Berkhout Maryse D, Ioannou Athanasia, de Ram Carol, Boeren Sjef, Plugge Caroline M, Belzer Clara
Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, Wageningen 6708 WE, The Netherlands.
Laboratory of Food Chemistry, Wageningen University and Research, Bornse Weilanden 9, Wageningen 6708 WG, The Netherlands.
Glycobiology. 2024 Dec 10;34(12). doi: 10.1093/glycob/cwae085.
Specific human gut microbes inhabit the outer mucus layer of the gastrointestinal tract. Certain residents of this niche can degrade the large and complex mucin glycoproteins that constitute this layer and utilise the degradation products for their metabolism. In turn, this microbial mucin degradation drives specific microbiological ecological interactions in the human gut mucus layer. However, the exact nature of these interactions remains unknown. In this study, we designed and studied an in vitro mucin-degrading synthetic community that included mucin O-glycan degraders and cross-feeding microorganisms by monitoring community composition and dynamics through a combination of 16S rRNA gene amplicon sequencing and qPCR, mucin glycan degradation with PGC-LC-MS/MS, production of mucin-degrading enzymes and other proteins through metaproteomics, and metabolite production with HPLC. We demonstrated that specialist and generalist mucin O-glycan degraders stably co-exist and found evidence for cross-feeding relationships. Cross-feeding on the products of mucin degradation by other gut microbes resulted in butyrate production, hydrogenotrophic acetogenesis, sulfate reduction and methanogenesis. Metaproteomics analysis revealed that mucin glycan degraders Akkermansia muciniphila, Bacteroides spp. and Ruminococcus torques together contributed 92% of the total mucin O-glycan degrading enzyme pool of this community. Furthermore, comparative proteomics showed that in response to cultivation in a community compared to monoculture, mucin glycan degraders increased carbohydrate-active enzymes whereas we also found indications for niche differentiation. These results confirm the complexity of mucin-driven microbiological ecological interactions and the intricate role of carbohydrate-active enzymes in the human gut mucus layer.
特定的人类肠道微生物栖息于胃肠道的外黏液层。该生态位的某些常驻微生物能够降解构成此层的大型复杂黏蛋白糖蛋白，并利用降解产物进行新陈代谢。反过来，这种微生物对黏蛋白的降解推动了人类肠道黏液层中特定的微生物生态相互作用。然而，这些相互作用的确切性质仍然未知。在本研究中，我们设计并研究了一个体外黏蛋白降解合成群落，该群落包括黏蛋白O-聚糖降解菌和交叉饲喂微生物，通过16S rRNA基因扩增子测序和qPCR相结合的方法监测群落组成和动态变化，利用PGC-LC-MS/MS分析黏蛋白聚糖降解情况，通过宏蛋白质组学分析黏蛋白降解酶和其他蛋白质的产生情况，并用HPLC分析代谢产物的产生情况。我们证明了专性和兼性黏蛋白O-聚糖降解菌能够稳定共存，并发现了交叉饲喂关系的证据。其他肠道微生物对黏蛋白降解产物的交叉饲喂导致了丁酸盐的产生、氢营养型乙酸生成、硫酸盐还原和甲烷生成。宏蛋白质组学分析表明，黏蛋白聚糖降解菌嗜黏蛋白阿克曼氏菌、拟杆菌属和扭链瘤胃球菌共同贡献了该群落总黏蛋白O-聚糖降解酶库的92%。此外，比较蛋白质组学表明，与单培养相比，在群落中培养时，黏蛋白聚糖降解菌增加了碳水化合物活性酶，同时我们也发现了生态位分化的迹象。这些结果证实了黏蛋白驱动的微生物生态相互作用的复杂性以及碳水化合物活性酶在人类肠道黏液层中的复杂作用。
