Comparative meta-RNA-seq of the vaginal microbiota and differential expression by Lactobacillus iners in health and dysbiosis.

Abstract:

BACKGROUND:Bacterial vaginosis (BV), the most common vaginal condition of reproductive-aged women, is associated with a highly diverse and heterogeneous microbiota. Here we present a proof-of-principle analysis to uncover the function of the microbiota using meta-RNA-seq to uncover genes and pathways that potentially differentiate healthy vaginal microbial communities from those in the dysbiotic state of bacterial vaginosis (BV). RESULTS:The predominant organism, Lactobacillus iners, was present in both conditions and showed a differing expression profile in BV compared to healthy. Despite its minimal genome, L. iners differentially expressed over 10% of its gene complement. Notably, in a BV environment L. iners increased expression of a cholesterol-dependent cytolysin, and of mucin and glycerol transport and related metabolic enzymes. Genes belonging to a CRISPR system were greatly upregulated suggesting that bacteriophage influence the community. Reflective of L. iners, the bacterial community as a whole demonstrated a preference for glycogen and glycerol as carbon sources under BV conditions. The predicted end-products of metabolism under BV conditions include an abundance of succinate and other short-chain fatty-acids, while healthy conditions are predicted to largely contain lactic acid. CONCLUSIONS:Our study underscores the importance of understanding the functional activity of the bacterial community in addition to characterizing the population structure when investigating the human microbiome.

journal_name

Microbiome

journal_title

Microbiome

authors

Macklaim JM,Fernandes AD,Di Bella JM,Hammond JA,Reid G,Gloor GB

doi

10.1186/2049-2618-1-12

subject

Has Abstract

pub_date

2013-04-12 00:00:00

pages

12

issue

1

issn

2049-2618

pii

2049-2618-1-12

journal_volume

1

pub_type

杂志文章
  • Dichotomous development of the gut microbiome in preterm infants.

    abstract:BACKGROUND:Preterm infants are at risk of developing intestinal dysbiosis with an increased proportion of Gammaproteobacteria. In this study, we sought the clinical determinants of the relative abundance of feces-associated Gammaproteobacteria in very low birth weight (VLBW) infants. Fecal microbiome was characterized ...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-018-0547-8

    authors: Ho TTB,Groer MW,Kane B,Yee AL,Torres BA,Gilbert JA,Maheshwari A

    更新日期:2018-09-12 00:00:00

  • Uncovering complex microbiome activities via metatranscriptomics during 24 hours of oral biofilm assembly and maturation.

    abstract:BACKGROUND:Dental plaque is composed of hundreds of bacterial taxonomic units and represents one of the most diverse and stable microbial ecosystems associated with the human body. Taxonomic composition and functional capacity of mature plaque is gradually shaped during several stages of community assembly via processe...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-018-0591-4

    authors: Edlund A,Yang Y,Yooseph S,He X,Shi W,McLean JS

    更新日期:2018-12-06 00:00:00

  • (Dis)Trust your gut: the gut microbiome in age-related inflammation, health, and disease.

    abstract::Chronic inflammation represents one of the most consistent biologic features of aging. However, the precise etiology of persistent low-grade increases in inflammation remains unclear. Recent evidence suggests that the gut microbiome may play a key role in age-related inflammation. Indeed, several studies have indicate...

    journal_title:Microbiome

    pub_type: 杂志文章,评审

    doi:10.1186/s40168-017-0296-0

    authors: Buford TW

    更新日期:2017-07-14 00:00:00

  • Diet shapes the gut microbiome of pigs during nursing and weaning.

    abstract:BACKGROUND:The newborn mammal is rapidly colonized by a complex microbial community, whose importance for host health is becoming increasingly clear. Understanding the forces that shape the early community, especially during the nursing period, is critical to gain insight into how this consortium of microbes is assembl...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-015-0091-8

    authors: Frese SA,Parker K,Calvert CC,Mills DA

    更新日期:2015-07-01 00:00:00

  • 16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice.

