scholarly journals Bioinformatics Analysis of Oral, Vaginal, and Rectal Microbial Profiles during Pregnancy: A Pilot Study on the Bacterial Co-Residence in Pregnant Women

2021 ◽  
Vol 9 (5) ◽  
pp. 1027
Author(s):  
Megumi Fudaba ◽  
Tomonori Kamiya ◽  
Daisuke Tachibana ◽  
Masayasu Koyama ◽  
Naoko Ohtani
Keyword(s):  
Preterm Labor ◽  
Bacterial Species ◽  
Bacterial Genome ◽  
Amplicon Sequencing ◽  
Bioinformatic Analysis ◽  
Lactobacillus Species ◽  
Sequencing Data ◽  
Associated Bacteria ◽  
16S Rrna Amplicon Sequencing ◽  
Threatened Preterm Labor

Preterm birth (PTB) and threatened preterm labor (TPL), an important pre-PTB state, are major obstetric complications during pregnancy. However, their triggers have not been fully elucidated. The vagina is dominated by Lactobacillus species (categorized as community state types; CSTs I, II, III, and V) or by mixed anaerobes (CST IV). An abundance of the latter is associated with bacterial vaginosis (BV) and BV-triggered PTB/TPL. To identify factors that influence the diversity of vaginal microbiota associated with BV and CST IV (BV-type) bacterial profile, we performed a bioinformatic analysis of the microbial taxa using 16S rRNA amplicon sequencing data of bacterial genome in oral, vaginal, and rectal samples collected from 58 pregnant Japanese women. Interestingly, common residence of BV-associated bacteria in the vagina and rectum was individually detected in the CST IV (non-Lactobacillus dominated) group by species-level Spearman correlation coefficient analysis, suggesting that the rectum acts as a reservoir of BV-associated bacterial species in the CST IV group. The current study provides evidence of bacterial co-residence in vagina and rectum in the non-Lactobacillus dominated group, which could be targeted to reduce the risk of preterm incidence in pregnancy.

scholarly journals Preterm Birth Is Correlated With Increased Oral Originated Microbiome in the Gut

2021 ◽  
Vol 11 ◽  
Author(s):  
Chunhua Yin ◽  
Jingrui Chen ◽  
Xuena Wu ◽  
Yeling Liu ◽  
Quan He ◽  
...  
Keyword(s):  
Preterm Birth ◽  
Gut Microbiome ◽  
Preterm Labor ◽  
Amplicon Sequencing ◽  
Oral Bacteria ◽  
Gut Bacteria ◽  
Oral Microbiome ◽  
16S Rrna Amplicon Sequencing ◽  
Threatened Preterm Labor ◽  
Adverse Pregnancy

BackgroundPreterm birth is one of the leading causes of perinatal morbidity and mortality. Gut microbiome dysbiosis is closely related to adverse pregnancy outcomes. However, the role of the gut microbiome in the pathogenesis of preterm birth remains poorly studied.MethodWe collected fecal samples from 41 women (cases presenting with threatened preterm labor =19, 11 of which delivered preterm; gestational age-matched no-labor controls, all of which delivered at term = 22) were recruited for the study. We performed 16S rRNA amplicon sequencing to compare the composition of the gut microbiome in threatened preterm labor cases and controls and among women who delivered preterm and at term. By annotating taxonomic biomarkers with the Human Oral Microbiome Database, we observed an increased abundance of potential oral-to-gut bacteria in preterm patients.ResultsPatients with preterm birth showed a distinct gut microbiome dysbiosis compared with those who delivered at term. Opportunistic pathogens, particularly Porphyromonas, Streptococcus, Fusobacterium, and Veillonella, were enriched, whereas Coprococcus and Gemmiger were markedly depleted in the preterm group. Most of the enriched bacteria were annotated oral bacteria using the Human Oral Microbiome Database. These potential oral-to-gut bacteria were correlated with clinical parameters that reflected maternal and fetal status.ConclusionsThis study suggests that patients who deliver preterm demonstrate altered gut microbiome that may contain higher common oral bacteria.

