---
_id: '14449'
abstract:
- lang: eng
  text: The rapid development of machine learning (ML) techniques has opened up the
    data-dense field of microbiome research for novel therapeutic, diagnostic, and
    prognostic applications targeting a wide range of disorders, which could substantially
    improve healthcare practices in the era of precision medicine. However, several
    challenges must be addressed to exploit the benefits of ML in this field fully.
    In particular, there is a need to establish “gold standard” protocols for conducting
    ML analysis experiments and improve interactions between microbiome researchers
    and ML experts. The Machine Learning Techniques in Human Microbiome Studies (ML4Microbiome)
    COST Action CA18131 is a European network established in 2019 to promote collaboration
    between discovery-oriented microbiome researchers and data-driven ML experts to
    optimize and standardize ML approaches for microbiome analysis. This perspective
    paper presents the key achievements of ML4Microbiome, which include identifying
    predictive and discriminatory ‘omics’ features, improving repeatability and comparability,
    developing automation procedures, and defining priority areas for the novel development
    of ML methods targeting the microbiome. The insights gained from ML4Microbiome
    will help to maximize the potential of ML in microbiome research and pave the
    way for new and improved healthcare practices.
acknowledgement: "This study is based upon work from COST Action ML4Microbiome “Statistical
  and machine learning techniques in human microbiome studies” (CA18131), supported
  by COST (European Cooperation in Science and Technology), www.cost.eu. MB acknowledges
  support through the Metagenopolis grant ANR-11-DPBS-0001. IM-I acknowledges support
  by the “Miguel Servet Type II” program (CPII21/00013) of the ISCIII-Madrid (Spain),
  co-financed by the FEDER.\r\nThe authors are grateful to all COST Action CA18131
  “Statistical and machine learning techniques in human microbiome studies” members
  for their contribution to the COST Action objectives, and to COST (European Cooperation
  in Science and Technology) for the economic support, www.cost.eu. WG2 and WG3 thank
  Emmanuelle Le Chatelier and Pauline Barbet (Université Paris-Saclay, INRAE, MetaGenoPolis,
  78350, Jouy-en-Josas, France) for preparing the shotgun CRC benchmark dataset."
article_number: '1257002'
article_processing_charge: Yes
article_type: original
author:
- first_name: Domenica
  full_name: D’Elia, Domenica
  last_name: D’Elia
- first_name: Jaak
  full_name: Truu, Jaak
  last_name: Truu
- first_name: Leo
  full_name: Lahti, Leo
  last_name: Lahti
- first_name: Magali
  full_name: Berland, Magali
  last_name: Berland
- first_name: Georgios
  full_name: Papoutsoglou, Georgios
  last_name: Papoutsoglou
- first_name: Michelangelo
  full_name: Ceci, Michelangelo
  last_name: Ceci
- first_name: Aldert
  full_name: Zomer, Aldert
  last_name: Zomer
- first_name: Marta B.
  full_name: Lopes, Marta B.
  last_name: Lopes
- first_name: Eliana
  full_name: Ibrahimi, Eliana
  last_name: Ibrahimi
- first_name: Aleksandra
  full_name: Gruca, Aleksandra
  last_name: Gruca
- first_name: Alina
  full_name: Nechyporenko, Alina
  last_name: Nechyporenko
- first_name: Marcus
  full_name: Frohme, Marcus
  last_name: Frohme
- first_name: Thomas
  full_name: Klammsteiner, Thomas
  last_name: Klammsteiner
- first_name: Enrique Carrillo De Santa
  full_name: Pau, Enrique Carrillo De Santa
  last_name: Pau
- first_name: Laura Judith
  full_name: Marcos-Zambrano, Laura Judith
  last_name: Marcos-Zambrano
- first_name: Karel
  full_name: Hron, Karel
  last_name: Hron
- first_name: Gianvito
  full_name: Pio, Gianvito
  last_name: Pio
- first_name: Andrea
  full_name: Simeon, Andrea
  last_name: Simeon
- first_name: Ramona
  full_name: Suharoschi, Ramona
  last_name: Suharoschi
- first_name: Isabel
  full_name: Moreno-Indias, Isabel
  last_name: Moreno-Indias
- first_name: Andriy
  full_name: Temko, Andriy
  last_name: Temko
- first_name: Miroslava
  full_name: Nedyalkova, Miroslava
  last_name: Nedyalkova
- first_name: Elena Simona
  full_name: Apostol, Elena Simona
  last_name: Apostol
- first_name: Ciprian Octavian
  full_name: Truică, Ciprian Octavian
  last_name: Truică
- first_name: Rajesh
  full_name: Shigdel, Rajesh
  last_name: Shigdel
- first_name: Jasminka Hasić
  full_name: Telalović, Jasminka Hasić
  last_name: Telalović
- first_name: Erik
  full_name: Bongcam-Rudloff, Erik
  last_name: Bongcam-Rudloff
- first_name: Piotr
  full_name: Przymus, Piotr
  last_name: Przymus
- first_name: Naida Babić
  full_name: Jordamović, Naida Babić
  last_name: Jordamović
- first_name: Laurent
  full_name: Falquet, Laurent
  last_name: Falquet
- first_name: Sonia
  full_name: Tarazona, Sonia
  last_name: Tarazona
- first_name: Alexia
  full_name: Sampri, Alexia
  last_name: Sampri
- first_name: Gaetano
  full_name: Isola, Gaetano
  last_name: Isola
- first_name: David
  full_name: Pérez-Serrano, David
  last_name: Pérez-Serrano
- first_name: Vladimir
  full_name: Trajkovik, Vladimir
  last_name: Trajkovik
- first_name: Lubos
  full_name: Klucar, Lubos
  last_name: Klucar
- first_name: Tatjana
  full_name: Loncar-Turukalo, Tatjana
  last_name: Loncar-Turukalo
- first_name: Aki S.
