Bifidobacteria represent one of the first colonizers of the mammalian gut, where such colonization is facilitated by their saccharolytic capabilities. Genomic analyses of bifidobacteria have revealed ...intriguing genetic strategies employed by these bacteria to access a variety of dietary and host-produced glycans. Bifidobacterial genome evolution therefore represents a fascinating example of how their chromosomes were molded to contain a large number of genes involved in carbohydrate metabolism. One of the reasons as to why bifidobacteria are such dominant and prevalent members of the (early) microbiota is that they may access glycans in the gut through mutualistic cross-feeding or resource-sharing activities, which is indicative of ‘social behavior’ among bifidobacterial strains.
Bifidobacteria represent key members of the gut microbiota in the early phases of life of animals that subject their offspring to parental care.
The first microbiota assemblage is believed to play pivotal roles in human health, both in infancy and at later stages of life.
Dietary and/or host-derived glycans represent a potent evolutionary force that has shaped the bifidobacterial pan-genome.
In silico and functional genomic analyses of bifidobacterial genomes revealed species-specific adaptation to a glycan-rich gut environment.
A key determinant of microbial dynamics in the gut microbiota results from nutrient competition and sharing.
Bifidobacteria play an important ecological role in shaping the gut microbiome.
Bifidobacteria exhibit social behavior through carbohydrate resource sharing in the gut.
Alterations in intestinal microbiota composition are associated with several chronic conditions, including obesity and inflammatory diseases. The microbiota of older people displays greater ...inter-individual variation than that of younger adults. Here we show that the faecal microbiota composition from 178 elderly subjects formed groups, correlating with residence location in the community, day-hospital, rehabilitation or in long-term residential care. However, clustering of subjects by diet separated them by the same residence location and microbiota groupings. The separation of microbiota composition significantly correlated with measures of frailty, co-morbidity, nutritional status, markers of inflammation and with metabolites in faecal water. The individual microbiota of people in long-stay care was significantly less diverse than that of community dwellers. Loss of community-associated microbiota correlated with increased frailty. Collectively, the data support a relationship between diet, microbiota and health status, and indicate a role for diet-driven microbiota alterations in varying rates of health decline upon ageing.
Summary
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.
The human gut represents a highly complex ecosystem, which is densely colonized by a myriad of microorganisms that influence the physiology, immune function and health status of the host. Among the ...many members of the human gut microbiota, there are microorganisms that have co-evolved with their host and that are believed to exert health-promoting or probiotic effects. Probiotic bacteria isolated from the gut and other environments are commercially exploited, and although there is a growing list of health benefits provided by the consumption of such probiotics, their precise mechanisms of action have essentially remained elusive. Genomics approaches have provided exciting new opportunities for the identification of probiotic effector molecules that elicit specific responses to influence the physiology and immune function of their human host. In this review, we describe the current understanding of the intriguing relationships that exist between the human gut and key members of the gut microbiota such as bifidobacteria and lactobacilli, discussed here as prototypical groups of probiotic microorganisms.
Abstract
Lactococcus lactis is used extensively worldwide for the production of a variety of fermented dairy products. The ability of L. lactis to successfully grow and acidify milk has long been ...known to be reliant on a number of plasmid-encoded traits. The recent availability of low-cost, high-quality genome sequencing, and the quest for novel, technologically desirable characteristics, such as novel flavour development and increased stress tolerance, has led to a steady increase in the number of available lactococcal plasmid sequences. We will review both well-known and very recent discoveries regarding plasmid-encoded traits of biotechnological significance. The acquired lactococcal plasmid sequence information has in recent years progressed our understanding of the origin of lactococcal dairy starter cultures. Salient points on the acquisition and evolution of lactococcal plasmids will be discussed in this review, as well as prospects of finding novel plasmid-encoded functions.
A review of recent findings, novel traits and insights to plasmid evolution emerging from the increasing availability of lactococcal plasmid sequences.
