A New Phylogenetic Framework for the Animal-Adapted Mycobacterium tuberculosis Complex.


:Tuberculosis (TB) affects humans and other animals and is caused by bacteria from the Mycobacterium tuberculosis complex (MTBC). Previous studies have shown that there are at least nine members of the MTBC infecting animals other than humans; these have also been referred to as ecotypes. However, the ecology and the evolution of these animal-adapted MTBC ecotypes are poorly understood. Here we screened 12,886 publicly available MTBC genomes and newly sequenced 17 animal-adapted MTBC strains, gathering a total of 529 genomes of animal-adapted MTBC strains. Phylogenomic and comparative analyses confirm that the animal-adapted MTBC members are paraphyletic with some members more closely related to the human-adapted Mycobacterium africanum Lineage 6 than to other animal-adapted strains. Furthermore, we identified four main animal-adapted MTBC clades that might correspond to four main host shifts; two of these clades are hypothesized to reflect independent cattle domestication events. Contrary to what would be expected from an obligate pathogen, MTBC nucleotide diversity was not positively correlated with host phylogenetic distances, suggesting that host tropism in the animal-adapted MTBC seems to be driven by contact rates and demographic aspects of the host population rather by than host relatedness. By combining phylogenomics with ecological data, we propose an evolutionary scenario in which the ancestor of Lineage 6 and all animal-adapted MTBC ecotypes was a generalist pathogen that subsequently adapted to different host species. This study provides a new phylogenetic framework to better understand the evolution of the different ecotypes of the MTBC and guide future work aimed at elucidating the molecular mechanisms underlying host range.


Front Microbiol


Brites D,Loiseau C,Menardo F,Borrell S,Boniotti MB,Warren R,Dippenaar A,Parsons SDC,Beisel C,Behr MA,Fyfe JA,Coscolla M,Gagneux S




Has Abstract


2018-11-27 00:00:00








  • Systemic effector and regulatory immune responses to chlamydial antigens in trachomatous trichiasis.

    abstract::Trachomatous trichiasis (TT) caused by repeated or chronic ocular infection with Chlamydia trachomatis is the result of a pro-fibrotic ocular immune response. At the conjunctiva, the increased expression of both inflammatory (IL1B, TNF) and regulatory cytokines (IL10) have been associated with adverse clinical outcome...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章


    authors: Gall A,Horowitz A,Joof H,Natividad A,Tetteh K,Riley E,Bailey RL,Mabey DC,Holland MJ

    更新日期:2011-02-10 00:00:00

  • Characterization of a Merkel Cell Polyomavirus-Positive Merkel Cell Carcinoma Cell Line CVG-1.

    abstract::Merkel cell polyomavirus (MCV) plays a causal role in ∼80% of Merkel cell carcinomas (MCC). MCV is clonally integrated into the MCC tumor genome, which results in persistent expression of large T (LT) and small T (sT) antigen oncoproteins encoded by the early locus. In MCV-positive MCC tumors, LT is truncated by prema...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章


    authors: Velásquez C,Amako Y,Harold A,Toptan T,Chang Y,Shuda M

    更新日期:2018-04-11 00:00:00

  • The Naphthalene Catabolic Genes of Pseudomonas putida BS3701: Additional Regulatory Control.

    abstract::Pseudomonas microorganisms are used for bioremediation of soils contaminated with petroleum hydrocarbons. The overall remediation efficiency is largely dependent on the presence of macro- and micronutrients. Widely varying concentrations of available nitrogen and iron (Fe) in soils were shown to affect residual hydroc...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章


    authors: Pozdnyakova-Filatova I,Petrikov K,Vetrova A,Frolova A,Streletskii R,Zakharova M

    更新日期:2020-06-05 00:00:00

  • Important Role of a Putative Lytic Transglycosylase Cj0843c in β-Lactam Resistance in Campylobacter jejuni.

