scholarly journals A multi-view model for relative and absolute microbial abundances

2019 ◽  
Author(s):  
Brian D. Williamson ◽  
James P. Hughes ◽  
Amy D. Willis
Keyword(s):  
Relative Abundance ◽  
Estimation Error ◽  
Bacterial Species ◽  
Critical Role ◽  
Sensitivity Study ◽  
Universal Primers ◽  
Rrna Gene ◽  
Absolute Abundance ◽  
Abundance Data ◽  
The Absolute

AbstractThe absolute abundance of bacterial taxa in human host-associated environments play a critical role in reproductive and gastrointestinal health. However, obtaining the absolute abundance of many bacterial species is typically prohibitively expensive. In contrast, relative abundance data for many species is comparatively cheap and easy to collect (e.g., with universal primers for the 16S rRNA gene). In this paper, we propose a method to jointly model relative abundance data for many taxa and absolute abundance data for a subset of taxa. Our method provides point and interval estimates for the absolute abundance of all taxa. Crucially, our proposal accounts for differences in the efficiency of taxon detection in the relative and absolute abundance data. We show that modeling taxon-specific efficiencies substantially reduces the estimation error for absolute abundance, and controls the coverage of interval estimators. We demonstrate the performance of our proposed method via a simulation study, a sensitivity study where we jackknife the taxa with observed absolute abundances, and a study of women with bacterial vaginosis.

scholarly journals Rumen Sampling Methods Bias Bacterial Communities Observed

2021 ◽  
Author(s):  
Jill V. Hagey ◽  
Maia Laabs ◽  
Elizabeth A. Maga ◽  
Edward J. DePeters
Keyword(s):  
Relative Abundance ◽  
Critical Role ◽  
Cost Effective ◽  
Feed Additives ◽  
Rrna Gene ◽  
Stomach Tube ◽  
Fecal Samples ◽  
Rumen Microbes ◽  
Lower Abundance ◽  
The Family

AbstractThe rumen is a complex ecosystem that plays a critical role in our efforts to improve feed efficiency of cattle and reduce their environmental impacts. Sequencing of the 16S rRNA gene provides a powerful tool to survey shifts in the microbial community in response to feed additives and dietary changes. Oral stomach tubing a cow for a rumen sample is a rapid, cost-effective alternative to rumen cannulation for acquiring rumen samples. In this study, we determined how sampling method, as well as type of sample collected (liquid vs solid), bias the microbial populations observed. The abundance of major archaeal populations was not different at the family level in samples acquired via rumen cannula or stomach tube. Liquid samples were enriched for the order WCHB1-41 (phylum Kiritimatiellaeota) as well as the family Prevotellaceae and had significantly lower abundance of Lachnospiraceae compared with grab samples from the rumen cannula. Solid samples most closely resembled the grab samples; therefore, inclusion of particulate matter is important for an accurate representation of the rumen microbes. Stomach tube samples were the most variable and were most representative of the liquid phase. In comparison with a grab sample, stomach tube samples had significantly lower abundance of Lachnospiraceae, Fibrobacter and Treponema. Fecal samples did not reflect the community composition of the rumen, as fecal samples had significantly higher relative abundance of Ruminococcaceae and significantly lower relative abundance of Lachnospiraceae compared with samples from the rumen.

scholarly journals Composition and diversity of the subgingival microbiome and its relationship with age in postmenopausal women: an epidemiologic investigation

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Michael J. LaMonte ◽  
Robert J. Genco ◽  
Michael J. Buck ◽  
Daniel I. McSkimming ◽  
Lu Li ◽  
...  
Keyword(s):  
Postmenopausal Women ◽  
Relative Abundance ◽  
Multiple Testing ◽  
Statistical Significance ◽  
Bacterial Species ◽  
Age Groups ◽  
Later Life ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Age Range