    abstract:BACKGROUND:Characterisation of the bacterial composition of the gut microbiota is increasingly carried out with a view to establish the role of different bacterial species in causation or prevention of disease. It is thus essential that the methods used to determine the microbial composition are robust. Here, several w...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-015-0087-4

    authors: Walker AW,Martin JC,Scott P,Parkhill J,Flint HJ,Scott KP

    更新日期:2015-06-22 00:00:00

  • Fine metagenomic profile of the Mediterranean stratified and mixed water columns revealed by assembly and recruitment.

    abstract:BACKGROUND:The photic zone of aquatic habitats is subjected to strong physicochemical gradients. To analyze the fine-scale variations in the marine microbiome, we collected seven samples from a single offshore location in the Mediterranean at 15 m depth intervals during a period of strong stratification, as well as two...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-018-0513-5

    authors: Haro-Moreno JM,López-Pérez M,de la Torre JR,Picazo A,Camacho A,Rodriguez-Valera F

    更新日期:2018-07-10 00:00:00

  • Seasonal and algal diet-driven patterns of the digestive microbiota of the European abalone Haliotis tuberculata, a generalist marine herbivore.

    abstract:BACKGROUND:Holobionts have a digestive microbiota with catabolic abilities allowing the degradation of complex dietary compounds for the host. In terrestrial herbivores, the digestive microbiota is known to degrade complex polysaccharides from land plants while in marine herbivores, the digestive microbiota is poorly c...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-018-0430-7

    authors: Gobet A,Mest L,Perennou M,Dittami SM,Caralp C,Coulombet C,Huchette S,Roussel S,Michel G,Leblanc C

    更新日期:2018-03-27 00:00:00

  • Mobile antibiotic resistome in wastewater treatment plants revealed by Nanopore metagenomic sequencing.

    abstract:BACKGROUND:Wastewater treatment plants (WWTPs) are recognized as hotspots for horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). Despite our understanding of the composition and distribution of ARGs in WWTPs, the genetic location, host, and fate of ARGs remain largely unknown. RESULTS:In this study,...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-019-0663-0

    authors: Che Y,Xia Y,Liu L,Li AD,Yang Y,Zhang T

    更新日期:2019-03-21 00:00:00

  • Differential dynamics of microbial community networks help identify microorganisms interacting with residue-borne pathogens: the case of Zymoseptoria tritici in wheat.

    abstract:BACKGROUND:Wheat residues are a crucial determinant of the epidemiology of Septoria tritici blotch, as they support the sexual reproduction of the causal agent Zymoseptoria tritici. We aimed to characterize the effect of infection with this fungal pathogen on the microbial communities present on wheat residues and to i...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-019-0736-0

    authors: Kerdraon L,Barret M,Laval V,Suffert F

    更新日期:2019-08-30 00:00:00

  • Picodroplet partitioned whole genome amplification of low biomass samples preserves genomic diversity for metagenomic analysis.

    abstract:BACKGROUND:Whole genome amplification (WGA) is a challenging, key step in metagenomic studies of samples containing minute amounts of DNA, such as samples from low biomass environments. It is well known that multiple displacement amplification (MDA), the most commonly used WGA method for microbial samples, skews the ge...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-016-0197-7

    authors: Hammond M,Homa F,Andersson-Svahn H,Ettema TJ,Joensson HN

    更新日期:2016-10-06 00:00:00

  • Improved OTU-picking using long-read 16S rRNA gene amplicon sequencing and generic hierarchical clustering.

    abstract:BACKGROUND:High-throughput bacterial 16S rRNA gene sequencing followed by clustering of short sequences into operational taxonomic units (OTUs) is widely used for microbiome profiling. However, clustering of short 16S rRNA gene reads into biologically meaningful OTUs is challenging, in part because nucleotide variation...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-015-0105-6

    authors: Franzén O,Hu J,Bao X,Itzkowitz SH,Peter I,Bashir A

    更新日期:2015-10-05 00:00:00

  • Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers.

