Balance Trees Reveal Microbial Niche Differentiation.

Abstract:

:Advances in sequencing technologies have enabled novel insights into microbial niche differentiation, from analyzing environmental samples to understanding human diseases and informing dietary studies. However, identifying the microbial taxa that differentiate these samples can be challenging. These issues stem from the compositional nature of 16S rRNA gene data (or, more generally, taxon or functional gene data); the changes in the relative abundance of one taxon influence the apparent abundances of the others. Here we acknowledge that inferring properties of individual bacteria is a difficult problem and instead introduce the concept of balances to infer meaningful properties of subcommunities, rather than properties of individual species. We show that balances can yield insights about niche differentiation across multiple microbial environments, including soil environments and lung sputum. These techniques have the potential to reshape how we carry out future ecological analyses aimed at revealing differences in relative taxonomic abundances across different samples. IMPORTANCE By explicitly accounting for the compositional nature of 16S rRNA gene data through the concept of balances, balance trees yield novel biological insights into niche differentiation. The software to perform this analysis is available under an open-source license and can be obtained at https://github.com/biocore/gneiss. Author Video: An author video summary of this article is available.

journal_name

mSystems

journal_title

mSystems

authors

Morton JT,Sanders J,Quinn RA,McDonald D,Gonzalez A,Vázquez-Baeza Y,Navas-Molina JA,Song SJ,Metcalf JL,Hyde ER,Lladser M,Dorrestein PC,Knight R

doi

10.1128/mSystems.00162-16

subject

Has Abstract

pub_date

2017-01-17 00:00:00

issue

1

issn

2379-5077

pii

mSystems00162-16

journal_volume

2

pub_type

杂志文章

相关文献

mSystems文献大全
  • Comparative Genomics and Metabolomics in the Genus Nocardia.

    abstract::Using automated genome analysis tools, it is often unclear to what degree genetic variability in homologous biosynthetic pathways relates to structural variation. This hampers strain prioritization and compound identification and can lead to overinterpretation of chemical diversity. Here, we assessed the metabolic pot...

    journal_title:mSystems

    pub_type: 杂志文章

    doi:10.1128/mSystems.00125-20

    authors: Männle D,McKinnie SMK,Mantri SS,Steinke K,Lu Z,Moore BS,Ziemert N,Kaysser L

    更新日期:2020-06-02 00:00:00

  • Proton Nuclear Magnetic Resonance Metabolomics Corroborates Serine Hydroxymethyltransferase as the Primary Target of 2-Aminoacrylate in a ridA Mutant of Salmonella enterica.

    abstract::The reactive intermediate deaminase RidA (EC 3.5.99.10) is conserved across all domains of life and deaminates reactive enamine species. When Salmonella entericaridA mutants are grown in minimal medium, 2-aminoacrylate (2AA) accumulates, damages several pyridoxal 5'-phosphate (PLP)-dependent enzymes, and elicits an ob...

    journal_title:mSystems

    pub_type: 杂志文章

    doi:10.1128/mSystems.00843-19

    authors: Borchert AJ,Gouveia GJ,Edison AS,Downs DM

    更新日期:2020-03-10 00:00:00

  • Gut Microbiota and Host Thermoregulation in Response to Ambient Temperature Fluctuations.

    abstract::Ambient temperature (Ta ) is an important factor in shaping phenotypic plasticity. Plasticity is generally beneficial for animals in adapting to their environments. Gut microbiota are crucial in regulating host physiological and behavioral processes. However, whether the gut microbiota play a role in regulating host p...

    journal_title:mSystems

    pub_type: 杂志文章

    doi:10.1128/mSystems.00514-20

    authors: Khakisahneh S,Zhang XY,Nouri Z,Wang DH

    更新日期:2020-10-20 00:00:00

  • Diagnosing and Predicting Mixed-Culture Fermentations with Unicellular and Guild-Based Metabolic Models.

    abstract::Multispecies microbial communities determine the fate of materials in the environment and can be harnessed to produce beneficial products from renewable resources. In a recent example, fermentations by microbial communities have produced medium-chain fatty acids (MCFAs). Tools to predict, assess, and improve the perfo...

    journal_title:mSystems

    pub_type: 杂志文章

    doi:10.1128/mSystems.00755-20

    authors: Scarborough MJ,Hamilton JJ,Erb EA,Donohue TJ,Noguera DR

    更新日期:2020-09-29 00:00:00

  • Synergy among Microbiota and Their Hosts: Leveraging the Hawaiian Archipelago and Local Collaborative Networks To Address Pressing Questions in Microbiome Research.