Abstract Background The extent to which the composition and diversity of the oral microbiome varies with age is not clearly understood. Methods The 16S rRNA gene of subgingival plaque in 1219 women, aged 53–81 years, was sequenced and its taxonomy annotated against the Human Oral Microbiome Database (v.14.5). Composition of the subgingival microbiome was described in terms of centered log(2)-ratio (CLR) transformed OTU values, relative abundance, and prevalence. Correlations between microbiota abundance and age were evelauted using Pearson Product Moment correlations. P-values were corrected for multiple testing using the Bonferroni method. Results Of the 267 species identified overall, Veillonella dispar was the most abundant bacteria when described by CLR OTU (mean 8.3) or relative abundance (mean 8.9%); whereas Streptococcus oralis, Veillonella dispar and Veillonella parvula were most prevalent (100%, all) when described as being present at any amount. Linear correlations between age and several CLR OTUs (Pearson r = − 0.18 to 0.18), of which 82 (31%) achieved statistical significance (P < 0.05). The correlations lost significance following Bonferroni correction. Twelve species that differed across age groups (each corrected P < 0.05); 5 (42%) were higher in women ages 50–59 compared to ≥70 (corrected P < 0.05), and 7 (48%) were higher in women 70 years and older. Conclusions We identified associations between several bacterial species and age across the age range of postmenopausal women studied. Understanding the functions of these bacteria could identify intervention targets to enhance oral health in later life.

scholarly journals Pressure ulcers microbiota dynamics and wound evolution

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Catherine Dunyach-Remy ◽  
Florian Salipante ◽  
Jean-Philippe Lavigne ◽  
Maxime Brunaud ◽  
Christophe Demattei ◽  
...  
Keyword(s):  
Spinal Cord ◽  
Relative Abundance ◽  
Pressure Ulcers ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Sequencing Analysis ◽  
Neurological Rehabilitation ◽  
Rehabilitation Centre ◽  
Promising Target ◽  
Cord Injury

AbstractBacterial species and their role in delaying the healing of pressure ulcers (PU) in spinal cord injury (SCI) patients have not been well described. This pilot study aimed to characterise the evolution of the cutaneous microbiota of PU in SCI cohort. Twenty-four patients with SCI from a French neurological rehabilitation centre were prospectively included. PU tissue biopsies were performed at baseline (D0) and 28 days (D28) and analysed using 16S rRNA gene-based sequencing analysis of the V3–V4 region. At D0, if the overall relative abundance of genus highlighted a large proportion of Staphylococcus, Anaerococcus and Finegoldia had a significantly higher relative abundance in wounds that stagnated or worsened in comparison with those improved at D28 (3.74% vs 0.05%; p = 0.015 and 11.02% versus 0.16%; p = 0.023, respectively). At D28, Proteus and Morganella genera were only present in stagnated or worsened wounds with respectively 0.02% (p = 0.003) and 0.01% (p = 0.02). Moreover, Proteus, Morganella, Anaerococcus and Peptoniphilus were associated within the same cluster, co-isolated from biopsies that had a poor evolution. This pathogroup could be a marker of wound degradation and Proteus could represent a promising target in PU management.

scholarly journals Complementing 16S rRNA Gene Amplicon Sequencing with Total Bacterial Load To Infer Absolute Species Concentrations in the Vaginal Microbiome

mSystems ◽  
2020 ◽  
Vol 5 (2) ◽  
Author(s):  
Florencia A. Tettamanti Boshier ◽  
Sujatha Srinivasan ◽  
Anthony Lopez ◽  
Noah G. Hoffman ◽  
Sean Proll ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Relative Abundance ◽  
Bacterial Species ◽  
Bacterial Load ◽  
Amplicon Sequencing ◽  
Individual Species ◽  
Rrna Gene ◽  
Vaginal Microbiome ◽  
Bacterial Concentrations