scholarly journals Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Caitlin M. Singleton ◽  
Francesca Petriglieri ◽  
Jannie M. Kristensen ◽  
Rasmus H. Kirkegaard ◽  
Thomas Y. Michaelsen ◽  
...  
Keyword(s):  
16S Rrna ◽  
Wastewater Treatment Plants ◽  
In Situ Hybridisation ◽  
Amplicon Sequencing ◽  
Rrna Genes ◽  
Fluorescence In Situ Hybridisation ◽  
Sequencing Data ◽  
High Quality ◽  
16S Rrna Amplicon Sequencing ◽  
Long Read

AbstractMicroorganisms play crucial roles in water recycling, pollution removal and resource recovery in the wastewater industry. The structure of these microbial communities is increasingly understood based on 16S rRNA amplicon sequencing data. However, such data cannot be linked to functional potential in the absence of high-quality metagenome-assembled genomes (MAGs) for nearly all species. Here, we use long-read and short-read sequencing to recover 1083 high-quality MAGs, including 57 closed circular genomes, from 23 Danish full-scale wastewater treatment plants. The MAGs account for ~30% of the community based on relative abundance, and meet the stringent MIMAG high-quality draft requirements including full-length rRNA genes. We use the information provided by these MAGs in combination with >13 years of 16S rRNA amplicon sequencing data, as well as Raman microspectroscopy and fluorescence in situ hybridisation, to uncover abundant undescribed lineages belonging to important functional groups.

scholarly journals SCAPP: an algorithm for improved plasmid assembly in metagenomes

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
David Pellow ◽  
Alvah Zorea ◽  
Maraike Probst ◽  
Ori Furman ◽  
Arik Segal ◽  
...  
Keyword(s):  
Bacterial Species ◽  
Bacterial Genome ◽  
Biological Knowledge ◽  
Assessment Procedure ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Human Gut ◽  
Double Stranded Dna ◽  
Wide Range ◽  
Python Package

Abstract Background Metagenomic sequencing has led to the identification and assembly of many new bacterial genome sequences. These bacteria often contain plasmids: usually small, circular double-stranded DNA molecules that may transfer across bacterial species and confer antibiotic resistance. These plasmids are generally less studied and understood than their bacterial hosts. Part of the reason for this is insufficient computational tools enabling the analysis of plasmids in metagenomic samples. Results We developed SCAPP (Sequence Contents-Aware Plasmid Peeler)—an algorithm and tool to assemble plasmid sequences from metagenomic sequencing. SCAPP builds on some key ideas from the Recycler algorithm while improving plasmid assemblies by integrating biological knowledge about plasmids. We compared the performance of SCAPP to Recycler and metaplasmidSPAdes on simulated metagenomes, real human gut microbiome samples, and a human gut plasmidome dataset that we generated. We also created plasmidome and metagenome data from the same cow rumen sample and used the parallel sequencing data to create a novel assessment procedure. Overall, SCAPP outperformed Recycler and metaplasmidSPAdes across this wide range of datasets. Conclusions SCAPP is an easy to use Python package that enables the assembly of full plasmid sequences from metagenomic samples. It outperformed existing metagenomic plasmid assemblers in most cases and assembled novel and clinically relevant plasmids in samples we generated such as a human gut plasmidome. SCAPP is open-source software available from: https://github.com/Shamir-Lab/SCAPP.

scholarly journals Dramatic differences in gut bacterial densities help to explain the relationship between diet and habitat in rainforest ants

2017 ◽  
Author(s):  
Jon G Sanders ◽  
Piotr Lukasik ◽  
Megan E Frederickson ◽  
Jacob A Russell ◽  
Ryuichi Koga ◽  
...  
Keyword(s):  
16S Rrna ◽  
Microbial Diversity ◽  
Tropical Rainforest ◽  
Amplicon Sequencing ◽  
Sequencing Data ◽  
Lowland Tropical Forest ◽  
16S Rrna Amplicon Sequencing ◽  
Microbial Symbionts ◽  
Microbial Symbiosis ◽  
Diversity Profiles

