Gene Sets for Utilization of Primary and Secondary Nutrition Supplies in the Iberian Lynx

Recent studies have indicated the existence of an extensive trans-genomic trans-mural co-metabolism between gut microbes and animal hosts that is diet-, host phylogeny- and provenance-influenced. Here, we analyzed the biodiversity at the level of small subunit rRNA gene sequence and the metabolic composition of 18 Mbp of consensus metagenome sequences and activity characteristics of bacterial intra-cellular extracts, in wild Iberian lynx (Lynx pardinus) fecal samples.

journal.pone.0051521.g001

Overview of the relative abundance of phylogenetic prokaryotic groups recovered from the lynx distal gut based on SSU rRNA tag sequences extracted from the pyrosequences.

Bacterial signatures (14.43% of all of the Firmicutes reads and 6.36% of total reads) related to the uncultured anaerobic commensals Anaeroplasma spp., which are typically found in ovine and bovine rumen, were first identified. The lynx gut was further characterized by an over-representation of ‘presumptive’ aquaporin aqpZ genes and genes encoding ‘active’ lysosomal-like digestive enzymes that are possibly needed to acquire glycerol, sugars and amino acids from glycoproteins, glyco(amino)lipids, glyco(amino)glycans and nucleoside diphosphate sugars. Lynx gut was highly enriched (28% of the total glycosidases) in genes encoding α-amylase and related enzymes, although it exhibited low rate of enzymatic activity indicative of starch degradation. The preponderance of β-xylosidase activity in protein extracts further suggests lynx gut microbes being most active for the metabolism of β-xylose containing plant N-glycans, although β-xylosidases sequences constituted only 1.5% of total glycosidases.

These collective and unique bacterial, genetic and enzymatic activity signatures suggest that the wild lynx gut microbiota not only harbors gene sets underpinning sugar uptake from primary animal tissues (with the monotypic dietary profile of the wild lynx consisting of 80–100% wild rabbits) but also for the hydrolysis of prey-derived plant biomass. Although, the present investigation corresponds to a single sample and some of the statements should be considered qualitative, the data most likely suggests a tighter, more coordinated and complex evolutionary and nutritional ecology scenario of carnivore gut microbial communities than has been previously assumed.

The Iberian lynx (Lynx pardinus) is native to the Iberian Peninsula and is considered the most endangered felid species in the world. Iberian lynxes are confined to two isolated populations in southern Spain in the Doñana-Aljarafe and Sierra Morena areas, and only 88 and 224 individuals, respectively, are estimated to remain. To save this species from extinction, an EU LIFE Nature project is underway that includes habitat preservation, lynx population monitoring, and rabbit population management. Additionally, cryopreservation of lynx genetic material and a captive ex situ breeding project were initiated to preserve the genetic diversity of the species and to produce new specimens for future reintroduction.

At present, this species is critically endangered due to the decline of its basic prey (the wild European rabbit, Oryctolagus cuniculus), an increase in non-natural mortality, the fragmentation and loss of its habitat and the effects of infectious disease. The identification of heavy metals in the tissues of some lynxes also suggests that anthropogenic activities (such as mining) that do contaminate their water reservoirs in Southern Spain (Doñana and Sierra Morena), may impact lynx health and survival. Comparative analysis of the gestagens and the estrogen levels in four lynx species has indicated the possible role of qualitative and quantitative variations in gut bacteria composition as determinants of specific life stages. This idea is consistent with the fact that gut harbors a vast ensemble of microbes that perform vital processes for host physiology and nutrition.

Reference: Alcaide M, Messina E, Richter M, Bargiela R, Peplies J, et al. (2012) Gene Sets for Utilization of Primary and Secondary Nutrition Supplies in the Distal Gut of Endangered Iberian Lynx. PLoS ONE 7(12): e51521. doi:10.1371/journal.pone.0051521

Source: PLOS ONE, 23/december/2012


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