ABSTRACT Whereas 16S rRNA gene amplicon sequencing quantifies relative abundances of bacterial taxa, variation in total bacterial load between samples restricts its ability to reflect absolute concentrations of individual bacterial species. Quantitative PCR (qPCR) can quantify individual species, but it is not practical to develop a suite of qPCR assays for every bacterium present in a diverse sample. We sought to determine the accuracy of an inferred measure of bacterial concentration using total bacterial load and relative abundance. We analyzed 1,320 samples from 20 women with a history of frequent bacterial vaginosis who self-collected vaginal swabs daily over 60 days. We inferred bacterial concentrations by taking the product of species relative abundance (assessed by 16S rRNA gene amplicon sequencing) and bacterial load (measured by broad-range 16S rRNA gene qPCR). Log10-converted inferred concentrations correlated with targeted qPCR (r = 0. 935, P < 2.2e–16) for seven key bacterial species. The mean inferred concentration error varied across bacteria, with rarer bacteria associated with larger errors. A total of 92% of the >0.5-log10 errors occurred when the relative abundance was <10%. Many errors occurred during early bacterial expansion from or late contraction to low abundance. When the relative abundance of a species is >10%, inferred concentrations are reliable proxies for targeted qPCR in the vaginal microbiome. However, targeted qPCR is required to capture bacteria at low relative abundance and is preferable for characterizing growth and decay kinetics of single species. IMPORTANCE Microbiome studies primarily use 16S rRNA gene amplicon sequencing to assess the relative abundance of bacterial taxa in a community. However, these measurements do not accurately reflect absolute taxon concentrations. We sought to determine whether the product of species’ relative abundance and total bacterial load measured by broad-range qPCR is an accurate proxy for individual species’ concentrations, as measured by taxon-specific qPCR assays. Overall, the inferred bacterial concentrations were a reasonable proxy of species-specific qPCR values, particularly when bacteria are present at a higher relative abundance. This approach offers an opportunity to assess the concentrations of bacterial species and how they change in a community over time without developing individual qPCR assays for each taxon.

Presence of Bacteria in Spontaneous Achilles Tendon Ruptures

2017 ◽  
Vol 45 (9) ◽  
pp. 2061-2067 ◽  
Author(s):  
Christer G. Rolf ◽  
Sai-Chuen Fu ◽  
Chelsea Hopkins ◽  
Ju Luan ◽  
Margaret Ip ◽  
...  
Keyword(s):  
Achilles Tendon ◽  
Acl Reconstruction ◽  
Bacterial Infections ◽  
Bacterial Species ◽  
Hamstring Tendon ◽  
Universal Primers ◽  
Rrna Gene ◽  
Low Grade ◽  
Bacterial Dna ◽  
Normal Tendon

Background: The structural pathology of Achilles tendon (AT) ruptures resembles tendinopathy, but the causes remain unknown. Recently, a number of diseases were found to be attributed to bacterial infections, resulting in low-grade inflammation and progressive matrix disturbance. The authors speculate that spontaneous AT ruptures may also be influenced by the presence of bacteria. Hypothesis: Bacteria are present in ruptured ATs but not in healthy tendons. Study Design: Cross-sectional study; Level of evidence, 3. Methods: Patients with spontaneous AT ruptures and patients undergoing anterior cruciate ligament (ACL) reconstruction were recruited for this study. During AT surgical repair, excised tendinopathic tissue was collected, and healthy tendon samples were obtained as controls from hamstring tendon grafts used in ACL reconstruction. Half of every sample was reserved for DNA extraction and the other half for histology. Polymerase chain reaction (PCR) was conducted using 16S rRNA gene universal primers, and the PCR products were sequenced for the identification of bacterial species. A histological examination was performed to compare tendinopathic changes in the case and control samples. Results: Five of 20 AT rupture samples were positive for the presence of bacterial DNA, while none of the 23 hamstring tendon samples were positive. Sterile operating and experimental conditions and tests on samples, controlling for harvesting and processing procedures, ruled out the chance of postoperative bacterial contamination. The species identified predominantly belonged to the Staphylococcus genus. AT rupture samples exhibited histopathological features characteristic of tendinopathy, and most healthy hamstring tendon samples displayed normal tendon features. There were no apparent differences in histopathology between the bacterial DNA–positive and bacterial DNA–negative AT rupture samples. Conclusion: The authors have demonstrated the presence of bacterial DNA in ruptured AT samples. It may suggest the potential involvement of bacteria in spontaneous AT ruptures.

