What is the role of cyclic di-GMP signaling within the human gut microbiome?

There is currently little understanding of the role of the bacterial second messenger cyclic di-GMP (c-di-GMP) in the human gut microbiome. C-di-GMP is synthesized by highly conserved diguanylate cyclase (DGC) enzymes and degraded by highly conserved phosphodiesterase (PDE) enzymes. To begin to assess the prevalence of c-di-GMP signaling in the gut microbiome, we found on average 1.0 DGC and 0.8 PDE enzymes per million base pairs of metagenomic DNA derived from stool samples. Specific species encoding substantial numbers of GGDEF and EAL domains were the commensal species

Genetically identical co-housed pigs as models for dietary studies of gut microbiomes

The impact of diet on the microbial composition in the gastrointestinal tract (GIT) has been well documented. However, quantifying the role of the diet in shaping microbial composition in humans has been difficult due to the influence of host genetics and the environment. To test the influence of diets on the GIT microbiome independently of host genotype and environment, two genetically identical co-housed pigs were used in an A-B-A-B design across four 14-day periods using two distinct diets that differed in dietary fiber source, soybean hulls or wheat bran. Shifts in fecal microbiomes were assessed with respect to dietary changes by 454-pyrosequencing analysis using the V3 region of the 16S rRNA genes. Similarity analysis revealed that the GIT microbiome distinctly clustered by diets rather than by individual. Diversity analysis showed that the diet fed had an influence on GIT microbiome diversity, which was host specific. While many bacterial taxa and KEGG orthologs reacted similarly to switches in diet, some bacterial taxa and KEGG orthologs reacted differentially in each of the pigs. While diet changed the GIT microbiome composition of isogenic co-housed pigs, inter-individual variations from epigenetics were not entirely eliminated by the use of cloned pigs.

Invertebrate systems for hypothesis-driven microbiome research

A number of novel, invertebrate systems have emerged as excellent models for the study of microbiomes. Due to their small size, evolutionary diversity, ease of culture, and – in many cases – relatively simple gut communities, invertebrates of many different orders can be tools to drive hypothesis-driven microbiome research. In this review we highlight several host systems amenable to microbiota analyses and specific questions that can be easily addressed in those systems. These questions address functional equivalence across similar habitats, host-specificity and coevolution of host-microbe interactions, and acquisition and transmission dynamics of host-associated communities. We propose that host systems be chosen based on the question of interest, and that insect systems are excellent tools for the vast behavioral, ecological, and genetic diversity that allows them to address a variety of these questions.

Co-evolution in context: The importance of studying gut microbiomes in wild animals

Because the gut microbiota contributes to host nutrition, health and behavior, and gut microbial community composition differs according to host phylogeny, co-evolution is believed to have been an important mechanism in the formation of the host-gut microbe relationship. However, current research is not ideal for examining this theme. Most studies of the gut microbiota are performed in controlled settings, but gut microbial community composition is strongly influenced by environmental factors. To truly explore the co-evolution of host and microbe, it is necessary to have data describing host-microbe dynamics in natural environments with variation in factors such as climate, food availability, disease prevalence, and host behavior. In this review, I use current knowledge of host-gut microbe dynamics to explore the potential interactions between host and microbe in natural habitats. These interactions include the influence of host habitat on gut microbial community composition as well as the impacts of the gut microbiota on host fitness in a given habitat. Based on what we currently know, the potential connections between host habitat, the gut microbiota, and host fitness are great. Studies of wild animals will be an essential next step to test these connections and to advance our understanding of host-gut microbe co-evolution.

Heterococcus sp. DN1 draft genome: focus on cold tolerance and lipid production

A yellow-green alga,