Genetic insights into the dark matter of the mammalian gut microbiota through targeted genome reconstruction

Abstract

Whole metagenomic shotgun (WMS) sequencing has dramatically enhanced our ability to study microbial genomics. The possibility to unveil the genetic makeup of bacteria that cannot be easily isolated has significantly expanded our microbiological horizon. Here, we report an approach aimed at uncovering novel bacterial species by the use of targeted WMS sequencing. Employing in silico data retrieved from metabolic modelling to formulate a chemically defined medium (CDM), we were able to isolate and subsequently sequence the genomes of six putative novel species of bacteria from the gut of non-human primates.

Imbalance of the intestinal virome and altered viral-bacterial interactions caused by a conditional deletion of the vitamin D receptor

“…27 The virome includes eukaryotic viruses, endogenous retroviruses, bacterial viruses (i.e., bacteriophages), and archaeal viruses and is one of the least understood components of the microbiota. 28,29 Fecal virome was involved in many diseases using samples from both human patients and mouse model, such as colitis and diabetes. [30][31][32][33][34] Dysbiosis of the microbiome not only leads to intestinal inflammatory and infectious diseases but also to diseases beyond the gastrointestinal tract.…”

Bifidobacteria: insights into the biology of a key microbial group of early life gut microbiota

“…Recently, with the advent of metagenomics approaches, insights have been obtained concerning the socalled "dark matter" of microbial populations residing in an environment and being represented by bacteria that are detected by sequencing but which appear to be recalcitrant to cultivation. The use of such novel approaches to disentangle bifidobacterial communities that reside in stool samples of all main representatives of mammalian species not only revealed that bifidobacterial presence is a common feature of the mammalian gut but also that a substantial part of the biodiversity of this bacterial genus is still far from being fully discovered [2] . In fact, the existence of many novel bifidobacterial phylotypes has been discovered, present in the gut of various mammals including the human gut, some of which occurring at very low abundance, although being shared by various mammalian species [2] .…”

“…The use of such novel approaches to disentangle bifidobacterial communities that reside in stool samples of all main representatives of mammalian species not only revealed that bifidobacterial presence is a common feature of the mammalian gut but also that a substantial part of the biodiversity of this bacterial genus is still far from being fully discovered [2] . In fact, the existence of many novel bifidobacterial phylotypes has been discovered, present in the gut of various mammals including the human gut, some of which occurring at very low abundance, although being shared by various mammalian species [2] . Notably, in this context, the application of shotgun metagenomics, followed by metabolic reconstruction involving those biological samples that were shown to encompass putative novel bifidobacterial species, allowed the delineation of detailed metabolic insights concerning the utilization of plant-derived complex carbon sources by these novel bifidobacterial phylotypes.…”

“…It has been described how the genomes of bifidobacterial taxa typically present during early life such as Bifidobacterium bifidum, Bifidobacterium breve, and Bifidobacterium longum subsp. infantis [2,4,11,30] are also enriched in GH-encoding genes involved in the metabolism of HMOs and mucins, both being host-associated glycans. Various genetic traits involved in HMO breakdown are typically identified in the genomes of members of these three bifidobacterial species, while they are generally absent from chromosomes of other bifidobacterial species, and they further support the notion of highly specialized genetic adaptations of these bifidobacterial species to the infant gut [27] .…”

“…number steadily increasing over the last five years thanks to the very considerable efforts made by various microbiologists through the assessment of bifidobacterial communities from a wide variety of animals and through the use of metagenomics-based approaches [2][3][4][5] . The phylogenetic analysis of this genus, as based on genomic data, has highlighted the occurrence of genetic variability that allows subdivision of members of the Bifidobacterium genus into seven main phylogenetic/phylogenomic clusters.…”