HadzaPrevotellaRequire Diet-derived Microbiota Accessible Carbohydrates to Persist in Mice

Abstract

Industrialization has transformed the gut microbiota, reducing the prevalence ofPrevotellarelative toBacteroides. Here, we isolateBacteroidesandPrevotellastrains from the microbiota of Hadza hunter-gatherers of Tanzania, a population with high levels ofPrevotella. We demonstrate that plant-derived microbiota-accessible carbohydrates (MACs) are required for persistence ofPrevotella copribut notBacteroides thetaiotaomicron in vivo. Differences in carbohydrate metabolism gene content, expression, and in vitro growth reveal that HadzaPrevotellastrains specialize in degrading plant carbohydrates, while HadzaBacteroidesisolates use both plant and host-derived carbohydrates, a difference mirrored inBacteroidesfrom non-Hadza populations. When competing directly,P. coprirequires plant-derived MACs to maintain colonization in the presence ofB. thetaiotaomicron, as a no MAC diet eliminatesP. copricolonization.Prevotella'sreliance on plant-derived MACs andBacteroides'ability to use host mucus carbohydrates could explain the reduced prevalence ofPrevotellain populations consuming a low-MAC, industrialized diet.

The transition from a non-westernized to westernized gut microbiome in Indian-Immigrants and Indo-Canadians is associated with dietary acculturation

“…9 The subsequent loss of P.copri in our Indo- Immigrant and Indo-Canadian cohorts aligned with their reduction of a high carbohydrate, high fiber diet, which was a trend previously explored among Hadza and Nepali groups. 45 Plant-derived microbiota-accessible carbohydrates (MACs) are required to maintain abundances of P. copri , whereas other species such as Bacteroides thetaiotaomicron can utilize both plant and animal- derived MACs, allowing for persistence in the gut. 45 This relationship therefore suggests that the Prevotella spp.…”

“…45 Plant-derived microbiota-accessible carbohydrates (MACs) are required to maintain abundances of P. copri , whereas other species such as Bacteroides thetaiotaomicron can utilize both plant and animal- derived MACs, allowing for persistence in the gut. 45 This relationship therefore suggests that the Prevotella spp. abundance in the Indian gut is highly linked to their specific dietary patterns.…”

Metagenomic Immunoglobulin Sequencing (MIG-Seq) Exposes Patterns of IgA Antibody Binding in the Healthy Human Gut Microbiome

“…More detailed instructions on gene annotation and parsing can be found here: https://instrain.readthedocs.io/en/latest/user_manual.html#gene-annotation. CAZyme substrate annotations were based on previously-used definitions 54 .…”

Segatella copri strains adopt distinct roles within a single individual's gut

“…Gellman et al . found that supplementing the mice with plant-derived microbiota-accessible carbohydrates enables colonization and maintenance of S. copri strains in mice 12 . In practice, this complicates experimental setups and may not be universally applicable for all research purposes.…”

“…It is an obligate anaerobe with understudied nutritional preferences, and, despite the tremendous amount of genetic diversity reported within this clade 1,3,9,10 , until recently, there has been only one strain available from public strain collections. Furthermore, this strain has been recalcitrant to genetic modification and to colonization in mice 11,12 . Overall, these constraints have led to large gaps in experimental evidence supporting these purported roles.…”