Although the health-promoting roles of bifidobacteria are widely accepted, the diversity of bifidobacteria among the human intestinal microbiota is still poorly understood. We performed a census of ...bifidobacterial populations from human intestinal mucosal and fecal samples by plating them on selective medium, coupled with molecular analysis of selected rRNA gene sequences (16S rRNA gene and internally transcribed spacer ITS 16S-23S spacer sequences) of isolated colonies. A total of 900 isolates were collected, of which 704 were shown to belong to bifidobacteria. Analyses showed that the culturable bifidobacterial population from intestinal and fecal samples include six main phylogenetic taxa, i.e., Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Bifidobacterium adolescentis, Bifidobacterium pseudolongum, Bifidobacterium breve, and Bifidobacterium bifidum, and two species mostly detected in fecal samples, i.e., Bifidobacterium dentium and Bifidobacterium animalis subp. lactis. Analysis of bifidobacterial distribution based on age of the subject revealed that certain identified bifidobacterial species were exclusively present in the adult human gut microbiota whereas others were found to be widely distributed. We encountered significant intersubject variability and composition differences between fecal and mucosa-adherent bifidobacterial communities. In contrast, a modest diversification of bifidobacterial populations was noticed between different intestinal regions within the same individual (intrasubject variability). Notably, a small number of bifidobacterial isolates were shown to display a wide ecological distribution, thus suggesting that they possess a broad colonization capacity.
Shotgun metagenomic sequencing is a valuable tool for the taxonomic and functional profiling of microbial communities. However, this approach is challenging in samples, such as milk, where a low ...microbial abundance, combined with high levels of host DNA, result in inefficient and uneconomical sequencing. Here we evaluate approaches to deplete host DNA or enrich microbial DNA prior to sequencing using three commercially available kits. We compared the percentage of microbial reads obtained from each kit after shotgun metagenomic sequencing. Using bovine and human milk samples, we determined that host depletion with the MolYsis complete5 kit significantly improved microbial sequencing depth compared to other approaches tested. Importantly, no biases were introduced. Additionally, the increased microbial sequencing depth allowed for further characterization of the microbiome through the generation of metagenome-assembled genomes (MAGs). Furthermore, with the use of a mock community, we compared three common classifiers and determined that Kraken2 was the optimal classifier for these samples. This evaluation shows that microbiome analysis can be performed on both bovine and human milk samples at a much greater resolution without the need for more expensive deep-sequencing approaches.
Random transposon mutagenesis allows for relatively rapid, genome-wide surveys to detect genes involved in functional traits, by performing screens of mutant libraries. This approach has been widely ...applied to identify genes responsible for activities of interest in multiple eukaryote and prokaryote organisms, although most studies on microorganisms have focused on pathogenic and clinically relevant bacteria. In this chapter we describe the implementation of an in vitro Tn5-based transposome strategy to generate a large collection of random mutants in the gut commensal Bifidobacterium breve UCC2003, and discuss considerations when applying this mutagenesis system to other Bifidobacterium species or strains of interest.
Summary
Fresh potable water is an indispensable drink which humans consume daily in substantial amounts. Nonetheless, very little is known about the composition of the microbial community inhabiting ...drinking water or its impact on our gut microbiota. In the current study, an exhaustive shotgun metagenomics analysis of the tap water microbiome highlighted the occurrence of a highly genetic biodiversity of the microbial communities residing in fresh water and the existence of a conserved core tap water microbiota largely represented by novel microbial species, representing microbial dark matter. Furthermore, genome reconstruction of this microbial dark matter from water samples unveiled homologous sequences present in the faecal microbiome of humans from various geographical locations. Accordingly, investigation of the faecal microbiota content of a subject that daily consumed tap water for 3 years provides proof for horizontal transmission and colonization of water bacteria in the human gut.
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Human milk oligosaccharides (HMO) are complex sugars which are found in breast milk at significant concentrations and with unique structural diversity. These sugars are the fourth ...most abundant component of human milk after water, lipids, and lactose and yet provide no direct nutritional value to the infant. Recent research has highlighted that HMOs have various functional roles to play in infant development. These sugars act as prebiotics by promoting growth of beneficial intestinal bacteria thereby generating short-chain fatty acids which are critical for gut health. HMOs also directly modulate host-epithelial immune responses and can selectively reduce binding of pathogenic bacteria and viruses to the gut epithelium preventing the emergence of a disease. This review covers current knowledge related to the functional biology of HMOs and their associated impact on infant gut health.
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