Microscale spatial analysis provides evidence for adhesive monopolization of dietary nutrients by specific intestinal bacteria

Abstract

Each species of intestinal bacteria requires a nutritional source to maintain its population in the intestine. Dietary factors are considered to be major nutrients; however, evidence directly explaining the in situ utilization of dietary factors is limited. Microscale bacterial distribution would provide clues to understand bacterial lifestyle and nutrient utilization. However, the detailed bacterial localization around dietary factors in the intestine remains uninvestigated. Therefore, we explored microscale habitats in the murine intestine by using histology and fluorescent in situ hybridization, focusing on dietary factors. This approach successfully revealed several types of bacterial colonization. In particular, bifidobacterial colonization and adhesion on granular starch was frequently and commonly observed in the jejunum and distal colon. To identify the bacterial composition of areas around starch granules and areas without starch, laser microdissection and next-generation sequencing-based 16S rRNA microbial profiling was performed. It was found that Bifidobacteriaceae were significantly enriched by 4.7 fold in peri-starch areas compared to ex-starch areas. This family solely consisted of Bifidobacterium pseudolongum. In contrast, there was no significant enrichment among the other major families. This murine intestinal B. pseudolongum had starch-degrading activity, confirmed by isolation from the mouse feces and in vitro analysis. Collectively, our results demonstrate the significance of starch granules as a major habitat and potential nutritional niche for murine intestinal B. pseudolongum. Moreover, our results suggest that colonizing bifidobacteria effectively utilize starch from the closest location and maintain the location. This may be a bacterial strategy to monopolize solid dietary nutrients. We believe that our analytical approach could possibly be applied to other nutritional factors, and can be a powerful tool to investigate in vivo relationships between bacteria and environmental factors in the intestine.

Spatial metagenomic characterization of microbial biogeography in the gut

“…The local spatial organization of the gut microbiome influences various properties including colonization 10 , 17 – 19 , metabolism 11 , host-microbe and inter-microbial interactions 20 and community stability 1 , 21 , 22 . However, current microbiome profiling approaches such as metagenomic sequencing require homogenization of input material which means that underlying spatial information is lost.…”

“…We next explored whether these observed spatial distributions reflect specific associations between individual taxa that may result from processes such as positive or negative interspecies interactions (e.g., cooperative metabolism 24 ; contact-dependent killing 20 ) or local habitat filtering 11 . Across abundant and prevalent OTUs (>2% abundance in >10% of clusters, n=24), we assessed whether their pairwise co-occurrences were detected more or less frequently than expected in comparison to a null model of independent, random assortment of OTUs (Methods, Fisher’s exact test, p < 0.05, FDR = 0.05).…”

“…We further investigated whether MaP-seq could identify individual taxa with unique or altered spatial patterns. While the cecum harbored the densest community and the highest degree of species mixing of the three sites ( Fig 3a – b ), we hypothesized that specific taxa may self-aggregate to a higher degree than others, for example by uniquely utilizing a specific metabolite 11 . Assessing the aggregation of abundant taxa revealed a Lachnospiraceae (OTU 7; putatively of the genus Dorea , 60% confidence by RDP) that clustered two-fold greater than the average clustering metric value of all taxa ( Supplementary Fig.…”

Spatial organization of a model 15-member human gut microbiota established in gnotobiotic mice

“…In the gut, microbes can adhere to the epithelium and mucins (19)(20)(21); these components of the ecosystem are arranged nonrandomly in ways that could lead to spatial structuring of adherent community members (22,23). Similarly, partially digested food particles in the lumen could serve as sites of attachment (24)(25)(26)(27)(28). Differential replication of a microbe based on its localization in the mucus layer or the lumen (29) could itself generate a spatially structured microbial consortium or could amplify differences established by differential adherence.…”

Bifidobacterium pseudolongum in the Ceca of Rats Fed Hi-Maize Starch Has Characteristics of a Keystone Species in Bifidobacterial Blooms

“…In other words, the glycogen debranching enzyme is possibly a misnomer in the case of B. pseudolongum. With respect to the rodent bowel, we propose that B. pseudolongum has the characteristics of a keystone species in the microbiota because it can adhere to starch granules in the digesta (26), and although in low abundance, it possesses the ability to degrade Hi-Maize starch to an extent that could generate, through maltose syntrophy, a bloom of B. animalis, a species which itself has poor ability to degrade the resistant starch. Care is needed in defining a species as a keystone of the community and requires the consideration of traits, context, diversity, trophism, and temporal factors (6).…”