    abstract::Despite increasing acknowledgment that microorganisms underpin the healthy functioning of basically all multicellular life, few cross-disciplinary teams address the diversity and function of microbiota across organisms and ecosystems. Our newly formed consortium of junior faculty spanning fields such as ecology and ge...

    journal_title:mSystems

    pub_type: 杂志文章

    doi:10.1128/mSystems.00159-17

    authors: Hynson NA,Frank KL,Alegado RA,Amend AS,Arif M,Bennett GM,Jani AJ,Medeiros MCI,Mileyko Y,Nelson CE,Nguyen NH,Nigro OD,Prisic S,Shin S,Takagi D,Wilson ST,Yew JY

    更新日期:2018-03-13 00:00:00

  • Randomized Lasso Links Microbial Taxa with Aquatic Functional Groups Inferred from Flow Cytometry.

    abstract::High-nucleic-acid (HNA) and low-nucleic-acid (LNA) bacteria are two operational groups identified by flow cytometry (FCM) in aquatic systems. A number of reports have shown that HNA cell density correlates strongly with heterotrophic production, while LNA cell density does not. However, which taxa are specifically ass...

    journal_title:mSystems

    pub_type: 杂志文章

    doi:10.1128/mSystems.00093-19

    authors: Rubbens P,Schmidt ML,Props R,Biddanda BA,Boon N,Waegeman W,Denef VJ

    更新日期:2019-09-10 00:00:00

  • Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes.

    abstract::Soil metagenomics has been touted as the "grand challenge" for metagenomics, as the high microbial diversity and spatial heterogeneity of soils make them unamenable to current assembly platforms. Here, we aimed to improve soil metagenomic sequence assembly by applying the Moleculo synthetic long-read sequencing techno...

    journal_title:mSystems

    pub_type: 杂志文章

    doi:10.1128/mSystems.00045-16

    authors: White RA 3rd,Bottos EM,Roy Chowdhury T,Zucker JD,Brislawn CJ,Nicora CD,Fansler SJ,Glaesemann KR,Glass K,Jansson JK

    更新日期:2016-06-28 00:00:00

  • Predicting Phenotypic Polymyxin Resistance in Klebsiella pneumoniae through Machine Learning Analysis of Genomic Data.

    abstract::Polymyxins are used as treatments of last resort for Gram-negative bacterial infections. Their increased use has led to concerns about emerging polymyxin resistance (PR). Phenotypic polymyxin susceptibility testing is resource intensive and difficult to perform accurately. The complex polygenic nature of PR and our in...

    journal_title:mSystems

    pub_type: 杂志文章

    doi:10.1128/mSystems.00656-19

    authors: Macesic N,Bear Don't Walk OJ IV,,Pe'er I,Tatonetti NP,Peleg AY,Uhlemann AC

    更新日期:2020-05-26 00:00:00

  • Integration of Metabolomics and Transcriptomics Reveals a Complex Diet of Mycobacterium tuberculosis during Early Macrophage Infection.

    abstract::Nutrient acquisition from the host environment is crucial for the survival of intracellular pathogens, but conceptual and technical challenges limit our knowledge of pathogen diets. To overcome some of these technical roadblocks, we exploited an experimentally accessible model for early infection of human macrophages ...

    journal_title:mSystems

    pub_type: 杂志文章

    doi:10.1128/mSystems.00057-17

    authors: Zimmermann M,Kogadeeva M,Gengenbacher M,McEwen G,Mollenkopf HJ,Zamboni N,Kaufmann SHE,Sauer U

    更新日期:2017-08-22 00:00:00

  • Metabolic Modeling of Streptococcus mutans Reveals Complex Nutrient Requirements of an Oral Pathogen.

    abstract::Streptococcus mutans is a Gram-positive bacterium that thrives under acidic conditions and is a primary cause of tooth decay (dental caries). To better understand the metabolism of S. mutans on a systematic level, we manually constructed a genome-scale metabolic model of the S. mutans type strain UA159. The model, cal...

    journal_title:mSystems

    pub_type: 杂志文章

    doi:10.1128/mSystems.00529-19

    authors: Jijakli K,Jensen PA

    更新日期:2019-10-29 00:00:00

  • Ecology and Host Identity Outweigh Evolutionary History in Shaping the Bat Microbiome.

