Low-abundant bacteria drive compositional changes in the gut microbiota after dietary alteration

Abstract

BackgroundAs the importance of beneficial bacteria is better recognized, understanding the dynamics of symbioses becomes increasingly crucial. In many gut symbioses, it is essential to understand whether changes in host diet play a role in the persistence of the bacterial gut community. In this study, termites were fed six dietary sources and the microbial community was monitored over a 49-day period using 16S rRNA gene sequencing. A deep backpropagation artificial neural network (ANN) was used to learn how the six different lignocellulose food sources affected the temporal composition of the hindgut microbiota of the termite as well as taxon-taxon and taxon-substrate interactions.ResultsShifts in the termite gut microbiota after diet change in each colony were observed using 16S rRNA gene sequencing and beta diversity analyses. The artificial neural network accurately predicted the relative abundances of taxa at random points in the temporal study and showed that low-abundant taxa maintain community driving correlations in the hindgut.ConclusionsThis combinatorial approach utilizing 16S rRNA gene sequencing and deep learning revealed that low-abundant bacteria that often do not belong to the core community are drivers of the termite hindgut bacterial community composition.Electronic supplementary materialThe online version of this article (10.1186/s40168-018-0469-5) contains supplementary material, which is available to authorized users.

Macrobdella decora: Old World Leech Gut Microbial Community Structure Conserved in a New World Leech

“…It is possible that this is due to a small sample size as we compared 13 unfed M. decora from MA and seven from CT and previous studies of synthetic and natural microbial communities found that insufficient sampling could yield an artificial difference between geographically separated communities (60, 61). As has been noted previously in the termite gut (58), the difference in community composition is based on minor members of the community and is reminiscent of a similar pattern observed in community differences between suppliers of H. verbana (data not shown). We therefore hypothesize that the conserved members of the community have been evolutionarily maintained in hirudinid leeches despite species-diversification and continent-dividing events.…”

“…In addition to confirming a similar core and common microbiome between the two leech hosts, our study also identified a rich rare microbiome. Previous research in a variety of environments has concluded that although a relatively small number of OTUs may dominate samples, low-abundance populations may be responsible for driving changes in observed phylogenetic diversity (57, 58). Rare species may have a significant role in metabolic cycles and may be a hidden driver of ecosystem functioning (59).…”

“…Extracted DNA samples were analyzed by amplifying the V4 hypervariable region of the 16S ribosomal RNA (rRNA) gene using primers designed in (73). PCR reactions were prepared as in (58) and sequenced using an Ilumina MiSeq (Illumina San Diego, CA U.S.A.) with custom sequencing primers added to the reagent cartridge (73) and sequenced 2 × 250bp. The sequence data was deposited in the NCBI SRA under project ID PRJNA544194.…”

Ecological specificity of the metagenome in a set of lower termite species supports contribution of the microbiome to adaptation of the host

“…We compared their functional repertoire to that of three wood-dwelling species Prorhinotermes simplex, Cryptotermes secundus, and Cryptotermes domesticus. Because there can be substantial variation in microbial communities between colonies [52][53][54][55], we analyzed five C. domesticus, eight C. secundus, seven P. simplex, five R. flavipes, and four R. grassei replicate colonies. We focused on the persistent, long-term differences between microbiomes by controlling shortterm effects caused by the influx of transient microbes.…”

“…Similarly, differences in local food supply can lead to transient, short-term effects on the termite microbiome [55]. Consequently, such short-term differences reflect environmental differences at termite collection sites, rather than potentially adaptive, evolved differences between host-species-specific microbiomes.…”