    abstract:BACKGROUND:Alterations of gut microbiota are associated with colorectal cancer (CRC) in different populations and several bacterial species were found to contribute to the tumorigenesis. The potential use of gut microbes as markers for early diagnosis has also been reported. However, cohort specific noises may distort ...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-018-0451-2

    authors: Dai Z,Coker OO,Nakatsu G,Wu WKK,Zhao L,Chen Z,Chan FKL,Kristiansen K,Sung JJY,Wong SH,Yu J

    更新日期:2018-04-11 00:00:00

  • Correction to: An exploration of Prevotella-rich microbiomes in HIV and men who have sex with men.

    abstract::Following publication of the original article [1], the authors reported an error in Fig. 2. The original Fig. 2 has been incorrectly replaced with the Supplementary Fig. 2. The correct Fig. 2 is presented here. ...

    journal_title:Microbiome

    pub_type: 杂志文章,已发布勘误

    doi:10.1186/s40168-020-00829-6

    authors: Armstrong AJS,Shaffer M,Nusbacher NM,Griesmer C,Fiorillo S,Schneider JM,Neff CP,Li SX,Fontenot AP,Campbell T,Palmer BE,Lozupone CA

    更新日期:2020-04-06 00:00:00

  • Rhizosphere microbiomes diverge among Populus trichocarpa plant-host genotypes and chemotypes, but it depends on soil origin.

    abstract:BACKGROUND:Plants have developed defense strategies for phytopathogen and herbivore protection via coordinated metabolic mechanisms. Low-molecular weight metabolites produced within plant tissues, such as salicylic acid, represent one such mechanism which likely mediates plant - microbe interactions above and below gro...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-019-0668-8

    authors: Veach AM,Morris R,Yip DZ,Yang ZK,Engle NL,Cregger MA,Tschaplinski TJ,Schadt CW

    更新日期:2019-05-18 00:00:00

  • The unsolved problem of otitis media in indigenous populations: a systematic review of upper respiratory and middle ear microbiology in indigenous children with otitis media.

    abstract:BACKGROUND:Otitis media (OM) imposes a great burden of disease in indigenous populations around the world, despite a variety of treatment and prevention programs. Improved understanding of the pathogenesis of OM in indigenous populations is required to advance treatment and reduce prevalence. We conducted a systematic ...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-018-0577-2

    authors: Coleman A,Wood A,Bialasiewicz S,Ware RS,Marsh RL,Cervin A

    更新日期:2018-11-05 00:00:00

  • Rumen metagenome and metatranscriptome analyses of low methane yield sheep reveals a Sharpea-enriched microbiome characterised by lactic acid formation and utilisation.

    abstract:BACKGROUND:Enteric fermentation by farmed ruminant animals is a major source of methane and constitutes the second largest anthropogenic contributor to global warming. Reducing methane emissions from ruminants is needed to ensure sustainable animal production in the future. Methane yield varies naturally in sheep and i...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-016-0201-2

    authors: Kamke J,Kittelmann S,Soni P,Li Y,Tavendale M,Ganesh S,Janssen PH,Shi W,Froula J,Rubin EM,Attwood GT

    更新日期:2016-10-19 00:00:00

  • Optimal screening and donor management in a public stool bank.

    abstract:BACKGROUND:Fecal microbiota transplantation is an effective treatment for recurrent Clostridium difficile infection and is being investigated as a treatment for other microbiota-associated diseases. To facilitate these activities, an international public stool bank has been created, which screens donors and processes s...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-015-0140-3

    authors: Kazerouni A,Burgess J,Burns LJ,Wein LM

    更新日期:2015-12-17 00:00:00

  • Pre-pregnancy weight, gestational weight gain, and the gut microbiota of mothers and their infants.

