scholarly journals The Problem with ‘Microbiome’

Diversity ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 138
Author(s):  
Stuart Donachie ◽  
Claire Fraser ◽  
Ethan Hill ◽  
Marguerite Butler
Keyword(s):  
16S Rrna ◽  
Microbial Diversity ◽  
Sensu Stricto ◽  
Ribosomal Gene ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Community Members ◽  
Etiologic Agents ◽  
Microbiome Research ◽  
Marine Microbial Diversity

The term “microbiome” is currently applied predominantly to assemblages of organisms with 16S rRNA genes. In this context, “microbiome” is a misnomer that has been conferred a wide-ranging primacy over terms for community members lacking such genes, e.g., mycobiome, eukaryome, and virome, yet these are also important subsets of microbial communities. Widespread convenient and affordable 16S rRNA sequencing pipelines have accelerated continued use of such a “microbiome”, but at what intellectual and practical costs? Here we show that the use of “microbiome” in ribosomal gene-based studies has been egregiously misapplied, and discuss potential impacts. We argue that the current focus of “microbiome” research, predominantly on only ‘bacteria’, presents a dangerous narrowing of scope which encourages dismissal and even ignorance of other organisms’ contributions to microbial diversity, sensu stricto, and as etiologic agents; we put this in context by discussing cases in both marine microbial diversity and the role of pathogens in global amphibian decline. Fortunately, the solution is simple. We must use descriptive nouns that strictly reflect the outcomes attainable by the methods used. “Microbiome”, as a descriptive noun, should only be used when diversity in the three recognized domains is explored.

scholarly journals High Diversity in Iron Cycling Microbial Communities in Acidic, Iron-Rich Water of the Pyhäsalmi Mine, Finland

Geofluids ◽  
2019 ◽  
Vol 2019 ◽  
pp. 1-17 ◽  
Author(s):  
Malin Bomberg ◽  
Jarno Mäkinen ◽  
Marja Salo ◽  
Päivi Kinnunen
Keyword(s):  
16S Rrna ◽  
Microbial Diversity ◽  
Microbial Communities ◽  
Mine Water ◽  
Ferrous Iron ◽  
Great Part ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Iron Oxidizers

Microbial communities of iron-rich water in the Pyhäsalmi mine, Finland, were investigated with high-throughput amplicon sequencing and qPCR targeting bacteria, archaea, and fungi. In addition, the abundance ofLeptospirillumandAcidithiobacilluswas assessed with genus-specific qPCR assays, and enrichment cultures targeting aerobic ferrous iron oxidizers and ferric iron reducers were established. The acidic (pH 1.4–2.3) mine water collected from 240 m, 500 m, and 600 m depth from within the mine had a high microbial diversity consisting of 63-114 bacterial, 10-13 archaeal, and 104-117 fungal genera. The most abundant microorganisms in the mine water were typical acid mine drainage (AMD) taxa, such as acidophilic, iron-oxidizingLeptospirillum,Acidiphilum,Acidithiobacillus,Ferrovum, andThermoplasma. The fungi belonged mostly to the phylum Ascomycetes, although a great part of the fungal sequences remained unclassified. The number of archaeal 16S rRNA genes in the mine water was between 0.3 and 1.2 × 107copies mL−1in the samples from 500 m and 600 m, but only 3.9 × 103at 240 m and archaea were in general not enriched in cultures. The number of fungal 5.8S rRNA genes was high only in the mine water from 500 m and 600 m, where 0.2–3.4 × 104spore equivalents mL−1were detected. A high number ofLeptospirillum16S rRNA genes, 0.6–1.6 × 1010copies mL−1, were detected at 500 m and 600 m depth and in cultures containing ferrous iron, showing the importance of iron oxidizers in this environment. The abundance of bacteria in general was between 103and 10616S rRNA gene copies mL−1. Our results showed a high microbial diversity in the acid- and iron-impacted waters of the Pyhäsalmi mine, whereLeptospirillumbacteria were especially prominent. These iron oxidizers are also the main nitrogen-fixing microorganisms in this ecosystem.

scholarly journals Genetic diversity of 16S rRNA and mcrA genes from methanogenic archaeas

2020 ◽  
Vol 42 ◽  
pp. e49877
Author(s):  
Keyla Vitoria Marques Xavier ◽  
Eden Silva e Souza ◽  
Erick de Aquino Santos ◽  
Michely Correia Diniz
Keyword(s):  
Genetic Diversity ◽  
16S Rrna ◽  
Descriptive Analysis ◽  
Methanogenic Archaea ◽  
Ribosomal Gene ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Terrestrial Environments ◽  
Methyl Coenzyme M Reductase ◽  
Potential Use