scholarly journals Complementing 16S rRNA gene amplicon sequencing with estimates of total bacterial load to infer absolute species concentrations in the vaginal microbiome

2019 ◽  
Author(s):  
Florencia Tettamanti Boshier ◽  
Sujatha Srinivasan ◽  
Anthony Lopez ◽  
Noah G. Hoffman ◽  
Sean Proll ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Vaginosis ◽  
Relative Abundance ◽  
Bacterial Species ◽  
Bacterial Load ◽  
Amplicon Sequencing ◽  
Individual Species ◽  
Rrna Gene ◽  
Associated Bacteria

Whereas 16S rRNA gene amplicon sequencing quantifies relative abundances of bacterial taxa, variation in total bacterial load between samples restricts its ability to reflect absolute concentration of individual species. Quantitative PCR (qPCR) can quantify individual species, but it is not practical to develop a suite of qPCR assays for every bacterium present in a diverse sample. We analyzed 1320 samples from 20 women with a history of frequent bacterial vaginosis, who self-collected vaginal swabs daily over 60 days. We inferred bacterial concentrations by taking the product of species relative abundance (assessed by 16S rRNA gene amplicon sequencing) and total bacterial load (measured by broad-range 16S rRNA gene qPCR). Log10-converted inferred concentrations correlated with targeted qPCR (r = 0. 935, p<2.2e-16) for seven key bacterial species. The mean inferred concentration error varied across bacteria, with rarer bacterial vaginosis-associated bacteria associated with larger errors. 92% of errors >0.5 log10 occurred when relative abundance was <10%. Many errors occurred during early bacterial expansion or late contraction. When relative abundance of a species is >10%, inferred concentrations are reliable proxies for targeted qPCR. However, targeted qPCR is required to capture bacteria at low relative abundance, particularly with BV-associated bacteria during the early onset of bacterial vaginosis.

scholarly journals Contemporary fisheries stock assessment: many issues still remain

2014 ◽  
Vol 72 (1) ◽  
pp. 7-18 ◽  
Author(s):  
Mark N. Maunder ◽  
Kevin R. Piner
Keyword(s):  
Information Content ◽  
Relative Abundance ◽  
Stock Assessment ◽  
Diagnostic Methods ◽  
Natural Mortality ◽  
Absolute Abundance ◽  
Substantial Impact ◽  
Composition Data ◽  
The Absolute ◽  
Management Advice

Abstract Interpretation of data used in fisheries assessment and management requires knowledge of population (e.g. growth, natural mortality, and recruitment), fisheries (e.g. selectivity), and sampling processes. Without this knowledge, assumptions need to be made, either implicitly or explicitly based on the methods used. Incorrect assumptions can have a substantial impact on stock assessment results and management advice. Unfortunately, there is a lack of understanding of these processes for most, if not all, stocks and even for processes that have traditionally been assumed to be well understood (e.g. growth and selectivity). We use information content of typical fisheries data that is informative about absolute abundance to illustrate some of the main issues in fisheries stock assessment. We concentrate on information about absolute abundance from indices of relative abundance combined with catch, and age and length-composition data and how the information depends on knowledge of population, fishing, and sampling processes. We also illustrate two recently developed diagnostic methods that can be used to evaluate the absolute abundance information content of the data. Finally, we discuss some of the reasons for the slowness of progress in fisheries stock assessment.

scholarly journals Measuring the absolute abundance of the microbiome by adding yeast containing 16S rRNA gene from a hyperthermophile

