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FEMS Microbiol Ecol. 2017 Feb;93(2). pii: fiw240. doi: 10.1093/femsec/fiw240. Epub 2016 Dec 2.

DNA extraction protocols may influence biodiversity detected in the intestinal microbiome: a case study from wild Prussian carp, Carassius gibelio.

Author information

1
Institute of Systematics and Ecology of Animals of Siberian Branch of Russian Academy of Sciences, Novosibirsk 630091, Russia.
2
IRTA-SCR, San Carlos de la Rapita, Tarragona 43540, Spain.
3
Department of Biochemistry and Microbiology, Tomsk State University, Tomsk 634050, Russia.
4
Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Nekouzskii raion, Yaroslavskaya oblast 152742, Russia.
5
Institute of Systematics and Ecology of Animals of Siberian Branch of Russian Academy of Sciences, Novosibirsk 630091, Russia yarmak85@mail.ru.

Abstract

In this investigation, we examined the influence of different DNA extraction protocols on results obtained for intestinal microbiota of Prussian carp. We showed that significant differences were observed in numbers of reads, OTUs, Shannon index and taxonomic composition between two different DNA extraction protocols for intestine of Prussian carp (Carassius gibelio), and differences were also evident between microbial communities in the intestinal mucosa and intestinal content. Statistical analyses of 25 published articles also revealed a significant relationship between methods of DNA extraction and bacterial diversity in fish intestine of freshwater species. Microbial diversity, community structure, proportions of read numbers derived from each OTU and the total number of OTU's obtained by different DNA extraction protocols could lead to a bias in results obtained in some cases, and therefore researchers should be conservative in conclusions about community structures.

KEYWORDS:

Carassius gibelio; extraction of DNA; fish gut microbiota; genetic diversity; metagenomic sequencing

PMID:
27915284
DOI:
10.1093/femsec/fiw240
[Indexed for MEDLINE]

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