An insider's perspective: Bacteroides as a window into the microbiome

Abstract

Over the last decade, our appreciation for the contribution of resident gut microorganisms—the gut microbiota—to human health has surged. However, progress is limited by the sheer diversity and complexity of these microbial communities. Compounding the challenge, the majority of our commensal microorganisms are not close relatives of Escherichia coli or other model organisms and have eluded culturing and manipulation in the laboratory. In this Review, we discuss how over a century of study of the readily cultured, genetically tractable human gut Bacteroides has revealed important insights into the biochemistry, genomics and ecology that make a gut bacterium a gut bacterium. While genome and metagenome sequences are being produced at breakneck speed, the Bacteroides provide a significant ‘jump-start’ on uncovering the guiding principles that govern microbiota–host and inter-bacterial associations in the gut that will probably extend to many other members of this ecosystem.

Major shifts in gut microbiota during development and its relationship to growth in ostriches

“…One bacterial group that appears to be particularly important at this initial stage is Bacteroides , which was strongly positively associated with growth directly after hatching. Bacteroides are obligate gut bacteria that are known to actively modify their environment, making it more hospitable for themselves and other microorganisms (Wexler & Goodman, ), for example by reducing oxygen levels (Baughn & Malamy, ). In chickens, this taxon seems to be more abundant in the later stages of chick development (Lu et al, ; Oakley et al, ).…”

“…Data were filtered to only include taxa with a minimum abundance of 100 counts and where at least 10 individuals had nonzero counts. The p-values were corrected with the false discovery rate to q-values and taxa with q < 0.05 were and gplots (Warnes et al, 2018;Wickham, 2009).…”

The social network of microorganisms — how auxotrophies shape complex communities

“…Some members of the Bacteroidetes phylum are missing some or all of the genes that are necessary for the synthesis of B 12 (REF. 9 ). However, these organisms possess several B 12 -dependent enzymes that are essential for the metabolism of sugars, amino acids and fatty acids 23 , which suggests a distinct need for B 12 .…”

“…Until recently, interactions have been viewed as successional activities of various members, each providing the energy source for the next member. However, on the basis of recent studies, a new picture has emerged, which emphasizes interdependencies and convoluted networks of microorganisms that are not limited to the exchange of electron donors for growth 2 but include the exchange of amino acids 2–6 , vitamins 7–9 and other cofactors 10,11 (FIG. 1).…”

Acquired interbacterial defense systems protect against interspecies antagonism in the human gut microbiome

“…Some of these are basal and protect against a wide range of threats, whereas others, for instance CRISPR-Cas, represent adaptations unique to the specific threats encountered by a bacterial lineage (1)(2)(3). The density of bacteria in the mammalian gut microbiome can exceed 10 11 gm -1 ; therefore, overcoming contact-dependent interbacterial antagonism is likely a major hurdle to survival in this ecosystem (4,5). The type VI secretion system (T6SS) is a pathway predicted to be widely utilized by gut bacteria to mediate the delivery of toxic effector proteins to neighboring cells (6)(7)(8)(9).…”