Microbes inside—from diversity to function: the case of <i>Akkermansia</i>

Belzer, Clara; Vos, Willem M. de

doi:10.1038/ismej.2012.6

Cited by 565 publications

(464 citation statements)

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“…3 C and D). This result reinforces the concept that in vivo, A. muciniphila is primarily active as a mucin degrader (67) in contrast to B. acidifaciens, which is more versatile in its nutrient utilization strategy. The flexible foraging activity of B. acidifaciens raises the possibility that the presence of alternative nutrients could modify its activity in degrading host-derived compounds in the gut.…”

Section: Determining Compound Utilization Patterns Of Members Of the Gutsupporting

confidence: 87%

Tracking heavy water (D ₂ O) incorporation for identifying and sorting active microbial cells

Berry

Mader

Lee

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

372

512

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Microbial communities are essential to the function of virtually all ecosystems and eukaryotes, including humans. However, it is still a major challenge to identify microbial cells active under natural conditions in complex systems. In this study, we developed a new method to identify and sort active microbes on the single-cell level in complex samples using stable isotope probing with heavy water (D 2 O) combined with Raman microspectroscopy. Incorporation of D 2 O-derived D into the biomass of autotrophic and heterotrophic bacteria and archaea could be unambiguously detected via C-D signature peaks in single-cell Raman spectra, and the obtained labeling pattern was confirmed by nanoscaleresolution secondary ion MS. In fast-growing Escherichia coli cells, label detection was already possible after 20 min. For functional analyses of microbial communities, the detection of D incorporation from D 2 O in individual microbial cells via Raman microspectroscopy can be directly combined with FISH for the identification of active microbes. Applying this approach to mouse cecal microbiota revealed that the host-compound foragers Akkermansia muciniphila and Bacteroides acidifaciens exhibited distinctive response patterns to amendments of mucin and sugars. By Ramanbased cell sorting of active (deuterated) cells with optical tweezers and subsequent multiple displacement amplification and DNA sequencing, novel cecal microbes stimulated by mucin and/ or glucosamine were identified, demonstrating the potential of the nondestructive D 2 O-Raman approach for targeted sorting of microbial cells with defined functional properties for singlecell genomics.ecophysiology | single-cell microbiology | carbohydrate utilization | nitrifier | Raman microspectroscopy M icroorganisms play a vital role in many environments. They mediate global biogeochemical cycles, catalyze biotechnological processes, and contribute to health and disease in the human body. The in situ study of microbial activity in natural and engineered ecosystems is therefore of great interest. For this purpose, several elegant methods have been established that use either transcriptional or translational activity of community members (i.e., metatranscriptomics, metaproteomics) (1-3) or the incorporation of isotopically labeled substrates into biomolecules (4-10) to infer the ecophysiology of microbes in such systems. However, these bulk techniques do not offer sufficient spatial resolution to study microbial activities at the micrometer scale. Therefore, important information can be overlooked because microbial communities are frequently spatially structured (e.g., biofilms) (11) and contain populations with life cycles (12,13). Furthermore, even apparently identical cells in clonal populations can have strongly divergent activities (14).Consequently, microbial ecophysiology is ideally studied also at the level of the single cell, but only a restricted number of approaches exist for determining physiological properties of individual cells in a microbial community. For exa...

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Section: Determining Compound Utilization Patterns Of Members Of the Gutsupporting

confidence: 87%

Tracking heavy water (D ₂ O) incorporation for identifying and sorting active microbial cells

Berry

Mader

Lee

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

372

512

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“…Ideally, human colonic mucins would be coated on the carrier materials using an agarindependent method. Next, Akkermansia muciniphila, the only known Verrucomicrobia representative that is a marker for mucin degradation (Belzer and de Vos, 2012), did not attain high densities in the current setup. Recent studies demonstrated that Akkermansia degrades mucins in (distal) colon regions characterized by depleted nutrient levels and long residence times (Van den Abbeele et al, 2010Abbeele et al, , 2011a.…”

Section: Discussionmentioning

confidence: 67%

“…Furthermore, as opposed to the luminal content where the pH was maintained constant, local accumulation of acids in mucus may cause a lower pH, selecting for Firmicutes over Bacteroidetes and Proteobacteria (Duncan et al, 2009). In addition, mucins may also serve as a growth substrate for butyrate-producing Firmicutes, possibly via cross-feeding with mucin-degrading microbes that deliver partial breakdown products, acetate and/or lactate (Belzer and de Vos 2012), similar as reported for fructo-oligosaccharides (Belenguer et al, 2006;Falony et al, 2006). Independent of the underlying reason, the mucus colonization by specific butyrate-producing Firmicutes (especially Clostridium cluster XIVa) species provides novel insight in the ecology of these abundant human gut colonizers.…”

Section: Discussionmentioning

confidence: 99%

“…Furthermore, the importance of the intestinal mcrobiota follows from the number of diseases that have been correlated with a dysbiosed microbial composition, such as inflammatory bowel diseases (IBDs; Willing et al, 2009;Walker et al, 2011) or obesity (Turnbaugh et al, 2006). A novel focus in gut microbiology is to not only study microbes in the intestinal content but also those that colonize the mucus layer (Swidsinski et al, 2008;Van den Abbeele et al, 2011c;Belzer and de Vos, 2012). The rationale is that mucosal microbes can interact more closely with the epithelium than their luminal counterparts, which may be crucial for achieving immunomodulatory effects.…”

