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J Microbiol Methods. 2016 Nov;130:180-188. doi: 10.1016/j.mimet.2016.09.017. Epub 2016 Sep 26.

Effects of field conditions on fecal microbiota.

Author information

1
Purdue University, West Lafayette, IN 47906, USA. Electronic address: vreynolds@gmail.com.
2
San Diego Zoo Institute for Conservation Research, Escondido, CA 92027, USA. Electronic address: ctan@sandiegozoo.org.
3
Fanjingshan National Nature Reserve Administration, Tongren, China; University of Turin, Turin, Italy. Electronic address: fjshmonkey@gmail.com.
4
Fanjingshan National Nature Reserve Administration, Tongren, China. Electronic address: fjs03@qq.com.
5
Beijing Key Laboratory of Captive Wildlife Technologies, Beijing Zoo, Beijing 100044, China. Electronic address: cuiduoying@hotmail.com.
6
Zhejiang Institute of Microbiology, Hangzhou, China. Electronic address: hongxia6891@163.com.
7
Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA. Electronic address: rknight@ucsd.edu.
8
Department of Anthropology, Northwestern University, Evanston, IL 60208, USA. Electronic address: Katherine.amato@northwestern.edu.

Abstract

Gut microbiota can provide great insight into host health, and studies of the gut microbiota in wildlife are becoming more common. However, the effects of field conditions on gut microbial samples are unknown. This study addresses the following questions: 1) How do environmental factors such as sunlight and insect infestations affect fecal microbial DNA? 2) How does fecal microbial DNA change over time after defecation? 3) How does storage method affect microbial DNA? Fresh fecal samples were collected, pooled, and homogenized from a family group of 6 spider monkeys, Ateles geoffroyi. Samples were then aliquoted and subjected to varying light conditions (shade, sun), insect infestations (limited or not limited by netting over the sample), and sample preservation methods (FTA - Fast Technology for Analysis of nucleic acid - cards, or freezing in liquid nitrogen then storing at -20°C). Changes in the microbial communities under these conditions were assessed over 24h. Time and preservation method both effected fecal microbial community diversity and composition. The effect size of these variables was then assessed in relation to fecal microbial samples from 2 other primate species (Rhinopithecus bieti and R. brelichi) housed at different captive institutions. While the microbial community of each primate species was significantly different, the effects of time and preservation method still remained significant indicating that these effects are important considerations for fieldwork.

KEYWORDS:

Environmental conditions; Fecal microbial community; Fecal preservation; Gut microbiota; Primates

PMID:
27686380
DOI:
10.1016/j.mimet.2016.09.017
[Indexed for MEDLINE]

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