Methanogenic archaeas are found in aquatic and terrestrial environments and are fundamental in the conversion of organic matter into methane, a gas that has a potential use as renewable source of energy, which is also considered as one of the main agents of the greenhouse effect. The vast majority of microbial genomes can be identified by a conservative molecular marker, the 16S ribosomal gene. However, the mcrA gene have been using in studies of methanogenic archaea diversity as an alternative marker, highly conserved and present only in methanogens. This gene allows the expression of the enzyme Methyl-coenzyme M reductase, the main agent in converting by-products of anaerobic digestion into methane. In this context, we aimed to study the genetic diversity of mcrA and 16S rRNA genes sequences available in databases. The nucleotide sequences were selected from the NCBI. The heterozygosity and molecular diversity indexes were calculated using the Arlequin 3.5 software, with plots generated by package R v3.0. The diversity and heterozygosity indices for both genes may have been influenced by the number and size of the sequences. Descriptive analysis of genetic diversity generated by sequences deposited in databases allowed a detailed study of these molecules. It is known that the organisms in a population are genetically distinct, and that, despite having similarities in their gene composition, the differences are essential for their adaptation to different environments.

scholarly journals Growing the recalcitrant

2007 ◽  
Vol 28 (3) ◽  
pp. 127
Author(s):  
Peter H Janssen
Keyword(s):  
16S Rrna ◽  
Microbial Diversity ◽  
16S Rrna Genes ◽  
Rrna Genes

Unculturable microorganisms are those that have been identifiedby microscopy, by their activity or by detection of phylogenetic markers such as their 16S rRNA genes, and have not been able to be cultured, despite reasonable efforts having been made. Recent successes in the cultivation of so-called unculturable microorganisms have revealed that the key ingredient in therecipe for growing them in the laboratory is patience. Beyond that, there is probably no single secret to success and microbial diversity must be matched by experimental ingenuity.

A Highly Selective PCR Protocol for Detecting 16S rRNA Genes of the Genus Pseudomonas (Sensu Stricto) in Environmental Samples

1998 ◽  
Vol 64 (7) ◽  
pp. 2545-2553 ◽  
Author(s):  
Franco Widmer ◽  
Ramon J. Seidler ◽  
Patrick M. Gillevet ◽  
Lidia S. Watrud ◽  
George D. Di Giovanni
Keyword(s):  
16S Rrna ◽  
Environmental Samples ◽  
Restriction Analysis ◽  
Phylogenetic Analyses ◽  
Pcr Amplification ◽  
Sensu Stricto ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Human Pathogens ◽  
Soil Dna

ABSTRACT Pseudomonas species are plant, animal, and human pathogens; exhibit plant pathogen-suppressing properties useful in biological control; or express metabolic versatilities valued in biotechnology and bioremediation. Specific detection ofPseudomonas species in the environment may help us gain a more complete understanding of the ecological significance of these microorganisms. The objective of this study was to develop a PCR protocol for selective detection ofPseudomonas (sensu stricto) in environmental samples. Extensive database searches identified a highly selective PCR primer pair for amplification of Pseudomonas16S rRNA genes. A protocol that included PCR amplification and restriction analysis, a general cloning and sequencing strategy, and phylogenetic analyses was developed. The PCR protocol was validated by testing 50 target and 14 nontarget pure cultures, which confirmed the selectivity to 100%. Further validation used amplification of target sequences from purified bulk soil DNA followed by cloning of PCR products. Restriction analysis with HaeIII revealed eight different fragmentation patterns among 36 clones. Sequencing and phylogenetic analysis of 8 representative clones indicated that 91.7% of the products were derived from target organisms of the PCR protocol. Three patterns, representing only 8.3% of the 36 clones, were derived from non-Pseudomonas or chimeric PCR artifacts. Three patterns, representing 61.1% of the clones, clustered with sequences of confirmed Pseudomonas species, whereas two patterns, representing 30.6% of the clones, formed a novel phylogenetic cluster closely associated with Pseudomonas species. The results indicated that the Pseudomonas-selective PCR primers were highly specific and may represent a powerful tool forPseudomonas population structure analyses and taxonomic confirmations.

scholarly journals Seasonal Variation of Microbial Diversity of Coastal Sediment in Tongyeong, South Korea, Using 16S rRNA Gene Amplicon Sequencing