2021 ◽  
Vol 10 (4) ◽  
Author(s):  
Ju Yeong Kim ◽  
Myung‐hee Yi ◽  
Myungjun Kim ◽  
Seogwon Lee ◽  
Hye Su Moon ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
Absolute Abundance ◽  
The Absolute

scholarly journals Species-level evaluation of the human respiratory microbiome

GigaScience ◽  
2020 ◽  
Vol 9 (4) ◽  
Author(s):  
Olufunmilola Ibironke ◽  
Lora R McGuinness ◽  
Shou-En Lu ◽  
Yaquan Wang ◽  
Sabiha Hussain ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Bronchoalveolar Lavage ◽  
Relative Abundance ◽  
Bacterial Species ◽  
Species Level ◽  
Rrna Gene ◽  
Human Respiratory Tract ◽  
Oxford Nanopore ◽  
Ribosomal Operons ◽  
Gene Database

Abstract Background Changes to human respiratory tract microbiome may contribute significantly to the progression of respiratory diseases. However, there are few studies examining the relative abundance of microbial communities at the species level along the human respiratory tract. Findings Bronchoalveolar lavage, throat swab, mouth rinse, and nasal swab samples were collected from 5 participants. Bacterial ribosomal operons were sequenced using the Oxford Nanopore MinION to determine the relative abundance of bacterial species in 4 compartments along the respiratory tract. More than 1.8 million raw operon reads were obtained from the participants with ∼600,000 rRNA reads passing quality assurance/quality control (70–95% identify; &gt;1,200 bp alignment) by Discontiguous MegaBLAST against the EZ BioCloud 16S rRNA gene database. Nearly 3,600 bacterial species were detected overall (&gt;750 bacterial species within the 5 dominant phyla: Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, and Fusobacteria. The relative abundance of bacterial species along the respiratory tract indicated that most microbes (95%) were being passively transported from outside into the lung. However, a small percentage (&lt;5%) of bacterial species were at higher abundance within the lavage samples. The most abundant lung-enriched bacterial species were Veillonella dispar and Veillonella atypica while the most abundant mouth-associated bacterial species were Streptococcus infantis and Streptococcus mitis. Conclusions Most bacteria detected in lower respiratory samples do not seem to colonize the lung. However, &gt;100 bacterial species were found to be enriched in bronchoalveolar lavage samples (compared to mouth/nose) and may play a substantial role in lung health.

scholarly journals Association of Bitter Taste Receptor T2R38 Polymorphisms, Oral Microbiota, and Rheumatoid Arthritis

2021 ◽  
Vol 43 (3) ◽  
pp. 1460-1472
Author(s):  
Vivianne Cruz de Jesus ◽  
Manu Singh ◽  
Robert J. Schroth ◽  
Prashen Chelikani ◽  
Carol A. Hitchon
Keyword(s):  
Rheumatoid Arthritis ◽  
Relative Abundance ◽  
Bitter Taste ◽  
Bacterial Species ◽  
Taste Receptor ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Oral Microbiota ◽  
Microbial Composition ◽  
The Impact

The association of taste genetics and the oral microbiome in autoimmune diseases such as rheumatoid arthritis (RA) has not been reported. We explored a novel oral mucosal innate immune pathway involving the bitter taste G protein-coupled receptor T2R38. This case–control study aimed to evaluate whether T2R38 polymorphisms associate with the buccal microbial composition in RA. Genomic DNA was obtained from buccal swabs of 35 RA patients and 64 non-RA controls. TAS2R38 genotypes were determined by Sanger sequencing. The buccal microbiome was assessed by Illumina MiSeq sequencing of the V4-16S rRNA gene. Bacterial community differences were analyzed with alpha and beta diversity measures. Linear discriminant analysis effect size identified taxa discriminating between RA versus non-RA and across TAS2R38 genotypes. TAS2R38 genotype frequency was similar between RA and non-RA controls (PAV/PAV; PAV/AVI; AVI/AVI: RA 42.9%; 45.7%; 11.4% versus controls 32.8%; 48.4%; 18.8%, chi-square (2, N = 99) = 2.1, p = 0.35). The relative abundance of Porphyromonas, among others, differed between RA and non-RA controls. The relative abundance of several bacterial species also differed across TAS2R38 genotypes. These findings suggest an association between T2R38 polymorphisms and RA buccal microbial composition. However, further research is needed to understand the impact of T2R38 in oral health and RA development.

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