucus turnover, stimulating mucus production, and producing beneficial metabolites.

In this Perspective, Garza et al. revisit the keystone concept and discuss its relevance for microbial keystone taxa and functions. For this, they explore the different mechanisms behind keystoneness,...

Sda antigens [GalNAcβ1-4(Neu5Acα2-3)Galβ1-O-R] are present at the non-reducing termini of O-glycans of colonic mucins of human. Previously, we reported characterization of two glycoside hydrolase fami...

We uncover hundreds of inhibitory interactions between industrial and agricultural chemicals and gut bacteria. Systematic genetic analyses reveal bacterial survival mechanisms against pollutants and t...

Zagieboylo and colleagues demonstrate that the human commensal Bacteroides thetaiotaomicron secretes two self-targeting proteins that induce heterogeneity within its own population. Differential expre...

Akkermansia muciniphila is a specialist mucin glycan-degrader that is common in the human gut. A. muciniphila is associated with host health and therefore proposed as a next-generation probiotic. Howe...

Akkermansia muciniphila is a specialist mucin glycan-degrader that is common in the human gut. A. muciniphila is associated with host health and therefore proposed as a next-generation probiotic. Howe...

A long-read metagenomics method empowers faecal microbiota transplantation studies by precisely tracking bacteria from donors to recipients, distinguishing co-existing strains and revealing genomic ch...

Abstract. Akkermansia muciniphila, a mucin-degrading gut bacterium, contributes to intestinal homeostasis and metabolic disorders, yet its transcriptional

Akkermansia muciniphila, an obligate mucin degrader, is a major member of the human colonic microbiota and has been associated positive health outcomes. Mucins are complex glycoproteins that contain h...

Fibre-degrading gut anaerobes including important butyrate producers, lactate producers and utilizers, have been proposed here as next-generation probiotic

Bifidobacterium are beneficial members of the microbiota across animal hosts. Kujawska et al. demonstrate that bifidobacteria have likely co-evolved more closely with mammals, particularly primates, a...

The gastrointestinal (GI) tract is colonized by trillions of microorganisms living in a symbiotic relationship with the host. Commensal bacteria in the gut engage in cross-talks with epithelial and...

Bacteria and fungi can augment the flavour, composition and sustainability of foods, but more research is needed to push microbial foods — and consumer palates — to new heights.

The emergence of resistance to traditional antimicrobials increases the need to develop innovative approaches to understanding pathogen function. This study uses a computational data-driven approach t...

Abstract. The complexity of natural microbial communities poses significant challenges for predictive manipulation, driving the emergence of Synthetic Micr

To explore the interactions between a baby's gut microbes and mother's milk, a study applies a synthetic community of glycan degraders and cross-feeders.

To explore the interactions between different sugars and the gut microbes in an infant, a new study applies a synthetic community consisting of glycan degraders and cross-feeders.

The developing immune system must learn which microbes to tolerate and which to resist, but how this process unfolds is unclear. This study develops a mechanistic mathematical model of early-life gut ...

The colonic mucus layer is the primary interface between the host and the gut microbiota. It serves both as an ecological niche for bacteria and a bar…

This Perspective discusses the application of ecological principles of macro-ecosystems to microbiome engineering. The authors propose research priorities necessary to facilitate the application of th...

qPCR is used to measure soil microorganisms but can be affected by inhibitors, change in mastermix, and platform. This study measured precision and accurac

Precision microbiome programming for therapeutic applications is limited by challenges in achieving reproducible colonic colonization. Previously, we created an exclusive niche that we used to engraft...

Cancer therapies called checkpoint inhibitor drugs, which ratchet up the immune system, work better when this bacterium is around.

Dietary and gut glycans drive the composition of an in vitro synthetic community of infant gut microbes.

A comprehensive genomic analysis reveals species- and strain-level heterogeneity in carbohydrate utilization potential across bifidobacteria of human origin.

The degradation and utilization of mucin glycans depend on microbial composition and the interactions between the present bacteria.

In a unique cohort of twins followed from birth to 8 years of age, shotgun sequencing of stool samples reveals that the transmission, persistence and evolutionary adaptation of bacterial strains are s...