2021 ◽  
Vol 10 (27) ◽  
Author(s):  
Nur Indradewi Oktavitri ◽  
Jong-Oh Kim ◽  
Kyunghoi Kim
Keyword(s):  
Seasonal Variation ◽  
Microbial Community ◽  
16S Rrna ◽  
South Korea ◽  
Microbial Diversity ◽  
Amplicon Sequencing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Generation Sequencing

Benthic microbial diversity in Tongyeong, South Korea, was analyzed using next-generation sequencing of the 16S rRNA genes, to reveal the effects of seasonal variations on the microbial community in sediment. Proteobacteria was the dominant phylum, with a relative abundance of 61.5 to 68.1%.

scholarly journals Animal-to-Animal Variation in Fecal Microbial Diversity among Beef Cattle

2010 ◽  
Vol 76 (14) ◽  
pp. 4858-4862 ◽  
Author(s):  
Lisa M. Durso ◽  
Gregory P. Harhay ◽  
Timothy P. L. Smith ◽  
James L. Bono ◽  
Todd Z. DeSantis ◽  
...  
Keyword(s):  
Food Safety ◽  
16S Rrna ◽  
Beef Cattle ◽  
Microbial Diversity ◽  
Intestinal Microbiota ◽  
Animal Health ◽  
Methane Emissions ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Health Food

ABSTRACT The intestinal microbiota of beef cattle are important for animal health, food safety, and methane emissions. This full-length sequencing survey of 11,171 16S rRNA genes reveals animal-to-animal variation in communities that cannot be attributed to breed, gender, diet, age, or weather. Beef communities differ from those of dairy. Core bovine taxa are identified.

Microbial Diversity in a Brazilian Acid Moderate Drainage and Experimental Nickel Bioleaching System

2009 ◽  
Vol 71-73 ◽  
pp. 117-120 ◽  
Author(s):  
L. Alves ◽  
C. Bernardelli ◽  
V.A. Leão ◽  
Monica Teixeira ◽  
Edgardo R. Donati
Keyword(s):  
16S Rrna ◽  
Microbial Diversity ◽  
Mine Drainage ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Complete Characterization ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Universal Primers ◽  
Fish Analysis ◽  
Acidithiobacillus Thiooxidans

The aim of this work was to determine the microbial diversity of the acid mine drainage (AMD) material collected at an abandoned pyrite mine in Ouro Preto, Brazil. AMD samples were compared to a nickel sulfide column bioleaching pregnant solution which was used as reference. Fluorescent in situ hybridization analyses (FISH) and Denaturing Gradient Gel Electrophoresis (DGGE) were used. FISH analysis was carried out using specific 16S rRNA probes. The extracted DNA was amplified using universal primers for bacterial 16S rRNA genes and analyzed by DGGE. Acidithiobacillus. ferrooxidans was not detected in AMD samples. However, the presence of Acidithiobacillus thiooxidans was confirmed. In other hand, in the bioleaching tanks samples studied, both bacteria species were detected. The non-identified DNA bands were cloned and sequenced for complete characterization.

Molecular Assessment of Microbial Diversity and Community Structure at Uranium Mines of Jaduguda, India

2007 ◽  
Vol 20-21 ◽  
pp. 413-416 ◽  
Author(s):  
Pinaki Sar ◽  
Paltu K. Dhal ◽  
Ekramul Islam ◽  
Sufia K. Kazy
Keyword(s):  
16S Rrna ◽  
Microbial Diversity ◽  
Molecular Level ◽  
Restriction Analysis ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Uranium Mine ◽  
Rrna Gene ◽  
Wide Range ◽  
Mine Sites

Microbial diversity associated with uranium mine areas of Jaduguda, India has been investigated using a culture independent molecular approach. Soil samples collected from existing and proposed mine sites were analyzed for physicochemical parameters. Community DNA was extracted from five samples. Small subunit rRNA gene (16S rRNA) was PCR amplified using bacterial primers. The diversity of the total bacterial community was described at molecular level by amplified ribosomal DNA restriction analysis (ARDRA). Dominant bacterial groups (represents by OTUs) selected by ARDRA were identified by sequencing the 16S rRNA genes. From the bacterial rDNA clone library around 230 clones were used for further analysis. The unique OTUs and number of clones representing such OTUs were determined. Dominant OTUs were sequenced and identified. These phylotypes spanned a wide range within the bacterial domain occupying Proteobacteria, Acidobacteria, Bacteroidetes, Firmicutes, Cyanobacteria as major phyla. About 46 % of clones sequenced from various sites were identified as Proteobacteria. The present findings on microbial diversity at the molecular level are the first of its kind for uranium mine sites of India. Around 20 % of the clone sequences showed little affiliation with known taxa and probably represent new organisms adapted to this habitat.

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