16-s.biz Bacteria: A look in between the cracks

Mar Genomics. 2016 Aug 25. pii: S1874-7787(16)30089-7. doi: 10.1016/j.margen.2016.08.003. [Epub ahead of print]

Complex bacterial communities in the deep-sea sediments of the Bay of Bengal and volcanic Barren Island in the Andaman Sea.

Verma P1, Raghavan RV2, Jeon CO3, Lee HJ3, Priya PV4, Dharani G2, Kirubagaran R5.

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Abstract

Deep-sea environments are gaining global attention as potential sources of useful microorganisms, thereby warranting a better understanding of the diversity and genomic potential of the microbes present. To this end, here we provide the first insights into the composition of the bacterial communities in deep-sea sediment samples from the southwestern Bay of Bengal and the geographically distinct volcanic Barren Island in the Andaman Sea. High-throughput 16S rRNA gene sequencing of the sediments revealed the presence of >44,000 operational taxonomic units (OTUs) in each of the samples, suggesting high bacterial diversity. Actinobacteria was the most dominant phylum, representing >20% of the taxonomically assignable OTUs, followed by Firmicutes, Proteobacteria, and Chloroflexi. Numerous bacteria that are potentially involved in the sulfur cycle were observed in the Barren Island sediment sample, while bacteria with clinical and industrial potential were observed in the samples from the southwestern Bay of Bengal. Correlation analysis of the biotic and abiotic parameters showed that the differences in bacterial richness and community composition between the sampling sites were mainly dependent on sediment texture. Using a predictive functional metagenomic approach, this study also discusses the genetic variations that may provide an adaptive advantage to sediment bacterial communities for survival in these extreme deep-sea environments. The results from this study should aid future studies focused on bioprospecting and geochemical cycling in the deep sea.

Copyright © 2016 Elsevier B.V. All rights reserved.

KEYWORDS:

16S rRNA gene; Amplicon sequencing; Bacterial diversity; DGGE; Deep-sea environment; Illumina

PMID: 27570125 DOI: 10.1016/j.margen.2016.08.003

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22.

FEMS Microbiol Ecol. 2016 Aug 24. pii: fiw181. [Epub ahead of print]

Distribution and activity of the anaerobic methanotrophic community in a nitrogen-fertilized Italian paddy soil.

Vaksmaa A1, Lüke C2, van Alen T1, Valè G3, Lupotto E3, Jetten M1, Ettwig KF1.

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Abstract

In order to mitigate methane emissions from paddy fields, it is important to understand the sources and sinks. Most paddy fields are heavily fertilized with nitrite and nitrate which can be used as electron acceptors by anaerobic methanotrophs. Here we show that slurry incubations of Italian paddy field soil with nitrate and 13C-labelled methane have the potential for nitrate-dependent anaerobic oxidation of methane (79.9. nmol g-1 dw d-1). Community analysis based on 16S rRNA amplicon sequencing and qPCR of the water-logged soil and the rhizosphere showed that AOM-associated archaea (AAA), including Methanoperedens nitroreducens, comprised 9% (bulk soil) and 1% (rhizosphere) of all archaeal reads. The NC10 phylum bacteria made up less than 1% of all bacterial sequences. The phylogenetic analysis was complemented by qPCR showing that AAA ranged from 0.28 to 3.9×106 16S rRNA gene copies g-1 dw in bulk soil and 0.27 to 2.8×106 in the rhizosphere. The abundance of NC10 phylum bacteria was an order of magnitude lower. Revisiting published diversity studies, we found that AAA have been detected, but not linked to methane oxidation in several paddy fields. Our data suggests an important role of AAA in methane cycling in paddy fields.

© FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

KEYWORDS:

16s rRNA gene; AAA; Methanoperedens nitroreducens; amplicon sequencing; anaerobic oxidation of methane; microbial community; paddy fields; rice rhizosphere

PMID: 27562776 DOI: 10.1093/femsec/fiw181

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23.

FEMS Microbiol Ecol. 2016 Nov;92(11). pii: fiw182. doi: 10.1093/femsec/fiw182. Epub 2016 Aug 23.

Taxonomic and predicted metabolic profiles of the human gut microbiome in pre-Columbian mummies.

Santiago-Rodriguez TM1, Fornaciari G2, Luciani S3, Dowd SE4, Toranzos GA5, Marota I3, Cano RJ6.

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Abstract

Characterization of naturally mummified human gut remains could potentially provide insights into the preservation and evolution of commensal and pathogenic microorganisms, and metabolic profiles. We characterized the gut microbiome of two pre-Columbian Andean mummies dating to the 10-15th centuries using 16S rRNA gene high-throughput sequencing and metagenomics, and compared them to a previously characterized gut microbiome of an 11th century AD pre-Columbian Andean mummy. Our previous study showed that the Clostridiales represented the majority of the bacterial communities in the mummified gut remains, but that other microbial communities were also preserved during the process of natural mummification, as shown with the metagenomics analyses. The gut microbiome of the other two mummies were mainly comprised by Clostridiales or Bacillales, as demonstrated with 16S rRNA gene amplicon sequencing, many of which are facultative anaerobes, possibly consistent with the process of natural mummification requiring low oxygen levels. Metagenome analyses showed the presence of other microbial groups that were positively or negatively correlated with specific metabolic profiles. The presence of sequences similar to both Trypanosoma cruzi and Leishmania donovani could suggest that these pathogens were prevalent in pre-Columbian individuals. Taxonomic and functional profiling of mummified human gut remains will aid in the understanding of the microbial ecology of the process of natural mummification.

© FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

KEYWORDS:

Chagas’ disease; Firmicutes; ancient gut microbiomes; leishmaniasis; mummies

PMID: 27559027 DOI: 10.1093/femsec/fiw182

[PubMed - in process]

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24.

Front Nutr. 2016 Aug 8;3:26. doi: 10.3389/fnut.2016.00026. eCollection 2016.

Considerations For Optimizing Microbiome Analysis Using a Marker Gene.

de la Cuesta-Zuluaga J1, Escobar JS1.

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Abstract

Next-generation sequencing technologies have found a widespread use in the study of host-microbe interactions due to the increase in their throughput and their ever-decreasing costs. The analysis of human-associated microbial communities using a marker gene, particularly the 16S rRNA, has been greatly benefited from these technologies - the human gut microbiome research being a remarkable example of such analysis that has greatly expanded our understanding of microbe-mediated human health and disease, metabolism, and food absorption. 16S studies go through a series of in vitro and in silico steps that can greatly influence their outcomes. However, the lack of a standardized workflow has led to uncertainties regarding the transparency and reproducibility of gut microbiome studies. We, here, discuss the most common challenges in the archetypical 16S rRNA workflow, including the extraction of total DNA, its use as template in PCR with primers that amplify specific hypervariable regions of the gene, amplicon sequencing, the denoising and removal of low-quality reads, the detection and removal of chimeric sequences, the clustering of high-quality sequences into operational taxonomic units, and their taxonomic classification. We recommend the essential technical information that should be conveyed in publications for reproducibility of results and encourage non-experts to include procedures and available tools that mitigate most of the problems encountered in microbiome analysis.

 

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