scholarly journals How, when, and where relic DNA biases estimates of microbial diversity

2017 ◽  
Author(s):  
JT Lennon ◽  
ME Muscarella ◽  
SA Muscarella ◽  
BK Lehmkuhl
Keyword(s):  
Microbial Diversity ◽  
Dna Sequences ◽  
Species Abundance ◽  
Rrna Gene ◽  
Bacterial Dna ◽  
Soil Sediment ◽  
Species Abundance Distributions ◽  
Abundance And Diversity ◽  
Dna Pool ◽  
Biased Estimates

Extracellular or “relic” DNA is one of the largest pools of nucleic acids in the mbiosphere1,2. Relic DNA can influence a number of important ecological and evolutionary processes, but it may also bias estimates of microbial abundance and diversity, which has implications for understanding environmental, engineered, and host-associated ecosystems. We developed models capturing the fundamental processes that regulate the size and composition of the relic DNA pools to identify scenarios leading to biased estimates of biodiversity. Our models predict that bias increases with relic DNA pool size, but only when the species abundance distributions (SAD) of relic and intact DNA are distinct from one another. We evaluated our model predictions by quantifying relic DNA and assessing its contribution to bacterial diversity using 16S rRNA gene sequences collected from different ecosystem types, including soil, sediment, water, and the mammalian gut. On average, relic DNA made up 33 % of the total bacterial DNA pool, but exceeded 80 % in some samples. Despite its abundance, relic DNA had no effect on estimates of taxonomic and phylogenetic diversity, even in ecosystems where processes such as the physical protection of relic DNA are common and predicted by our models to generate bias. Rather, our findings are consistent with the expectation that relic DNA sequences degrade in proportion to their abundance and therefore may contribute minimally to estimates of microbial diversity.

scholarly journals How, When, and Where Relic DNA Affects Microbial Diversity

mBio ◽  
2018 ◽  
Vol 9 (3) ◽  
Author(s):  
J. T. Lennon ◽  
M. E. Muscarella ◽  
S. A. Placella ◽  
B. K. Lehmkuhl
Keyword(s):  
Nucleic Acids ◽  
Microbial Diversity ◽  
Species Abundance ◽  
Theoretical Models ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Dna Pools ◽  
Species Abundance Distributions ◽  
Dna Pool ◽  
Biased Estimates

ABSTRACTExtracellular or “relic” DNA is one of the largest pools of nucleic acids in the biosphere. Relic DNA can influence a number of important ecological and evolutionary processes, but it may also affect estimates of microbial abundance and diversity, which has implications for understanding environmental, engineered, and host-associated ecosystems. We developed models capturing the fundamental processes that regulate the size and composition of the relic DNA pools to identify scenarios leading to biased estimates of biodiversity. Our models predict that bias increases with relic DNA pool size, but only when the species abundance distributions (SADs) of relic and intact DNA are distinct from one another. We evaluated our model predictions by quantifying relic DNA and assessing its contribution to bacterial diversity using 16S rRNA gene sequences collected from different ecosystem types, including soil, sediment, water, and the mammalian gut. On average, relic DNA made up 33% of the total bacterial DNA pool but exceeded 80% in some samples. Despite its abundance, relic DNA had a minimal effect on estimates of taxonomic and phylogenetic diversity, even in ecosystems where processes such as the physical protection of relic DNA are common and predicted by our models to generate bias. Our findings are consistent with the expectation that relic DNA from different taxa degrades at a constant and equal rate, suggesting that it may not fundamentally alter estimates of microbial diversity.IMPORTANCEThe ability to rapidly obtain millions of gene sequences and transcripts from a range of environments has greatly advanced understanding of the processes that regulate microbial communities. However, nucleic acids extracted from complex samples do not come only from viable microorganisms. Dead microorganisms can generate large pools of relic DNA that distort insight into the ecology and evolution of microbial systems. Here, we develop a conceptual and quantitative framework for understanding how relic DNA influences the structure of microbiomes. Our theoretical models and empirical results demonstrate that a large relic DNA pool does not automatically lead to biased estimates of microbial diversity. Rather, relic DNA effects emerge in combination with microscale processes that alter the commonness and rarity of sequences found in heterogeneous DNA pools.