    abstract::Recent studies of mammalian microbiomes have identified strong phylogenetic effects on bacterial community composition. Bats (Mammalia: Chiroptera) are among the most speciose mammals on the planet and the only mammal capable of true flight. We examined 1,236 16S rRNA amplicon libraries of the gut, oral, and skin micr...

    journal_title:mSystems

    pub_type: 杂志文章

    doi:10.1128/mSystems.00511-19

    authors: Lutz HL,Jackson EW,Webala PW,Babyesiza WS,Kerbis Peterhans JC,Demos TC,Patterson BD,Gilbert JA

    更新日期:2019-11-12 00:00:00

  • Perinatal Bisphenol A Exposure Induces Chronic Inflammation in Rabbit Offspring via Modulation of Gut Bacteria and Their Metabolites.

    abstract::Bisphenol A (BPA) accumulates in the maturing gut and liver in utero and is known to alter gut bacterial profiles in offspring. Gut bacterial dysbiosis may contribute to chronic colonic and systemic inflammation. We hypothesized that perinatal BPA exposure-induced intestinal (and liver) inflammation in offspring is du...

    journal_title:mSystems

    pub_type: 杂志文章

    doi:10.1128/mSystems.00093-17

    authors: Reddivari L,Veeramachaneni DNR,Walters WA,Lozupone C,Palmer J,Hewage MKK,Bhatnagar R,Amir A,Kennett MJ,Knight R,Vanamala JKP

    更新日期:2017-10-10 00:00:00

  • Metabolic Reconstruction Elucidates the Lifestyle of the Last Diplomonadida Common Ancestor.

    abstract::The identification of ancestral traits is essential to understanding the evolution of any group. In the case of parasitic groups, this helps us understand the adaptation to this lifestyle and a particular host. Most diplomonads are parasites, but there are free-living members of the group nested among the host-associa...

    journal_title:mSystems

    pub_type: 杂志文章

    doi:10.1128/mSystems.00774-20

    authors: Jiménez-González A,Andersson JO

    更新日期:2020-12-22 00:00:00

  • Comparative Genome Analyses of Vibrio anguillarum Strains Reveal a Link with Pathogenicity Traits.

    abstract::Vibrio anguillarum is a marine bacterium that can cause vibriosis in many fish and shellfish species, leading to high mortalities and economic losses in aquaculture. Although putative virulence factors have been identified, the mechanism of pathogenesis of V. anguillarum is not fully understood. Here, we analyzed whol...

    journal_title:mSystems

    pub_type: 杂志文章

    doi:10.1128/mSystems.00001-17

    authors: Castillo D,Alvise PD,Xu R,Zhang F,Middelboe M,Gram L

    更新日期:2017-02-28 00:00:00

  • Intermittent Hypoxia and Hypercapnia Reproducibly Change the Gut Microbiome and Metabolome across Rodent Model Systems.

    abstract::Studying perturbations in the gut ecosystem using animal models of disease continues to provide valuable insights into the role of the microbiome in various pathological conditions. However, understanding whether these changes are consistent across animal models of different genetic backgrounds, and hence potentially ...

    journal_title:mSystems

    pub_type: 杂志文章

    doi:10.1128/mSystems.00058-19

    authors: Tripathi A,Xu ZZ,Xue J,Poulsen O,Gonzalez A,Humphrey G,Meehan MJ,Melnik AV,Ackermann G,Zhou D,Malhotra A,Haddad GG,Dorrestein PC,Knight R

    更新日期:2019-04-30 00:00:00

  • Comparative Genomics Reveals Ecological and Evolutionary Insights into Sponge-Associated Thaumarchaeota.

    abstract::Thaumarchaeota are frequently reported to associate with marine sponges (phylum Porifera); however, little is known about the features that distinguish them from their free-living thaumarchaeal counterparts. In this study, thaumarchaeal metagenome-assembled genomes (MAGs) were reconstructed from metagenomic data sets ...

    journal_title:mSystems

    pub_type: 杂志文章

    doi:10.1128/mSystems.00288-19

    authors: Zhang S,Song W,Wemheuer B,Reveillaud J,Webster N,Thomas T

    更新日期:2019-08-13 00:00:00

  • Reconciling Ecological and Engineering Design Principles for Building Microbiomes.

    abstract::Simplified microbial communities, or "benchtop microbiomes," enable us to manage the profound complexity of microbial ecosystems. Widespread activities aiming to design and control communities result in novel resources for testing ecological theories and also for realizing new biotechnologies. There is much to be gain...

