GUT HEAL ▶▶▶TH


Core metagenomic functions of the poultry microbiome


Let’s face it. As it is often presented, the microbiome seems terribly confusing. This is not news to anyone who has scrutinized a microbial profile like the 16s sequencing reports now common in the literature and the industry. However, looking at the all-important metagenome makes it decidedly simpler.


BY DR J.M. GEREMIA, MIDORI ANIMAL HEALTH AND DR MARIA WALSH, DSM M Figure 1:


Functional metagenomics can be used to study how the microbiome converts


undigested feed to thousands of active meta-


bolites that are either absorbed to affect host biology or


excreted to affect the


environment. 24 ▶ POULTRY WORLD | No. 7, 2020


icrobial profiles characterise taxonomic compo- sition. That is, they tell us the types and amounts of the various micro-organisms pres- ent in the gut. And they make one thing excep-


tionally clear: gut composition varies wildly from bird to bird, even when healthy and grown under identical conditions. This is not surprising. As a bird develops from hatch, the mi- cro-organisms that take hold in its gut are subject to a natural degree of randomness. It begs the question: How can some- thing as variable as microbial composition serve an industry where consistency is everything? Spoiler alert: the key to unlocking robustness and consistency in the microbiome is not microbial profiling. We must look


deeper, to the metagenome (the collection of all genes from across the microbiota). Your first reaction might be that this sounds even more complicated than microbial profiles. No, it is decidedly simpler and exceptionally powerful. Put simply, analysis of the metagenome can be used to understand the functions the microbiome can perform when it works in con- cert, as a unit. An analogy helps: if you think of the microbi- ome like an orchestra, the microbiota are the musicians, while the metagenome is the music they play.


More than a collection of bugs Following this logic, we recently discussed the merits of re- thinking the gut microbiome as an unit rather than a collec- tion of bugs. Figure 1 illustrates this thinking. Rather than fo- cus on organism identities, we consider the biochemical metabolites that run through them. The circles in Figure 1 rep- resent these metabolites while the lines denote the chemical reactions (microbial genes) that perform them. Via its path- ways, the gut microbiome converts undigested feed into thousands of metabolites. Many are nutritional to the host; others are excreted in the litter, runoff or are released into the atmosphere. Some gut metabolites are potent biomolecules that modulate systemic host functions, like inflammation, im- munity, muscle growth, colour, flavour and potentially even behavioural factors, like stress, activity level and appetite.


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