    abstract::Beta-lactam antibiotics are an important class of antibiotics for treating bacterial infections. Despite prevalent β-lactam resistance in Campylobacter jejuni, the leading bacterial cause of human diarrhea in developed countries, molecular mechanism of β-lactam resistance in C. jejuni is still largely unknown. In this...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章


    authors: Zeng X,Gillespie B,Lin J

    更新日期:2015-11-17 00:00:00

  • Fourth Generation Cephalosporin Resistance Among Salmonella enterica Serovar Enteritidis Isolates in Shanghai, China Conferred by bla CTX-M-55 Harboring Plasmids.

    abstract::In this study, we investigated the pattern of antimicrobial resistance in Salmonella enterica serotype Enteritidis isolates in Shanghai, China from 2005 to 2014. We found the first isolates with resistance to the fourth-generation cephalosporin cefepime starting in 2010. Furthermore, we analyzed the epidemic character...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章


    authors: Fu Y,Xu X,Zhang L,Xiong Z,Ma Y,Wei Y,Chen Z,Bai J,Liao M,Zhang J

    更新日期:2020-05-15 00:00:00

  • Cyclic Lipodepsipeptides From Pseudomonas spp. - Biological Swiss-Army Knives.

    abstract::Cyclic lipodepsipeptides produced by Pseudomonas spp. (Ps-CLPs) are biosurfactants that constitute a diverse class of versatile bioactive natural compounds with promising application potential. While chemically diverse, they obey a common structural blue-print, allowing the definition of 14 distinct groups with multip...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章,评审


    authors: Geudens N,Martins JC

    更新日期:2018-08-14 00:00:00

  • Substrate Pre-loading Influences Initial Colonization of GAC Biofilter Biofilms.

    abstract::Microbial community composition and stability affect pollutant removal for biological/granular activated carbon (BAC/GAC) processes. Here, we pre-loaded the organic carbon substrates sucrose, lactose, and Lysogeny Broth (LB) medium onto new GAC prior to use and then tested whether this substrate pre-loading promoted d...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章


    authors: Qin W,Hammes F

    更新日期:2021-01-12 00:00:00

  • Building of Pressure-Assisted Ultra-High Temperature System and Its Inactivation of Bacterial Spores.

    abstract::The pressure-assisted ultra-high temperature (PAUHT) system was built by using soybean oil as pressure-transmitting medium, and the multiple regression equation of soybean oil temperature change (ΔTP ) during pressurization as a function of initial temperature (Ti ) and set pressure (P) was developed: ΔTP = -13.45 + 0...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章


    authors: Liang D,Zhang L,Wang X,Wang P,Liao X,Wu X,Chen F,Hu X

    更新日期:2019-06-10 00:00:00

  • Potential TMA-Producing Bacteria Are Ubiquitously Found in Mammalia.

    abstract::Human gut bacteria metabolize dietary components such as choline and carnitine to trimethylamine (TMA) that is subsequently oxidized to trimethylamine-N-oxide (TMAO) by hepatic enzymes. Increased plasma levels of TMAO are associated with the development of cardiovascular and renal disease. In this study, we applied ge...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章


    authors: Rath S,Rud T,Pieper DH,Vital M

    更新日期:2020-01-09 00:00:00

  • Identification of Novel Genes Mediating Survival of Salmonella on Low-Moisture Foods via Transposon Sequencing Analysis.

    abstract::Salmonella enterica is the leading foodborne pathogen associated with outbreaks involving low-moisture foods (LMFs). However, the genes involved in Salmonella's long-term survival on LMFs remain poorly characterized. In this study, in-shell pistachios were inoculated with Tn5-based mutant libraries of S. Enteritidis P...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章


    authors: Jayeola V,McClelland M,Porwollik S,Chu W,Farber J,Kathariou S

    更新日期:2020-05-15 00:00:00

  • A Disulfide Bond in the Membrane Protein IgaA Is Essential for Repression of the RcsCDB System.

    abstract::IgaA is an integral inner membrane protein that was discovered as repressor of the RcsCDB phosphorelay system in the intracellular pathogen Salmonella enterica serovar Typhimurium. The RcsCDB system, conserved in many members of the family Enterobacteriaceae, regulates expression of varied processes including motility...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章


    authors: Pucciarelli MG,Rodríguez L,García-Del Portillo F

    更新日期:2017-12-22 00:00:00

  • Characterization and Metabolism Effect of Seed Endophytic Bacteria Associated With Peanut Grown in South China.