AbstractAbundance is a key parameter in microbial ecology, and important to estimates of potential metabolite flux, impacts of dispersal, and sensitivity of samples to technical biases such as laboratory contamination. However, modern amplicon-based sequencing techniques by themselves typically provide no information about the absolute abundance of microbes. Here, we use fluorescence microscopy and quantitative PCR as independent estimates of microbial abundance to test the hypothesis that microbial symbionts have enabled ants to dominate tropical rainforest canopies by facilitating herbivorous diets, and compare these methods to microbial diversity profiles from 16S rRNA amplicon sequencing. Through a systematic survey of ants from a lowland tropical forest, we show that the density of gut microbiota varies across several orders of magnitude among ant lineages, with median individuals from many genera only marginally above detection limits. Supporting the hypothesis that microbial symbiosis is important to dominance in the canopy, we find that the abundance of gut bacteria is positively correlated with stable isotope proxies of herbivory among canopy-dwelling ants, but not among ground-dwelling ants. Notably, these broad findings are much more evident in the quantitative data than in the 16S rRNA sequencing data. Our results help to resolve a longstanding question in tropical rainforest ecology, and have broad implications for the interpretation of sequence-based surveys of microbial diversity.

scholarly journals Compositional and functional analysis of the gut microbiota of Radix auricularia (Linnaeus) via high-throughput Illumina sequencing

2018 ◽  
Author(s):  
Zongfu Hu ◽  
Xi CHEN ◽  
Jie CHANG ◽  
Jianhua YU ◽  
Qing TONG ◽  
...  
Keyword(s):  
16S Rrna ◽  
Bacterial Species ◽  
Intestinal Bacteria ◽  
Amplicon Sequencing ◽  
Freshwater Snail ◽  
Gonadal Development ◽  
Growth Stages ◽  
Rrna Gene ◽  
16S Rrna Amplicon Sequencing ◽  
Radix Auricularia

Widely distributed across the world, the freshwater snail Radix auricularia plays an important role in freshwater systems. In this study, gut bacterial communities of R. auricularia were characterized using 16S rRNA amplicon sequencing, then intestinal bacteria were compared at different growth stages: adult snails (AS) (with complete gonadal development) and juvenile snails (JS) (with incomplete gonadal development). We obtained 251,072 high quality sequences which were clustered into 1,196 operational taxonomic units (OTUs) with 97% sequence identity. The predominant phyla were Proteobacteria and Cyanobacteria, followed by Chloroflexi, Firmicutes, and Actinobacteria. Other bacterial species such as Tenericutes, Bacteroidetes, Fusobacteria and Verrucomicrobia were present to a lesser extent. 52 bacterial families and 55 genera were found in > 1% of each sample. A large number of species could not be successfully identified. 469 core OTUs were found to make up 39.38% of all OTUs and 88.38% of all sequences. Samples obtained from juvenile organisms possessed higher ratios of Ruminococcaceae, Subdoligranulum, and Faecalibacterium than adult species. Furthermore, 16S rRNA gene data was used to predict function, showing that genes related to metabolism and environmental information processing were rich in snail samples.

scholarly journals A high-resolution pipeline for 16S-sequencing identifies bacterial strains in human microbiome

2019 ◽  
Author(s):  
Igor Segota ◽  
Tao Long
Keyword(s):  
Bacterial Species ◽  
Human Microbiome ◽  
Amplicon Sequencing ◽  
R Package ◽  
Strain Level ◽  
Sequencing Data ◽  
Bacterial Strains ◽  
16S Sequencing ◽  
16S Amplicon Sequencing ◽  
Sequencing Data Analysis

We developed a High-resolution Microbial Analysis Pipeline (HiMAP) for 16S amplicon sequencing data analysis, aiming at bacterial species or strain-level identification from human microbiome to enable experimental validation for causal effects of the associated bacterial strains on health and diseases. HiMAP achieved higher accuracy in identifying species in human microbiome mock community than other pipelines. HiMAP identified majority of the species, with strain-level resolution wherever possible, as detected by whole genome shotgun sequencing using MetaPhlAn2 and reported comparable relative abundances. HiMAP is an open-source R package available at https://github.com/taolonglab/himap.