    journal_title:mSystems

    pub_type: 杂志文章

    doi:10.1128/mSystems.00106-19

    authors: Bernstein HC

    更新日期:2019-05-28 00:00:00

  • Carbon Fate and Flux in Prochlorococcus under Nitrogen Limitation.

    abstract::Primary production by Prochlorococcus, the smallest known free-living photosynthetic organism in terms of both physical and genomic size, is thought to have a significant role in global carbon cycles. Despite its small size and low growth rate, Prochlorococcus numerically dominates the phytoplankton community in the n...

    journal_title:mSystems

    pub_type: 杂志文章

    doi:10.1128/mSystems.00254-18

    authors: Szul MJ,Dearth SP,Campagna SR,Zinser ER

    更新日期:2019-02-26 00:00:00

  • Species Designations Belie Phenotypic and Genotypic Heterogeneity in Oral Streptococci.

    abstract::Health-associated oral Streptococcus species are promising probiotic candidates to protect against dental caries. Ammonia production through the arginine deiminase system (ADS), which can increase the pH of oral biofilms, and direct antagonism of caries-associated bacterial species are desirable properties for oral pr...

    journal_title:mSystems

    pub_type: 杂志文章

    doi:10.1128/mSystems.00158-18

    authors: Velsko IM,Chakraborty B,Nascimento MM,Burne RA,Richards VP

    更新日期:2018-12-18 00:00:00

  • Data-Driven Models Reveal Mutant Cell Behaviors Important for Myxobacterial Aggregation.

    abstract::Single mutations frequently alter several aspects of cell behavior but rarely reveal whether a particular statistically significant change is biologically significant. To determine which behavioral changes are most important for multicellular self-organization, we devised a new methodology using Myxococcus xanthus as ...

    journal_title:mSystems

    pub_type: 杂志文章

    doi:10.1128/mSystems.00518-20

    authors: Zhang Z,Cotter CR,Lyu Z,Shimkets LJ,Igoshin OA

    更新日期:2020-07-14 00:00:00

  • Sex Bias in Gut Microbiome Transmission in Newly Paired Marmosets (Callithrix jacchus).

    abstract::Social behavior can alter the microbiome composition via transmission among social partners, but there have been few controlled experimental studies of gut microbiome transmission among social partners in primates. We collected longitudinal fecal samples from eight unrelated male-female pairs of marmoset monkeys prior...

    journal_title:mSystems

    pub_type: 杂志文章

    doi:10.1128/mSystems.00910-19

    authors: Zhu L,Clayton JB,Suhr Van Haute MJ,Yang Q,Hassenstab HR,Mustoe AC,Knights D,Benson AK,French JA

    更新日期:2020-03-24 00:00:00

  • Exploring Linkages between Taxonomic and Functional Profiles of the Human Microbiome.

    abstract::Microbiome studies typically focus on characterizing the taxonomic and functional profiles of the microbes within a community. Functional profiling is generally thought to be superior to taxonomic profiling for investigating human-microbe interactions, but there are several limitations and challenges to existing appro...

    journal_title:mSystems

    pub_type: 杂志文章

    doi:10.1128/mSystems.00163-17

    authors: Langille MGI

    更新日期:2018-03-27 00:00:00

  • Biomimetic Gut Model Systems for Development of Targeted Microbial Solutions for Enhancing Warfighter Health and Performance.

    abstract::The human gut microbiome plays a vital role in both health and disease states and as a mediator of cognitive and physical performance. Despite major advances in our understanding of the role of gut microbes in host physiology, mechanisms underlying human-microbiome dynamics have yet to be fully elucidated. This knowle...

    journal_title:mSystems

    pub_type: 杂志文章,评审

    doi:10.1128/mSystems.00487-20

    authors: Brinkac LM,Rahman N,Chua LL,Thomas S

    更新日期:2020-10-27 00:00:00

  • Transcriptome Analysis of Polyhydroxybutyrate Cycle Mutants Reveals Discrete Loci Connecting Nitrogen Utilization and Carbon Storage in Sinorhizobium meliloti.

    abstract::Polyhydroxybutyrate (PHB) and glycogen polymers are produced by bacteria as carbon storage compounds under unbalanced growth conditions. To gain insights into the transcriptional mechanisms controlling carbon storage in Sinorhizobium meliloti, we investigated the global transcriptomic response to the genetic disruptio...

    journal_title:mSystems

    pub_type: 杂志文章

    doi:10.1128/mSystems.00035-17

    authors: D'Alessio M,Nordeste R,Doxey AC,Charles TC

    更新日期:2017-09-12 00:00:00

  • Selected Immunological Mediators and Cervical Microbial Signatures in Women with Chlamydia trachomatis Infection.