    abstract:BACKGROUND:Recent evidence supports that the maternal gut microbiota impacts the initial infant gut microbiota. Since the gut microbiota may play a causal role in the development of obesity, it is important to understand how pre-pregnancy weight and gestational weight gain (GWG) impact the gut microbiota of mothers at ...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-017-0332-0

    authors: Stanislawski MA,Dabelea D,Wagner BD,Sontag MK,Lozupone CA,Eggesbø M

    更新日期:2017-09-04 00:00:00

  • The occurrence of potato common scab correlates with the community composition and function of the geocaulosphere soil microbiome.

    abstract:BACKGROUND:Soil microorganisms can mediate the occurrence of plant diseases. Potato common scab (CS) is a refractory disease caused by pathogenic Streptomyces that occurs worldwide, but little is known about the interactions between CS and the soil microbiome. In this study, four soil-root system compartments (geocaulo...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-019-0629-2

    authors: Shi W,Li M,Wei G,Tian R,Li C,Wang B,Lin R,Shi C,Chi X,Zhou B,Gao Z

    更新日期:2019-02-01 00:00:00

  • VALENCIA: a nearest centroid classification method for vaginal microbial communities based on composition.

    abstract:BACKGROUND:Taxonomic profiles of vaginal microbial communities can be sorted into a discrete number of categories termed community state types (CSTs). This approach is advantageous because collapsing a hyper-dimensional taxonomic profile into a single categorical variable enables efforts such as data exploration, epide...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-020-00934-6

    authors: France MT,Ma B,Gajer P,Brown S,Humphrys MS,Holm JB,Waetjen LE,Brotman RM,Ravel J

    更新日期:2020-11-23 00:00:00

  • Gut microbiota-derived propionate mediates the neuroprotective effect of osteocalcin in a mouse model of Parkinson's disease.

    abstract:BACKGROUND:Parkinson's disease (PD) is a neurodegenerative disorder with no absolute cure. The evidence of the involvement of gut microbiota in PD pathogenesis suggests the need to identify certain molecule(s) derived from the gut microbiota, which has the potential to manage PD. Osteocalcin (OCN), an osteoblast-secret...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-020-00988-6

    authors: Hou YF,Shan C,Zhuang SY,Zhuang QQ,Ghosh A,Zhu KC,Kong XK,Wang SM,Gong YL,Yang YY,Tao B,Sun LH,Zhao HY,Guo XZ,Wang WQ,Ning G,Gu YY,Li ST,Liu JM

    更新日期:2021-01-31 00:00:00

  • An integrated meta-omics approach reveals substrates involved in synergistic interactions in a bisphenol A (BPA)-degrading microbial community.

    abstract:BACKGROUND:Understanding microbial interactions in engineering bioprocesses is important to enhance and optimize performance outcomes and requires dissection of the multi-layer complexities of microbial communities. However, unraveling microbial interactions as well as substrates involved in complex microbial communiti...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-019-0634-5

    authors: Yu K,Yi S,Li B,Guo F,Peng X,Wang Z,Wu Y,Alvarez-Cohen L,Zhang T

    更新日期:2019-02-06 00:00:00

  • Genomic insights into potential interdependencies in microbial hydrocarbon and nutrient cycling in hydrothermal sediments.

    abstract:BACKGROUND:Deep-sea hydrothermal vents are hotspots for productivity and biodiversity. Thermal pyrolysis and circulation produce fluids rich in hydrocarbons and reduced compounds that stimulate microbial activity in surrounding sediments. Several studies have characterized the diversity of Guaymas Basin (Gulf of Califo...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-017-0322-2

    authors: Dombrowski N,Seitz KW,Teske AP,Baker BJ

    更新日期:2017-08-23 00:00:00

  • Facultative methanotrophs are abundant at terrestrial natural gas seeps.