scholarly journals 16S rRNA Gene Amplicon Sequencing Data of the Iron Quadrangle Ferruginous Caves (Brazil) Shows the Importance of Conserving This Singular and Threatened Geosystem

Diversity ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 494
Author(s):  
Camila G. C. Lemes ◽  
Morghana M. Villa ◽  
Érica B. Felestrino ◽  
Luiza O. Perucci ◽  
Renata A. B. Assis ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Diversity ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Metabolic Potential ◽  
Microbial Life ◽  
Iron Quadrangle ◽  
Abundance And Diversity

The Iron Quadrangle (IQ) is one of the main iron ore producing regions of the world. The exploitation of its reserves jeopardizes the high biological endemism associated with this region. This work aimed to understand the diversity and bacterial potential associated with IQ caves. Floor and ceiling samples of seven ferruginous caves and one quartzite cave were collected, and their microbial relative abundance and diversity were established by 16S rRNA gene amplicon sequencing data. The results showed that ferruginous caves present higher microbial abundance and greater microbial diversity compared to the quartzite cave. Many species belonging to genera found in these caves, such as Pseudonocardia and Streptacidiphilus, are known to produce biomolecules of biotechnological interest as macrolides and polyketides. Moreover, comparative analysis of microbial diversity and metabolic potential in a biofilm in pendant microfeature revealed that the microbiota associated with this structure is more similar to the floor rather than ceiling samples, with the presence of genera that may participate in the genesis of these cavities, for instance, Ferrovum, Geobacter, and Sideroxydans. These results provide the first glimpse of the microbial life in these environments and emphasize the need of conservation programs for these areas, which are under intense anthropogenic exploration.

Patterns in diversity and composition of the microbenthos of subarctic intertidal beaches with different morphodynamics

2020 ◽  
Vol 648 ◽  
pp. 19-38
Author(s):  
AI Azovsky ◽  
YA Mazei ◽  
MA Saburova ◽  
PV Sapozhnikov
Keyword(s):  
Species Abundance ◽  
Abundance Ratio ◽  
Wave Action ◽  
Coarse Grained ◽  
Sediment Properties ◽  
Β Diversity ◽  
Α Diversity ◽  
Wide Range ◽  
Similar Mode ◽  
Abundance And Diversity

Diversity and composition of benthic diatom algae and ciliates were studied at several beaches along the White and Barents seas: from highly exposed, reflective beaches with coarse-grained sands to sheltered, dissipative silty-sandy flats. For diatoms, the epipelic to epipsammic species abundance ratio was significantly correlated with the beach index and mean particle size, while neither α-diversity measures nor mean cell length were related to beach properties. In contrast, most of the characteristics of ciliate assemblages (diversity, total abundance and biomass, mean individual weight and percentage of karyorelictids) demonstrated a strong correlation to beach properties, remaining low at exposed beaches but increasing sharply in more sheltered conditions. β-diversity did not correlate with beach properties for either diatoms or ciliates. We suggest that wave action and sediment properties are the main drivers controlling the diversity and composition of the intertidal microbenthos. Diatoms and ciliates, however, demonstrated divergent response to these factors. Epipelic and epipsammic diatoms exhibited 2 different strategies to adapt to their environments and therefore were complementarily distributed along the environmental gradient and compensated for each other in diversity. Most ciliates demonstrated a similar mode of habitat selection but differed in their degree of tolerance. Euryporal (including mesoporal) species were relatively tolerant to wave action and therefore occurred under a wide range of beach conditions, though their abundance and diversity were highest in fine, relatively stable sediments on sheltered beaches, whereas the specific interstitial (i.e. genuine microporal) species were mostly restricted to only these habitats.