scholarly journals 77 Responses to alfalfa supplementation in mice

2019 ◽  
Vol 97 (Supplement_2) ◽  
pp. 45-46
Author(s):  
Krysten Fries-Craft ◽  
Justin Anast ◽  
Stephan Schmitz-Esser ◽  
Elizabeth A Bobeck
Keyword(s):  
Amplicon Sequencing ◽  
Chloroform Extract ◽  
Citrobacter Rodentium ◽  
Sequencing Data ◽  
Discrimination Analysis ◽  
16S Rrna Amplicon Sequencing ◽  
Linear Discrimination ◽  
Alfalfa Hay ◽  
Cytokine Analysis ◽  
System 2

Abstract Anecdotal evidence suggests health benefits from feeding late cutting alfalfa to non-ruminants, but there is a lack of published literature to support these claims. The objective was to compare early (1st) and late (5th) cutting alfalfa as ground hay, aqueous, or chloroform-extracted hay in combination with a gastrointestinal challenge to understand the effect of supplementation form and cutting on the overall health, microbiome, and immune system of mice. 163 C57BL/6J mice were housed for 35 d (Innovive system; 2–4 mice/cage) and fed treatments that consisted of an 18% protein rodent diet (alfalfa-free control), or control supplemented with 1st or 5th cutting 9% ground alfalfa hay, 0.25% aqueous extract (AAE), or 0.25% chloroform extract (CAE). After a 14 d enrichment period, 6 mice/treatment were euthanized for baseline tissue and digesta sampling, and remaining mice were orally gavaged with 2x1010 CFU Citrobacter rodentium. On d18, 22, 28, and 35, 4 mice/treatment were euthanized for sampling. Body weight (BW) and feed intake (FI) were recorded, 13 serum cytokines were measured, and changes in the microbial communities were analyzed using 16S rRNA amplicon sequencing. Data were analyzed using PROC MIXED and linear discrimination analysis effect size (LEfSe), with significance at P ≤ 0.05. No BW differences were observed between treatments at the key timepoints (P > 0.05). Mice fed hay diets ate 16% more per day during the enrichment period (P = 0.03), 19% more from d14–18 (P = 0.001), and 17% more from d18–22 (P = 0.03) versus mice fed AAE. Citrobacter rodentium infection was confirmed via MiSeq in colon digesta. Significant shifts in microbial taxa were observed in mice fed alfalfa hay regardless of cutting (P < 0.05). Cytokine analysis, flow cytometry, and microbiome analysis is ongoing. Preliminary results show that alfalfa form significantly impacts FI and microbiome while cutting impacts weight (P < 0.05).

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 SCAPP: An algorithm for improved plasmid assembly in metagenomes

2020 ◽  
Author(s):  
David Pellow ◽  
Alvah Zorea ◽  
Maraike Probst ◽  
Ori Furman ◽  
Arik Segal ◽  
...  
Keyword(s):  
Bacterial Species ◽  
Bacterial Genome ◽  
Biological Knowledge ◽  
Assessment Procedure ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Human Gut ◽  
Double Stranded Dna ◽  
Wide Range ◽  
Python Package

Background: Metagenomic sequencing has led to the identification and assembly of many new bacterial genome sequences. These bacteria often contain plasmids: usually small, circular double-stranded DNA molecules that may transfer across bacterial species and confer antibiotic resistance. These plasmids are generally less studied and understood than their bacterial hosts. Part of the reason for this is insufficient computational tools enabling the analysis of plasmids in metagenomic samples. Results: We developed SCAPP (Sequence Contents-Aware Plasmid Peeler) - an algorithm and tool to assemble plasmid sequences from metagenomic sequencing. SCAPP builds on some key ideas from the Recycler algorithm while improving plasmid assemblies by integrating biological knowledge about plasmids. We compared the performance of SCAPP to Recycler and metaplasmidSPAdes on simulated metagenomes, real human gut microbiome samples, and a human gut plasmidome dataset that we generated. We also created plasmidome and metagenome data from the same cow rumen sample and used the parallel sequencing data to create a novel assessment procedure. Overall, SCAPP outperformed Recycler and metaplasmidSPAdes across this wide range of datasets. Conclusions: SCAPP is an easy to use Python package that enables the assembly of full plasmid sequences from metagenomic samples. It outperformed existing metagenomic plasmid assemblers in most cases, and assembled novel and clinically relevant plasmids in samples we generated such as a human gut plasmidome. SCAPP is open-source software available from: https://github.com/Shamir-Lab/SCAPP.

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