    abstract::Endophytes are considered to be excellent biocontrol agents and biofertilizers, and are associated with plant growth promotion and health. In particular, seed-endophytic bacteria benefit the host plant's progeny via vertical transmission, and can play a role in plant growth and defense. However, seed-associated endoph...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章


    authors: Li L,Zhang Z,Pan S,Li L,Li X

    更新日期:2019-11-13 00:00:00

  • Potential Risk Areas of Aedes albopictus in South-Eastern Iran: A Vector of Dengue Fever, Zika, and Chikungunya.

    abstract::The possibility of the rapid and global spread of Zika, chikungunya, yellow fever, and dengue fever by Aedes albopictus is well documented and may be facilitated by changes in climate. To avert and manage health risks, climatic and topographic information can be used to model and forecast which areas may be most prone...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章


    authors: Nejati J,Bueno-Marí R,Collantes F,Hanafi-Bojd AA,Vatandoost H,Charrahy Z,Tabatabaei SM,Yaghoobi-Ershadi MR,Hasanzehi A,Shirzadi MR,Moosa-Kazemi SH,Sedaghat MM

    更新日期:2017-09-05 00:00:00

  • Characterization of Two Endo-β-1, 4-Xylanases from Myceliophthora thermophila and Their Saccharification Efficiencies, Synergistic with Commercial Cellulase.

    abstract::The xylanases with high specific activity and resistance to harsh conditions are of high practical value for biomass utilization. In the present study, two new GH11 xylanase genes, MYCTH_56237 and MYCTH_49824, have been cloned from thermophilic fungus Myceliophthora thermophila and expressed in Pichia pastoris. The sp...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章


    authors: Basit A,Liu J,Miao T,Zheng F,Rahim K,Lou H,Jiang W

    更新日期:2018-02-14 00:00:00

  • Comparison of Bacterial and Fungal Composition and Their Chemical Interaction in Free Tropospheric Air and Snow Over an Entire Winter Season at Mount Sonnblick, Austria.

    abstract::We investigated the interactions of air and snow over one entire winter accumulation period as well as the importance of chemical markers in a pristine free-tropospheric environment to explain variation in a microbiological dataset. To overcome the limitations of short term bioaerosol sampling, we sampled the atmosphe...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章


    authors: Els N,Greilinger M,Reisecker M,Tignat-Perrier R,Baumann-Stanzer K,Kasper-Giebl A,Sattler B,Larose C

    更新日期:2020-05-20 00:00:00

  • Transcriptional Regulation of the Type VI Secretion System 1 Genes by Quorum Sensing and ToxR in Vibrio parahaemolyticus.

    abstract::Vibrio parahaemolyticus, the leading cause of seafood-associated gastroenteritis, harbors two separate T6SSs on chromosomes 1 and 2, i.e., T6SS1 (VP1386-1420) and T6SS2 (VPA1025-1046). T6SS1 contains at least 7 putative operons: VP1386-1387, VP1388-1390, VP1392-1391, VP1393-1406, VP1400-1406, VP1409-1407, and VP1410-1...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章


    authors: Zhang Y,Gao H,Osei-Adjei G,Zhang Y,Yang W,Yang H,Yin Z,Huang X,Zhou D

    更新日期:2017-10-16 00:00:00

  • The MHC-II transactivator CIITA, a restriction factor against oncogenic HTLV-1 and HTLV-2 retroviruses: similarities and differences in the inhibition of Tax-1 and Tax-2 viral transactivators.

    abstract::The activation of CD4(+) T helper cells is strictly dependent on the presentation of antigenic peptides by MHC class II (MHC-II) molecules. MHC-II expression is primarily regulated at the transcriptional level by the AIR-1 gene product CIITA (class II transactivator). Thus, CIITA plays a pivotal role in the triggering...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章


    authors: Forlani G,Abdallah R,Accolla RS,Tosi G

    更新日期:2013-08-22 00:00:00

  • A New Method to Correct for Habitat Filtering in Microbial Correlation Networks.