scholarly journals Amplicon-sequencing of raw milk microbiota: impact of DNA extraction and library-PCR

2021 ◽  
Author(s):  
Annemarie Siebert ◽  
Katharina Hofmann ◽  
Lena Staib ◽  
Etienne V. Doll ◽  
Siegfried Scherer ◽  
...  
Keyword(s):  
Sample Preparation ◽  
Dna Extraction ◽  
Raw Milk ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Bacterial Dna ◽  
Microbiome Analysis ◽  
Eukaryotic Dna ◽  
Selective Lysis ◽  
The Impact

Abstract The highly complex raw milk matrix challenges the sample preparation for amplicon-sequencing due to low bacterial counts and high amounts of eukaryotic DNA originating from the cow. In this study, we optimized the extraction of bacterial DNA from raw milk for microbiome analysis and evaluated the impact of cycle numbers in the library-PCR. The selective lysis of eukaryotic cells by proteinase K and digestion of released DNA before bacterial lysis resulted in a high reduction of mostly eukaryotic DNA and increased the proportion of bacterial DNA. Comparative microbiome analysis showed that a combined enzymatic and mechanical lysis procedure using the DNeasy® PowerFood® Microbial Kit with a modified protocol was best suitable to achieve high DNA quantities after library-PCR and broad coverage of detected bacterial biodiversity. Increasing cycle numbers during library-PCR systematically altered results for species and beta-diversity with a tendency to overrepresentation or underrepresentation of particular taxa. To limit PCR bias, high cycle numbers should thus be avoided. An optimized DNA extraction yielding sufficient bacterial DNA and enabling higher PCR efficiency is fundamental for successful library preparation. We suggest that a protocol using ethylenediaminetetraacetic acid (EDTA) to resolve casein micelles, selective lysis of somatic cells, extraction of bacterial DNA with a combination of mechanical and enzymatic lysis, and restriction of PCR cycles for analysis of raw milk microbiomes is optimal even for samples with low bacterial numbers. Key points • Sample preparation for high-throughput 16S rRNA gene sequencing of raw milk microbiota. • Reduction of eukaryotic DNA by enzymatic digestion. • Shift of detected microbiome caused by high cycle numbers in library-PCR.

scholarly journals Effects of Psychotropics on the Microbiome in Patients With Depression and Anxiety: Considerations in a Naturalistic Clinical Setting

2020 ◽  
Author(s):  
Yoshihiro Tomizawa ◽  
Shunya Kurokawa ◽  
Daiki Ishii ◽  
Katsuma Miyaho ◽  
Chiharu Ishii ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbial Diversity ◽  
Depressive Disorders ◽  
Alpha Diversity ◽  
16S Rrna Gene Sequencing ◽  
Shannon Index ◽  
Rrna Gene ◽  
Depression And Anxiety ◽  
The Impact ◽  
Whole Tree

Abstract Background The antibacterial effects of psychotropics may be part of their pharmacological effects when treating depression. However, limited studies have focused on gut microbiota in relation to prescribed medication. Method We longitudinally investigated the relationship between patients’ prescribed medications and intestinal bacterial diversity in a naturalistic treatment course for patients with major depressive disorders and anxiety disorders. Patients were recruited and their stool was collected at 3 time points during their usual psychiatric treatments. Gut microbiota were analyzed using 16S rRNA gene sequencing. We examined the impact of psychotropics (i.e., antidepressants, anxiolytics, antipsychotics) on their gut microbial diversity and functions. Results We collected 246 stool samples from 40 patients. Despite no differences in microbial diversity between medication groups at the baseline, over the course of treatment, phylogenic diversity whole-tree diversity decreased in patients on antipsychotics compared with patients without (P = .027), and beta diversity followed this trend. Based on a fixed-effect model, antipsychotics predicted microbial diversity; the higher doses correlated with less diversity based on the Shannon index and phylogenic diversity whole tree (estimate = −0.00254, SE = 0.000595, P < .0001; estimate = −0.02644, SE = 0.00833, P = .002, respectively). Conclusion Antipsychotics may play a role in decreasing the alpha diversity of the gut microbiome among patients with depression and anxiety, and our results indicate a relationship with medication dosage. Future studies are warranted and should consider patients’ types and doses of antipsychotics in order to further elucidate the mechanisms of gut-brain interactions in psychiatric disorders.

