Eating for two: how metabolism establishes interspecies interactions in the gut

Abstract

In bacterial communities, "tight economic times" are the norm. Of the many challenges bacteria face in making a living, perhaps none are more important than generating energy, maintaining redox balance, and acquiring carbon and nitrogen to synthesize primary metabolites. The ability of bacteria to meet these challenges depends heavily on the rest of their community. Indeed, the most fundamental way in which bacteria communicate is by importing the substrates for metabolism and exporting metabolic end products. As an illustration of this principle, we will travel down a carbohydrate catabolic pathway common to many species of Bacteroides, highlighting the interspecies interactions established (often inevitably) at its key steps. We also discuss the metabolic considerations in maintaining the stability of host-associated microbial communities.

Figure 1. Simplified illustrative schematic of some trophic networks within the intestinal microbiota

Dietary or host-derived substrates may be metabolized by different microbial groups, which are divided in this schematic by major metabolic function (e.g., acetogen). The sequential action of glycolytic and fermentation pathways (shown within the green box representing a Bacteroides cell; ED= Entner–Doudoroff pathway, EMP= Embden-Meyerhof-Parnas pathway, and PP= pentose phosphate pathway) result in fermentation end-products that become the metabolic inputs for other syntrophic microbes, such as acetogens, sulfate-reducers and butyrate-producers, or the host.

Figure 2. A carbohydrate catabolic pathway from Bacteroides

This pathway serves as a template for our review. (A) Oligosaccharide foraging and hydrolysis to monosaccharides. (B) The Embden-Meyerhof-Parnas and Entner Doudoroff pathways convert process monosaccharides to PEP, generating ATP and NADH. (C) PEP carboxykinase fixes CO₂ by appending it to PEP, generating oxaloacetate in a reaction that generates one equivalent of ATP or GTP. (D) Fumarate serves as the terminal electron acceptor in a primitive Bacteroides electron transport chain, enabling anaerobic respiration. (E) Methylmalonyl-CoA mutase isomerizes succinate to methylmalonate, which is then decarboxylated to regenerate CO₂ and produce propionate as an end product. Double arrows represent multiple steps in a pathway.

Figure 3. Bacteroides’ primitive electron transport chain

A proposed model for the anaerobic electron transport chain common to many Bacteroides species is shown; this model is based on crystal structures of NADH dehydrogenase and fumarate reductase from other bacteria (Efremov et al., 2010; Lancaster et al., 1999). The chain would consist of two enzyme complexes: a proton-translocating NADH-quinone oxidoreductase (NADH dehydrogenase, left) and a quinol:fumarate reductase (fumarate reductase, right). The action of NADH dehydrogenase would shuttle electrons from the oxidation of NADH to NAD⁺ down a pathway involving a flavin cofactor and multiple iron-sulfur clusters, ultimately reducing a membrane-bound menaquinone. This menaquinone would carry the electrons to fumarate reductase, which would shuttle them down a pathway involving one or two heme cofactors, possibly a second quinone, multiple iron-sulfur clusters, and a flavin cofactor that would reduce the terminal electron acceptor fumarate to succinate. ‘BT-numerical’ labels are the locus tags for genes within the B. thetatiotaomicron (VPI-5482) genome.

Figure 4. A metabolic scorecard

The choice of a lower pathway for the metabolism of pyruvate by Clostridium pasteuranium is shown. Lactate, ethanol, acetate, butyrate, and butanol are the major metabolic end products; next to each one is a ‘scorecard’ showing, from left to right: equivalents of NADH reduced to NAD⁺; equivalents of ADP converted to ATP by substrate-level phosphorylation; equivalents of acid produced; and equivalents of H₂ produced (all figures are in units of per mole pyruvate). Double arrows represent multiple steps in a pathway; see text for details.

Figure 5. Amino acid acrobatics

(A) Bacteroides species can synthesize certain amino acids from short-chain fatty acids by a two step process: an initial reductive carboxylation to generate an alpha-ketoacid extended by one carbon, and its subsequent transamination to an amino acid. The amino group of the resulting amino acid derives originally from host NH₃ (possibly via urea), while the carboxylic acid comes from host CO₂. The bracketed NH₃ indicates that the proximal nitrogen donor for transamination is unknown. (B) The Stickland reaction, in which two amino acids are co-fermented, with one serving as electron donor and the other as electron acceptor. (C) Unusual fragmentations and rearrangements of amino acids, which allow certain Clostridium species to use amino acids as electron donors and acceptors.

Figure 6. Interspecies interactions in metabolic networks

(A) A toy model for carbon and nitrogen flows in the gut. Bacteroides’ ability to access protein-encapsulated plant carbohydrates via proteases may provide a source of amino acids for other genera such as Clostridium, which, in turn, provide a pool of free nitrogen (NH₄⁺) derived from amino acid deamination. The provision of short-chain fatty acids to the host is reciprocated by CO₂ excretion among other, to be defined metabolites. (B) Positive feedback loops in the gut (lumen in blue and mucus in light brown). Although the intestine is a dynamic environment, continually being perfused with new dietary components and microbial species, the relative temporal stability of microbiota composition suggests that communities may tend toward self-reinforcing configurations. These may be simple feedback loops in which a species’ metabolism creates a favorable local chemical milieu (e.g., optimal pH) for that species (c). Alternatively, multiple species may act syntrophically to reinforce advantageous metabolism of one another, and in some cases this may involve host responses. For example, the fermentation of host mucus to succinate by one species (represented in purple) may be accompanied by another microbe (represented in orange) converting succinate to butyrate, which in turn can be taken up by the host and lead to increased mucus production (b). Alternatively, a pathogen (green rods) may induce inflammation, which leads to host production of oxidative effectors that have the dual effect of killing mutualistic, pathogen-excluding anaerobes (represented as orange circles and purple rods) and providing terminal electron acceptors to the facultative pathogen. Both effects lead to additional pathogen expansion, pathogen invasion and more inflammation (a).