Nucleic Acid Isolation from Ecological Samples—Vertebrate Gut Flora

Nordgård, Lise; Traavik, Terje; Nielsen, Kaare M.

doi:10.1016/s0076-6879(05)95003-9

Cited by 12 publications

(7 citation statements)

References 37 publications

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“…Three different gut dissection was performed as per [32] with few modifications. Briefly, 1 gm of the sample from each bat was finely ground in a sterile mortar and pestle followed by suspending the aliquot in 1 ml of sterile distilled water.…”

Section: Characterization Of Bacteria Present In the Lesser Horseshoementioning

confidence: 99%

Culture-dependent and metagenomic analysis of lesser horseshoe bats’ gut microbiome revealing unique bacterial diversity and signatures of potential human pathogens

Selvin

Lanong

Syiem

et al. 2019

Microbial Pathogenesis

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A B S T R A C T Bats are highly diverse and ecologically important mammals. They harbor various bacteria, viruses, and fungal communities that are either beneficial or potentially pathogenic. Extensive metagenomic studies in bats are limited, particularly for the gut, and to date, there are no reports on the bacterial diversity of Rhinolophus monoceros from Meghalaya, India. There are limited studies on the isolation of potential harmful or beneficial bacteria and their interactions with the environment through culture-dependent approaches. Therefore, highthroughput screening was used to understand the population structure, genetic diversity, and ecological role of the microorganisms. High-throughput sequencing of the 16S rRNA marker for gene mapping showed that the gut samples constitute a diverse group of bacteria that is dominated by Proteobacteria, followed by Firmicutes. The bacterial genera Corynebacterium and Mycobacterium were also observed in the Illumina dataset. Illumina sequencing revealed eight bacterial phyla composed of 112 genera. The metagenomic analysis of the OTUs from the gut revealed diverse bacterial communities as well as zoonotic and human pathogens. There were differences in the bacterial communities between the two methods used in this study, which could be related to host specificity, diet, and habitat. The culture-dependent technique resulted in the isolation of 35 bacterial isolates, of which Bacillus cereus and B. anthracis are well-known bacterial pathogens that show virulent traits including hemolytic and proteolytic activities. Pseudomonas stutzeri is an opportunistic human pathogen that was also isolated and showed similar traits. Antibiotic sensitivity tests were performed on all 35 isolates, and different antibiotics were used for Gram-positive and -negative bacteria. The result showed that some isolates are resistant to antibiotics such as penicillin G and Cefoxitin. This report on gut bacterial communities could attract interest in the possibility of isolating and characterizing bacteria for the production of antibiotics, enzymes, plant growth promoters, and probiotics. However, the presence of potential pathogenic bacteria that may impose health hazards cannot be ignored and needs to be studied further.

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Section: Characterization Of Bacteria Present In the Lesser Horseshoementioning

confidence: 99%

Culture-dependent and metagenomic analysis of lesser horseshoe bats’ gut microbiome revealing unique bacterial diversity and signatures of potential human pathogens

Selvin

Lanong

Syiem

et al. 2019

Microbial Pathogenesis

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“…We extracted DNA using a modification of the method proposed by Nordgård et al [51]. Briefly, each intestinal region was dissected longitudinally, washed, and macerated with a plastic pestle in saline solution (0.85% NaCl and 0.1% Tween 80) to remove unattached bacteria from the gut walls, and to collect the bacteria in the intestinal content.…”

Section: Dna Extraction From Gut Samplesmentioning

confidence: 99%

Gut Bacterial Diversity of the House Sparrow (Passer domesticus) Inferred by 16S rRNA Sequence Analysis

Mirón¹,

Mira²,

Rocha‐Ramírez³

et al. 2014

Metagenomics

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Intestinal bacteria play an important role in animal health. They extract and process nutrients present in their host's diet, help to develop their host's immune system, and recycle organic compounds, water, and minerals. The gut bacterial diversity is poorly known in wild animals. This study is the first description of the diversity of bacteria along the whole intestine of a wild bird (Passer domesticus). Pyrosequencing of the 16S rRNA gene unveiled a high bacterial diversity, distributed in 11 bacterial phyla. The most abundant groups were Proteobacteria and Firmicutes. Bacterial diversity was greater in the upper section of the intestine and decreased toward the final portion of the gut. After a conservative denoising of the sequences, we found 4,436 OTUs in the gut of P. domesticus. Our data shows that the diversity of intestinal bacteria in the gut of wild birds is much larger than what had previously been estimated using fecal samples.

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“…Several methods for the extraction of DNA from the vertebrate gut have been described, 11,12 and a number of commercial kits are available. Some of these have been specifically developed for faecal analysis, as faeces contain several inhibitors of the polymerase chain reaction (PCR), such as bile salts, haemoglobin degradation products and complex polysaccharides.…”

Section: Introductionmentioning

confidence: 99%

Lyophilisation improves the extraction of PCR‐quality community DNA from pig faecal samples

Ruíz

Rubio

2009

J Sci Food Agric

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BACKGROUND: Faeces are increasingly used as sources of DNA for genetic and ecological studies. Although multiple methods to preserve faecal samples prior to DNA extraction have been used (e.g., 70% or absolute ethanol, freezing at −20• C or in liquid nitrogen) no information is at present available in the literature on the use of lyophilised faeces. Accordingly, the yield and quality of the community DNA obtained by using four different commercial DNA extraction kits (QIAamp DNA Stool Mini Kit, REALPURE Spin Kit, SPEEDTOOLS Tissue DNA Extraction Kit, and JETQUICK Tissue DNA Spin Kit) from fresh and lyophilised samples of faeces were studied here.

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Nucleic Acid Isolation from Ecological Samples—Vertebrate Gut Flora

Cited by 12 publications

References 37 publications

Culture-dependent and metagenomic analysis of lesser horseshoe bats’ gut microbiome revealing unique bacterial diversity and signatures of potential human pathogens

Culture-dependent and metagenomic analysis of lesser horseshoe bats’ gut microbiome revealing unique bacterial diversity and signatures of potential human pathogens

Gut Bacterial Diversity of the House Sparrow (Passer domesticus) Inferred by 16S rRNA Sequence Analysis

Lyophilisation improves the extraction of PCR‐quality community DNA from pig faecal samples

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