scholarly journals Microbial Diversity of Terrestrial Geothermal Springs in Armenia and Nagorno-Karabakh: A Review

2021 ◽  
Vol 9 (7) ◽  
pp. 1473
Author(s):  
Ani Saghatelyan ◽  
Armine Margaryan ◽  
Hovik Panosyan ◽  
Nils-Kåre Birkeland
Keyword(s):  
16S Rrna ◽  
Microbial Diversity ◽  
High Altitude ◽  
Hot Springs ◽  
Hot Spring ◽  
Abiotic Factors ◽  
Rrna Gene ◽  
Geothermal Springs ◽  
Bacterial Phyla ◽  
Terrestrial Hot Springs

The microbial diversity of high-altitude geothermal springs has been recently assessed to explore their biotechnological potential. However, little is known regarding the microbiota of similar ecosystems located on the Armenian Highland. This review summarizes the known information on the microbiota of nine high-altitude mineralized geothermal springs (temperature range 25.8–70 °C and pH range 6.0–7.5) in Armenia and Nagorno-Karabakh. All these geothermal springs are at altitudes ranging from 960–2090 m above sea level and are located on the Alpide (Alpine–Himalayan) orogenic belt, a seismically active region. A mixed-cation mixed-anion composition, with total mineralization of 0.5 mg/L, has been identified for these thermal springs. The taxonomic diversity of hot spring microbiomes has been examined using culture-independent approaches, including denaturing gradient gel electrophoresis (DGGE), 16S rRNA gene library construction, 454 pyrosequencing, and Illumina HiSeq. The bacterial phyla Proteobacteria, Bacteroidetes, Cyanobacteria, and Firmicutes are the predominant life forms in the studied springs. Archaea mainly include the phyla Euryarchaeota, Crenarchaeota, and Thaumarchaeota, and comprise less than 1% of the prokaryotic community. Comparison of microbial diversity in springs from Karvachar with that described for other terrestrial hot springs revealed that Proteobacteria, Bacteroidetes, Actinobacteria, and Deinococcus–Thermus are the common bacterial groups in terrestrial hot springs. Contemporaneously, specific bacterial and archaeal taxa were observed in different springs. Evaluation of the carbon, sulfur, and nitrogen metabolism in these hot spring communities has revealed diversity in terms of metabolic activity. Temperature seems to be an important factor in shaping the microbial communities of these springs. Overall, the diversity and richness of the microbiota are negatively affected by increasing temperature. Other abiotic factors, including pH, mineralization, and geological history, also impact the structure and function of the microbial community. More than 130 bacterial and archaeal strains (Bacillus, Geobacillus, Parageobacillus, Anoxybacillus, Paenibacillus, Brevibacillus Aeribacillus, Ureibacillus, Thermoactinomyces, Sporosarcina, Thermus, Rhodobacter, Thiospirillum, Thiocapsa, Rhodopseudomonas, Methylocaldum, Desulfomicrobium, Desulfovibrio, Treponema, Arcobacter, Nitropspira, and Methanoculleus) have been reported, some of which may be representative of novel species (sharing 91–97% sequence identity with their closest matches in GenBank) and producers of thermozymes and biomolecules with potential biotechnological applications. Whole-genome shotgun sequencing of T. scotoductus K1, as well as of the potentially new Treponema sp. J25 and Anoxybacillus sp. K1, were performed. Most of the phyla identified by 16S rRNA were also identified using metagenomic approaches. Detailed characterization of thermophilic isolates indicate the potential of the studied springs as a source of biotechnologically valuable microbes and biomolecules.