Section: Introductionmentioning

confidence: 99%

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Butyrate-producing Clostridium cluster XIVa species specifically colonize mucins in an in vitro gut model

et al. 2012

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The human gut is colonized by a complex microbiota with multiple benefits. Although the surfaceattached, mucosal microbiota has a unique composition and potential to influence human health, it remains difficult to study in vivo. Therefore, we performed an in-depth microbial characterization (human intestinal tract chip (HITChip)) of a recently developed dynamic in vitro gut model, which simulates both luminal and mucosal gut microbes (mucosal-simulator of human intestinal microbial ecosystem (M-SHIME)). Inter-individual differences among human subjects were confirmed and microbial patterns unique for each individual were preserved in vitro. Furthermore, in correspondence with in vivo studies, Bacteroidetes and Proteobacteria were enriched in the luminal content while Firmicutes rather colonized the mucin layer, with Clostridium cluster XIVa accounting for almost 60% of the mucin-adhered microbiota. Of the many acetate and/or lactate-converting butyrate producers within this cluster, Roseburia intestinalis and Eubacterium rectale most specifically colonized mucins. These 16S rRNA gene-based results were confirmed at a functional level as butyryl-CoA:acetate-CoA transferase gene sequences belonged to different species in the luminal as opposed to the mucin-adhered microbiota, with Roseburia species governing the mucosal butyrate production. Correspondingly, the simulated mucosal environment induced a shift from acetate towards butyrate. As not only inter-individual differences were preserved but also because compared with conventional models, washout of relevant mucin-adhered microbes was avoided, simulating the mucosal gut microbiota represents a breakthrough in modeling and mechanistically studying the human intestinal microbiome in health and disease. Finally, as mucosal butyrate producers produce butyrate close to the epithelium, they may enhance butyrate bioavailability, which could be useful in treating diseases, such as inflammatory bowel disease.

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“…A. muciniphila may represent 3-5% of the microbial community (18,19) in healthy subjects, and its abundance inversely correlates with body weight (20)(21)(22)(23) and type 1 diabetes (24) in mice and humans, although a recent metagenomic study found that some of the genes belonging to A. muciniphila were enriched in type 2 diabetic subjects (25).…”

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confidence: 99%

Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity

Everard

Belzer

Geurts

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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Obesity and type 2 diabetes are characterized by altered gut microbiota, inflammation, and gut barrier disruption. Microbial composition and the mechanisms of interaction with the host that affect gut barrier function during obesity and type 2 diabetes have not been elucidated. We recently isolated Akkermansia muciniphila, which is a mucin-degrading bacterium that resides in the mucus layer. The presence of this bacterium inversely correlates with body weight in rodents and humans. However, the precise physiological roles played by this bacterium during obesity and metabolic disorders are unknown. This study demonstrated that the abundance of A. muciniphila decreased in obese and type 2 diabetic mice. We also observed that prebiotic feeding normalized A. muciniphila abundance, which correlated with an improved metabolic profile. In addition, we demonstrated that A. muciniphila treatment reversed high-fat diet-induced metabolic disorders, including fat-mass gain, metabolic endotoxemia, adipose tissue inflammation, and insulin resistance. A. muciniphila administration increased the intestinal levels of endocannabinoids that control inflammation, the gut barrier, and gut peptide secretion. Finally, we demonstrated that all these effects required viable A. muciniphila because treatment with heat-killed cells did not improve the metabolic profile or the mucus layer thickness. In summary, this study provides substantial insight into the intricate mechanisms of bacterial (i.e., A. muciniphila) regulation of the cross-talk between the host and gut microbiota. These results also provide a rationale for the development of a treatment that uses this human mucus colonizer for the prevention or treatment of obesity and its associated metabolic disorders.RegIIIγ | LPS | gut permeability | Lactobacillus plantarum | antimicrobial peptides G ut microbiota were once characterized as bystanders in the intestinal tract, but their active role in intestinal physiology is now widely investigated. In particular, the mutualism that exists between gut microbiota and the host has received much attention. Obesity and type 2 diabetes are characterized by altered gut microbiota (1), inflammation (2), and gut barrier disruption (3-5). We recently demonstrated an association of obesity and type 2 diabetes with increased gut permeability, which induced metabolic endotoxemia and metabolic inflammation (3-5). Unequivocal evidence demonstrates that gut microbiota influence whole-body metabolism (1, 6) by affecting the energy balance (6), gut permeability (4, 5), serum lipopolysaccharides [i.e., metabolic endotoxemia (7)], and metabolic inflammation (3-5, 7) that are associated with obesity and associated disorders. However, the microbial composition and the exact mechanisms of interaction between these two partners that affect host-gut barrier function and metabolism remain unclear.The intestinal epithelium is the interface for the interaction between gut microbiota and host tissues (8). This barrier is enhanced by the presence of a mucus layer an...

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Microbes inside—from diversity to function: the case of Akkermansia

Cited by 565 publications

References 64 publications

Tracking heavy water (D ₂ O) incorporation for identifying and sorting active microbial cells

Tracking heavy water (D ₂ O) incorporation for identifying and sorting active microbial cells

Butyrate-producing Clostridium cluster XIVa species specifically colonize mucins in an in vitro gut model

Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity

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Microbes inside—from diversity to function: the case of Akkermansia

Cited by 565 publications

References 64 publications

Tracking heavy water (D 2 O) incorporation for identifying and sorting active microbial cells

Tracking heavy water (D 2 O) incorporation for identifying and sorting active microbial cells

Butyrate-producing Clostridium cluster XIVa species specifically colonize mucins in an in vitro gut model

Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity

Contact Info

Product

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About

Tracking heavy water (D ₂ O) incorporation for identifying and sorting active microbial cells

Tracking heavy water (D ₂ O) incorporation for identifying and sorting active microbial cells