    abstract::In the female genital ecosystem, the complex interplay between the host immune system and the resident microflora protects against urogenital pathogens, like Chlamydia trachomatisC. trachomatis is responsible for urethritis and cervicitis; however, most chlamydial infections are asymptomatic and, thus, not treated, po...

    journal_title:mSystems

    pub_type: 杂志文章

    doi:10.1128/mSystems.00094-19

    authors: Filardo S,Di Pietro M,Tranquilli G,Latino MA,Recine N,Porpora MG,Sessa R

    更新日期:2019-06-04 00:00:00

  • Getting the Hologenome Concept Right: an Eco-Evolutionary Framework for Hosts and Their Microbiomes.

    abstract::Given the complexity of host-microbiota symbioses, scientists and philosophers are asking questions at new biological levels of hierarchical organization-what is a holobiont and hologenome? When should this vocabulary be applied? Are these concepts a null hypothesis for host-microbe systems or limited to a certain spe...

    journal_title:mSystems

    pub_type: 杂志文章

    doi:10.1128/mSystems.00028-16

    authors: Theis KR,Dheilly NM,Klassen JL,Brucker RM,Baines JF,Bosch TC,Cryan JF,Gilbert SF,Goodnight CJ,Lloyd EA,Sapp J,Vandenkoornhuyse P,Zilber-Rosenberg I,Rosenberg E,Bordenstein SR

    更新日期:2016-03-29 00:00:00

  • Oral Microbiome Alterations Associated with Early Childhood Caries Highlight the Importance of Carbohydrate Metabolic Activities.

    abstract::Globally, dental caries is the most prevalent chronic oral disease and affects roughly half of all children. The aim of this report was to use metagenomic analyses to investigate the relationship between the oral microbiome and caries in preschool children. A total of 25 preschoolers, aged 3 to 5 years old with severe...

    journal_title:mSystems

    pub_type: 杂志文章

    doi:10.1128/mSystems.00450-19

    authors: Wang Y,Wang S,Wu C,Chen X,Duan Z,Xu Q,Jiang W,Xu L,Wang T,Su L,Wang Y,Chen Y,Zhang J,Huang Y,Tong S,Zhou C,Deng S,Qin N

    更新日期:2019-11-05 00:00:00

  • The Induction of Oxalate Metabolism In Vivo Is More Effective with Functional Microbial Communities than with Functional Microbial Species.

    abstract::For mammals, oxalate enters the body through the diet or is endogenously produced by the liver; it is removed by microbial oxalate metabolism in the gut and/or excretion in feces or urine. Deficiencies in any one of the these pathways can lead to complications, such as calcium oxalate urinary stones. While considerabl...

    journal_title:mSystems

    pub_type: 杂志文章

    doi:10.1128/mSystems.00088-17

    authors: Miller AW,Dale C,Dearing MD

    更新日期:2017-09-26 00:00:00

  • Isolation and Characterization of the Novel Phage JD032 and Global Transcriptomic Response during JD032 Infection of Clostridioides difficile Ribotype 078.

    abstract::Insights into the interaction between phages and their bacterial hosts are crucial for the development of phage therapy. However, only one study has investigated global gene expression of Clostridioides (formerly Clostridium) difficile carrying prophage, and transcriptional reprogramming during lytic infection has not...

    journal_title:mSystems

    pub_type: 杂志文章

    doi:10.1128/mSystems.00017-20

    authors: Li T,Zhang Y,Dong K,Kuo CJ,Li C,Zhu YQ,Qin J,Li QT,Chang YF,Guo X,Zhu Y

    更新日期:2020-05-05 00:00:00

  • Integrating CRISPR-Enabled Trackable Genome Engineering and Transcriptomic Analysis of Global Regulators for Antibiotic Resistance Selection and Identification in Escherichia coli.

    abstract::It is important to expedite our understanding of antibiotic resistance to address the increasing numbers of fatalities and environmental pollution due to the emergence of antibiotic resistance and multidrug-resistant strains. Here, we combined the CRISPR-enabled trackable genome engineering (CREATE) technology and tra...

    journal_title:mSystems

    pub_type: 杂志文章

    doi:10.1128/mSystems.00232-20

    authors: Chen C,Choudhury A,Zhang S,Garst AD,Song X,Liu X,Chen T,Gill RT,Wang Z

    更新日期:2020-04-21 00:00:00