scholarly journals Circulating bacterial signature is linked to metabolic disease and shifts with metabolic alleviation after bariatric surgery

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Rima M. Chakaroun ◽  
Lucas Massier ◽  
Anna Heintz-Buschart ◽  
Nedal Said ◽  
Joerg Fallmann ◽  
...  
Keyword(s):  
Metabolic Disease ◽  
Bariatric Surgery ◽  
Weight Loss ◽  
Metabolic Health ◽  
Rrna Gene ◽  
Clinical Group ◽  
Analytical Control ◽  
Bacterial Dna ◽  
Blood Samples ◽  
Living Bacteria

Abstract Background The microbiome has emerged as an environmental factor contributing to obesity and type 2 diabetes (T2D). Increasing evidence suggests links between circulating bacterial components (i.e., bacterial DNA), cardiometabolic disease, and blunted response to metabolic interventions. In this aspect, thorough next-generation sequencing-based and contaminant-aware approaches are lacking. To address this, we tested whether bacterial DNA could be amplified in the blood of subjects with obesity and high metabolic risk under strict experimental and analytical control and whether a putative bacterial signature is related to metabolic improvement after bariatric surgery. Methods Subjects undergoing bariatric surgery were recruited into sex- and BMI-matched subgroups with (n = 24) or without T2D (n = 24). Bacterial DNA in the blood was quantified and prokaryotic 16S rRNA gene amplicons were sequenced. A contaminant-aware approach was applied to derive a compositional microbial signature from bacterial sequences in all subjects at baseline and at 3 and 12 months after surgery. We modeled associations between bacterial load and composition with host metabolic and anthropometric markers. We further tested whether compositional shifts were related to weight loss response and T2D remission. Lastly, bacteria were visualized in blood samples using catalyzed reporter deposition (CARD)-fluorescence in situ hybridization (FISH). Results The contaminant-aware blood bacterial signature was associated with metabolic health. Based on bacterial phyla and genera detected in the blood samples, a metabolic syndrome classification index score was derived and shown to robustly classify subjects along their actual clinical group. T2D was characterized by decreased bacterial richness and loss of genera associated with improved metabolic health. Weight loss and metabolic improvement following bariatric surgery were associated with an early and stable increase of these genera in parallel with improvements in key cardiometabolic risk parameters. CARD-FISH allowed the detection of living bacteria in blood samples in obesity. Conclusions We show that the circulating bacterial signature reflects metabolic disease and its improvement after bariatric surgery. Our work provides contaminant-aware evidence for the presence of living bacteria in the blood and suggests a putative crosstalk between components of the blood and metabolism in metabolic health regulation.

scholarly journals Microbial Diversity of Septic Tank Effluent and a Soil Biomat

2009 ◽  
Vol 75 (10) ◽  
pp. 3348-3351 ◽  
Author(s):  
Jill Tomaras ◽  
Jason W. Sahl ◽  
Robert L. Siegrist ◽  
John R. Spear
Keyword(s):  
Sequence Analysis ◽  
Microbial Diversity ◽  
Gene Sequence ◽  
Septic Tank ◽  
Rrna Gene ◽  
Control Soil ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
Site Water ◽  
Septic Tank Effluent

ABSTRACT Microbial diversity of septic tank effluent (STE) and the biomat that is formed as a result of STE infiltration on soil were characterized by 16S rRNA gene sequence analysis. Results indicate that microbial communities are different within control soil, STE, and the biomat and that microbes found in STE are not found in the biomat. The development of a stable soil biomat appears to provide the best on-site water treatment or protection for subsequent groundwater interactions of STE.

Sign in / Sign up

Export Citation Format

Share Document