    abstract::Amplicon sequencing of 16S, ITS, and 18S regions of microbial genomes is a commonly used first step toward understanding microbial communities of interest for human health, agriculture, and the environment. Correlation network analysis is an emerging tool for investigating the interactions within these microbial commu...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章


    authors: Brisson V,Schmidt J,Northen TR,Vogel JP,Gaudin A

    更新日期:2019-03-20 00:00:00

  • The Human Gastric Microbiome Is Predicated upon Infection with Helicobacter pylori.

    abstract::The human gastric lumen is one of the most hostile environments of the human body suspected to be sterile until the discovery of Helicobacter pylori (H.p.). State of the art next generation sequencing technologies multiply the knowledge on H.p. functional genomics as well as on the colonization of supposed sterile hum...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章


    authors: Klymiuk I,Bilgilier C,Stadlmann A,Thannesberger J,Kastner MT,Högenauer C,Püspök A,Biowski-Frotz S,Schrutka-Kölbl C,Thallinger GG,Steininger C

    更新日期:2017-12-14 00:00:00

  • Citrus Leprosis Virus C Encodes Three Proteins With Gene Silencing Suppression Activity.

    abstract::Citrus leprosis virus C (CiLV-C) belongs to the genus Cilevirus, family Kitaviridae, and is considered the most devastating virus infecting citrus in Brazil, being the main viral pathogen responsible for citrus leprosis (CL), a severe disease that affects citrus orchards in Latin America. Here, proteins encoded by CiL...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章


    authors: Leastro MO,Castro DYO,Freitas-Astúa J,Kitajima EW,Pallás V,Sánchez-Navarro JÁ

    更新日期:2020-06-09 00:00:00

  • A Multifactorial Approach for Surveillance of Shigella spp. and Entero-Invasive Escherichia coli Is Important for Detecting (Inter)national Clusters.

    abstract::Shigella spp. and entero-invasive Escherichia coli (EIEC) can cause mild diarrhea to dysentery. In Netherlands, although shigellosis is a notifiable disease, there is no laboratory surveillance for Shigella spp. and EIEC in place. Consequently, the population structure for circulating Shigella spp. and EIEC isolates i...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章


    authors: van den Beld MJC,Reubsaet FAG,Pijnacker R,Harpal A,Kuiling S,Heerkens EM,Hoeve-Bakker BJAD,Noomen RCEA,Hendriks ACA,Borst D,van der Heide H,Kooistra-Smid AMDM,Rossen JWA

    更新日期:2020-10-19 00:00:00

  • Draft Genomic Analysis of an Avian Multidrug Resistant Morganella morganii Isolate Carrying qnrD1.

    abstract::Morganella morganii is a commensal bacterium and opportunistic pathogen often present in the gut of humans and animals. We report the 4.3 Mbp draft genome sequence of a M. morganii isolated in association with an Escherichia coli from broilers in Portugal that showed macroscopic lesions consistent with colisepticemia....

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章


    authors: Jones-Dias D,Clemente L,Moura IB,Sampaio DA,Albuquerque T,Vieira L,Manageiro V,Caniça M

    更新日期:2016-10-25 00:00:00

  • AmrZ and FleQ Co-regulate Cellulose Production in Pseudomonas syringae pv. Tomato DC3000.

    abstract::Pseudomonas syringae pv. tomato DC3000 carries the wssABCDEFGHI operon for the synthesis of acetylated cellulose, whose production is stimulated by increasing the intracellular levels of the second messenger c-di-GMP. This enhances air-liquid biofilm formation and generates a wrinkly colony morphotype in solid media. ...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章


    authors: Pérez-Mendoza D,Felipe A,Ferreiro MD,Sanjuán J,Gallegos MT

    更新日期:2019-04-17 00:00:00

  • Aedes aegypti Molecular Responses to Zika Virus: Modulation of Infection by the Toll and Jak/Stat Immune Pathways and Virus Host Factors.

