Chapter outline: Animal Gut Microbiomes

f. Animal Gut Microbiomes

Section 2.        Human gut – to include cross-reference to models (rodents and pigs) and in vitro models.

Hauke Smidt, Paul O’Toole, and J Marchesi

Overview of the of the explosion in the area and the large increase in interest and what is currently known in each niche

Current status and census on the

·        Oral cavity

·        Stomach

·        Small Intestine

·        Large intestine

Issues with diversity and host specificity – for prospective studies individuals will commonly become their own controls

Sampling the system – what’s current practise, issues with using fecal samples, mucosal vs fecal, animal data on diversity at different sites, endoscopy sampling and issues

Culturing vs non-culturing current methods

Culturing – approaches (Pure and defined mixed cultures, in vitro models) media and methods – all the “omic” tiers being used?

Obtaining nucleic acids DNA and RNA, protein?

Non-culturing methods – 16S (other biomarkers rpoB, cpn60?)

Profiling – ARISA, DGGE, LH-PCR, T-RFLP

NGS – 454 and Illumina – 16S inventories, Other NGS platforms Ion Torrent data

Sequence based metagenomics – reference to approaches and bioinformatics

Functional metagenomics

Metatranscriptomics, Metaproteomics, Metabolonomics

Models of the gut

An introduction covering ways to study the human gut at present, namely fecal samples, as well as small and large intestinal lumen and mucosa-samples taken from sudden death victims, samples collected via a catheter and samples from ileostomy patients. The disadvantage of these samples is that we cannot control and observe the microbiota activity in vivo in certain locations such as the jejunum.

In vitro models

Solutions can be the use of in vitro models, where a broad range of parameters can be measured during microbial fermentation. The best known in vitro models are TIM and SHIME, and most recent developments in the field, such as the M-SHIME, will be described, including differences in set-ups and possibilities/limitations with these models.

Animal models

In vitro models in general don’t allow studying interactions between the host and the microbiota. Animal models and in particular mammals provide an alternative way to study the in vivo responses to beneficial, commensal and pathogenic microorganisms in the GI tract. The main animals used to study the mammalian GI tract are rodents and pigs. Below we will discuss how they are used. However, to convert the knowledge gained from animal studies into the human situation, we need to consider the differences between animals and humans concerning their GI tract. Discuss the differences between animals and humans, including behavior of rodents and pigs: coprophagy.

Overview picture of the GI tract of humans, pigs and rodents

Conventional rodents

Rodents are often used to study the GI tract and relate this back to the human situation. These animals are relatively small, easy to keep and well known models to study medicines for humans.

Discuss some studies, like: obesity alters the gut microbiota from Ley, et al., 2005;….

Differences in microbiota composition. For example, in mice bifidobacteria are present, but in lower abundance than in humans. Discuss some other differences, besides the previously discussed physiological differences of the GI tract.

Germ-free animals

Preferred animals for germ-free and gnotobiotic studies are mice. These animals are used for two main reasons: to humanize them, to study one single bacterial species or a consortium of defined bacterial species. Discuss some well-known studies, like diet-induced obesity from Turnbaugh, et al., 2008;…

Humanized rodents

Rats and mice that are born germ-free can be humanized by feeding them a slurry of human feces (Mallett, et al., 1987). These are valuable models to study the human microbiota, but the difference in physiology can have an effect on the colonization of the human microbiota. 

Pigs

Pigs are an important livestock for humans for their meat production. Therefore these animals are studied intensively to optimise production. In recent years the majority of studies focused on the GI tract of pigs, since alternatives had to be found for feeding antibiotics. Besides pigs being important as a livestock, they are much more comparable in their physiology, anatomy and nutrition to humans. This makes these animals an important addition to the other animal models used to study the human GI tract. The following models will discussed in this section.

Germfree and gnotobiotic mini-pigs, including humanized mini-pigs for analysis of single bacterial species or consortium of defined bacterial species.

Piglet model for microbial colonization of infants and its further effect during the life span.

Other animals

Like: ruminants, drosophila and fish (zebrafish)