    abstract:BACKGROUND:Natural gas contains methane and the gaseous alkanes ethane, propane and butane, which collectively influence atmospheric chemistry and cause global warming. Methane-oxidising bacteria, methanotrophs, are crucial in mitigating emissions of methane as they oxidise most of the methane produced in soils and the...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-018-0500-x

    authors: Farhan Ul Haque M,Crombie AT,Ensminger SA,Baciu C,Murrell JC

    更新日期:2018-06-28 00:00:00

  • Interactive effects of temperature, organic carbon, and pipe material on microbiota composition and Legionella pneumophila in hot water plumbing systems.

    abstract:BACKGROUND:Several biotic and abiotic factors have been reported to influence the proliferation of microbes, including Legionella pneumophila, in hot water premise plumbing systems, but their combined effects have not been systematically evaluated. Here, we utilize simulated household water heaters to examine the effec...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-017-0348-5

    authors: Proctor CR,Dai D,Edwards MA,Pruden A

    更新日期:2017-10-04 00:00:00

  • Consistent responses of soil microbial taxonomic and functional attributes to mercury pollution across China.

    abstract:BACKGROUND:The ecological consequences of mercury (Hg) pollution-one of the major pollutants worldwide-on microbial taxonomic and functional attributes remain poorly understood and largely unexplored. Using soils from two typical Hg-impacted regions across China, here, we evaluated the role of Hg pollution in regulatin...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-018-0572-7

    authors: Liu YR,Delgado-Baquerizo M,Bi L,Zhu J,He JZ

    更新日期:2018-10-18 00:00:00

  • Direct and indirect effects of a pH gradient bring insights into the mechanisms driving prokaryotic community structures.

    abstract:BACKGROUND:pH is frequently reported as the main driver for prokaryotic community structure in soils. However, pH changes are also linked to "spillover effects" on other chemical parameters (e.g., availability of Al, Fe, Mn, Zn, and Cu) and plant growth, but these indirect effects on the microbial communities are rarel...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-018-0482-8

    authors: Lammel DR,Barth G,Ovaskainen O,Cruz LM,Zanatta JA,Ryo M,de Souza EM,Pedrosa FO

    更新日期:2018-06-11 00:00:00

  • Relative and contextual contribution of different sources to the composition and abundance of indoor air bacteria in residences.

    abstract:BACKGROUND:The study of the microbial communities in the built environment is of critical importance as humans spend the majority of their time indoors. While the microorganisms in living spaces, especially those in the air, can impact health and well-being, little is known of their identity and the processes that dete...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-015-0128-z

    authors: Miletto M,Lindow SE

    更新日期:2015-12-10 00:00:00

  • Transplanted human fecal microbiota enhanced Guillain Barré syndrome autoantibody responses after Campylobacter jejuni infection in C57BL/6 mice.

    abstract:BACKGROUND:Campylobacter jejuni is the leading antecedent infection to the autoimmune neuropathy Guillain-Barré syndrome (GBS), which is accompanied by an autoimmune anti-ganglioside antibody attack on peripheral nerves. Previously, we showed that contrasting immune responses mediate C. jejuni induced colitis and autoi...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/s40168-017-0284-4

    authors: Brooks PT,Brakel KA,Bell JA,Bejcek CE,Gilpin T,Brudvig JM,Mansfield LS

    更新日期:2017-08-08 00:00:00

  • CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction.

    abstract:BACKGROUND:Culture-independent molecular surveys targeting conserved marker genes, most notably 16S rRNA, to assess microbial diversity remain semi-quantitative due to variations in the number of gene copies between species. RESULTS:Based on 2,900 sequenced reference genomes, we show that 16S rRNA gene copy number (GC...

    journal_title:Microbiome

    pub_type: 杂志文章

    doi:10.1186/2049-2618-2-11

    authors: Angly FE,Dennis PG,Skarshewski A,Vanwonterghem I,Hugenholtz P,Tyson GW

    更新日期:2014-04-07 00:00:00