    abstract::Zika (ZIKV) and dengue virus (DENV) are transmitted to humans by Aedes mosquitoes. However, the molecular interactions between the vector and ZIKV remain largely unexplored. In this work, we further investigated the tropism of ZIKV in two different Aedes aegypti strains and show that the virus infection kinetics, tiss...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章


    authors: Angleró-Rodríguez YI,MacLeod HJ,Kang S,Carlson JS,Jupatanakul N,Dimopoulos G

    更新日期:2017-10-23 00:00:00

  • A Genetic and Chemical Perspective on Symbiotic Recruitment of Cyanobacteria of the Genus Nostoc into the Host Plant Blasia pusilla L.

    abstract::Liverwort Blasia pusilla L. recruits soil nitrogen-fixing cyanobacteria of genus Nostoc as symbiotic partners. In this work we compared Nostoc community composition inside the plants and in the soil around them from two distant locations in Northern Norway. STRR fingerprinting and 16S rDNA phylogeny reconstruction sho...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章


    authors: Liaimer A,Jensen JB,Dittmann E

    更新日期:2016-11-01 00:00:00

  • Antibiotic Resistance Genes and Bacterial Communities of Farmed Rainbow Trout Fillets (Oncorhynchus mykiss).

    abstract::The rise of antibiotic resistance is not only a challenge for human and animal health treatments, but is also posing the risk of spreading among bacterial populations in foodstuffs. Farmed fish-related foodstuffs, the food of animal origin most consumed worldwide, are suspected to be a reservoir of antibiotic resistan...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章


    authors: Helsens N,Calvez S,Prevost H,Bouju-Albert A,Maillet A,Rossero A,Hurtaud-Pessel D,Zagorec M,Magras C

    更新日期:2020-12-03 00:00:00

  • Progress on Structured Biosensors for Monitoring Aflatoxin B1 From Biofilms: A Review.

    abstract::Aspergillus exists commonly in many crops and any process of crop growth, harvest, storage, and processing can be polluted by this fungus. Once it forms a biofilm, Aspergillus can produce many toxins, such as aflatoxin B1 (AFB1), ochratoxin, zearalenone, fumonisin, and patulin. Among these toxins, AFB1 possesses the h...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章,评审


    authors: Wang Q,Yang Q,Wu W

    更新日期:2020-03-27 00:00:00

  • Antimicrobial Resistance Diversity Suggestive of Distinct Salmonella Typhimurium Sources or Selective Pressures in Food-Production Animals.

    abstract::Salmonella enterica subsp. enterica serovar Typhimurium is a common cause of enterocolitis in humans globally, with multidrug resistant (MDR) strains posing an enhanced threat. S. Typhimurium is also a pathogen in food-production animals, and these populations can act as reservoirs of the bacterium. Therefore, surveil...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章


    authors: Mellor KC,Petrovska L,Thomson NR,Harris K,Reid SWJ,Mather AE

    更新日期:2019-04-12 00:00:00

  • Complementary DNA/RNA-Based Profiling: Characterization of Corrosive Microbial Communities and Their Functional Profiles in an Oil Production Facility.

    abstract::DNA and RNA-based sequencing of the 16S rRNA gene and transcripts were used to assess the phylogenetic diversity of microbial communities at assets experiencing corrosion in an oil production facility. The complementary methodological approach, coupled with extensive bioinformatics analysis, allowed to visualize diffe...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章


    authors: Salgar-Chaparro SJ,Machuca LL

    更新日期:2019-11-07 00:00:00

  • Effects of Intravenous Infusion With Sodium Butyrate on Colonic Microbiota, Intestinal Development- and Mucosal Immune-Related Gene Expression in Normal Growing Pigs.

    abstract::This study aimed to investigate effects of intravenous infusion with sodium butyrate (SB) on colonic microbiota, intestinal mucosal immune and intestinal development in normal growing pigs. Twelve crossbred barrows (Duroc × Landrace × Large White) fitted with a medical polyethylene cannula via internal jugular vein we...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章


    authors: Chen X,Xu J,Su Y,Zhu W

    更新日期:2018-07-20 00:00:00