Habitat degradation impacts black howler monkey (Alouatta pigra) gastrointestinal microbiomes

1] Program in Ecology, Evolution and Conservation Biology, University of Illinois, Urbana, IL, USA [2] Department of Anthropology, University of Illinois, Urbana, IL, USA.
The ISME Journal (Impact Factor: 9.27). 03/2013; DOI: 10.1038/ismej.2013.16

ABSTRACT The gastrointestinal (GI) microbiome contributes significantly to host nutrition and health. However, relationships involving GI microbes, their hosts and host macrohabitats remain to be established. Here, we define clear patterns of variation in the GI microbiomes of six groups of Mexican black howler monkeys (Alouatta pigra) occupying a gradation of habitats including a continuous evergreen rainforest, an evergreen rainforest fragment, a continuous semi-deciduous forest and captivity. High throughput microbial 16S ribosomal RNA gene sequencing indicated that diversity, richness and composition of howler GI microbiomes varied with host habitat in relation to diet. Howlers occupying suboptimal habitats consumed less diverse diets and correspondingly had less diverse gut microbiomes. Quantitative real-time PCR also revealed a reduction in the number of genes related to butyrate production and hydrogen metabolism in the microbiomes of howlers occupying suboptimal habitats, which may impact host health.

1 Follower
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Recent gut microbiome studies in model organisms emphasize the effects of intrinsic and extrinsic factors on the variation of the bacterial composition and its impact on the overall health status of the host. Species occurring in the same habitat might share a similar microbiome, especially if they overlap in ecological and behavioral traits. So far, the natural variation in microbiomes of free-ranging wildlife species has not been thoroughly investigated. The few existing studies exploring microbiomes through 16S rRNA gene reads clustered sequencing reads into operational taxonomic units (OTUs) based on a similarity threshold (e.g., 97%). This approach, in combination with the low resolution of target databases, generally limits the level of taxonomic assignments to the genus level. However, distinguishing natural variation of microbiomes in healthy individuals from "abnormal" microbial compositions that affect host health requires knowledge of the "normal" microbial flora at a high taxonomic resolution. This gap can now be addressed using the recently published oligotyping approach, which can resolve closely related organisms into distinct oligotypes by utilizing subtle nucleotide variation. Here, we used Illumina MiSeq to sequence amplicons generated from the V4 region of the 16S rRNA gene to investigate the gut microbiome of two free-ranging sympatric Namibian carnivore species, the cheetah (Acinonyx jubatus) and the black-backed jackal (Canis mesomelas). Bacterial phyla with proportions >0.2% were identical for both species and included Firmicutes, Fusobacteria, Bacteroidetes, Proteobacteria and Actinobacteria. At a finer taxonomic resolution, black-backed jackals exhibited 69 bacterial taxa with proportions ≥0.1%, whereas cheetahs had only 42. Finally, oligotyping revealed that shared bacterial taxa consisted of distinct oligotype profiles. Thus, in contrast to 3% OTUs, oligotyping can detect fine-scale taxonomic differences between microbiomes.
    Frontiers in Microbiology 10/2014; 5(526):1-12. DOI:10.3389/fmicb.2014.00526 · 3.94 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: The gastrointestinal tract (GIT) microbiomes of production animals are now firmly established as a key feature underscoring animal health, development, and productivity. In particular, early gut colonization is critically important to the morphological and immunological development of the GIT, development of a functional fermentative environment, and neonatal resistance to pathogenic challenge. Although perturbations of an animal's GIT microbiome at any age can have profound consequences, perturbations during early GIT development can be particularly severe and result in significant and long-lasting sequelae. As the GIT microbiome matures, it exhibits significant diversity, ostensibly an important indicator of ecosystem health. Recognition of the immense importance of the GIT microbiota to the host has led to the development of probiotic and prebiotic feedstuffs with the express aim of ensuring animal health. We herein review the current collective understanding of the GIT microbiota of production animals.
    02/2014; 2:469-86. DOI:10.1146/annurev-animal-022513-114149
  • [Show abstract] [Hide abstract]
    ABSTRACT: The addition of 0.5-1 mm biostable biochar (10 g/L) to mesophilic anaerobic digesters inoculated with crushed granules (1 g-VS/L) and fed with 4, 6 and 8 g/L glucose shortened the methanogenic lag phase by 11.4%, 30.3% and 21.6% and raised the maximum methane production rate by 86.6%, 21.4% and 5.2%, respectively, compared with the controls without biochar. 75 μm biochar further shortened the lag phase by 38.0% and increased the methane production rate by 70.6% at 6 g/L glucose loading. Biochar also simultaneously enhanced the production and degradation of intermediate acids. The fingerprint and sequencing analysis used to examine the spatial distribution and temporal evolution of communities revealed that proportion of Archaea was higher in the biochar-added treatments and in the tightly-bound fractions. Methanosarcina located in the tightly-bound fractions on the biochar surface, and was most abundant in the larger 2-5 mm biochar particles. Methanosaeta was enriched in the loosely-bound fractions by all-size biochar particles and within the tightly-bound fractions by small biochar particles. Because biochar is cost-effective and can remain in digestate for direct use as soil amendment without separation, eco-compatible biochar may serve as a good substrate for highly-loaded digestion by inducing selective colonization of functional microbes. Copyright © 2014 Elsevier Ltd. All rights reserved.
    Water Research 11/2014; 68C:710-718. DOI:10.1016/j.watres.2014.10.052 · 5.32 Impact Factor

Full-text (2 Sources)

Available from
Jun 4, 2014