  full_name: Havulinna, Aki S.
  last_name: Havulinna
- first_name: Christian
  full_name: Jansen, Christian
  id: 837b2259-bcc9-11ed-a196-ae55927bc6e2
  last_name: Jansen
- first_name: Randi J.
  full_name: Bertelsen, Randi J.
  last_name: Bertelsen
- first_name: Marcus Joakim
  full_name: Claesson, Marcus Joakim
  last_name: Claesson
citation:
  ama: 'D’Elia D, Truu J, Lahti L, et al. Advancing microbiome research with machine
    learning: Key findings from the ML4Microbiome COST action. <i>Frontiers in Microbiology</i>.
    2023;14. doi:<a href="https://doi.org/10.3389/fmicb.2023.1257002">10.3389/fmicb.2023.1257002</a>'
  apa: 'D’Elia, D., Truu, J., Lahti, L., Berland, M., Papoutsoglou, G., Ceci, M.,
    … Claesson, M. J. (2023). Advancing microbiome research with machine learning:
    Key findings from the ML4Microbiome COST action. <i>Frontiers in Microbiology</i>.
    Frontiers. <a href="https://doi.org/10.3389/fmicb.2023.1257002">https://doi.org/10.3389/fmicb.2023.1257002</a>'
  chicago: 'D’Elia, Domenica, Jaak Truu, Leo Lahti, Magali Berland, Georgios Papoutsoglou,
    Michelangelo Ceci, Aldert Zomer, et al. “Advancing Microbiome Research with Machine
    Learning: Key Findings from the ML4Microbiome COST Action.” <i>Frontiers in Microbiology</i>.
    Frontiers, 2023. <a href="https://doi.org/10.3389/fmicb.2023.1257002">https://doi.org/10.3389/fmicb.2023.1257002</a>.'
  ieee: 'D. D’Elia <i>et al.</i>, “Advancing microbiome research with machine learning:
    Key findings from the ML4Microbiome COST action,” <i>Frontiers in Microbiology</i>,
    vol. 14. Frontiers, 2023.'
  ista: 'D’Elia D, Truu J, Lahti L, Berland M, Papoutsoglou G, Ceci M, Zomer A, Lopes
    MB, Ibrahimi E, Gruca A, Nechyporenko A, Frohme M, Klammsteiner T, Pau ECDS, Marcos-Zambrano
    LJ, Hron K, Pio G, Simeon A, Suharoschi R, Moreno-Indias I, Temko A, Nedyalkova
    M, Apostol ES, Truică CO, Shigdel R, Telalović JH, Bongcam-Rudloff E, Przymus
    P, Jordamović NB, Falquet L, Tarazona S, Sampri A, Isola G, Pérez-Serrano D, Trajkovik
    V, Klucar L, Loncar-Turukalo T, Havulinna AS, Jansen C, Bertelsen RJ, Claesson
    MJ. 2023. Advancing microbiome research with machine learning: Key findings from
    the ML4Microbiome COST action. Frontiers in Microbiology. 14, 1257002.'
  mla: 'D’Elia, Domenica, et al. “Advancing Microbiome Research with Machine Learning:
    Key Findings from the ML4Microbiome COST Action.” <i>Frontiers in Microbiology</i>,
    vol. 14, 1257002, Frontiers, 2023, doi:<a href="https://doi.org/10.3389/fmicb.2023.1257002">10.3389/fmicb.2023.1257002</a>.'
  short: D. D’Elia, J. Truu, L. Lahti, M. Berland, G. Papoutsoglou, M. Ceci, A. Zomer,
    M.B. Lopes, E. Ibrahimi, A. Gruca, A. Nechyporenko, M. Frohme, T. Klammsteiner,
    E.C.D.S. Pau, L.J. Marcos-Zambrano, K. Hron, G. Pio, A. Simeon, R. Suharoschi,
    I. Moreno-Indias, A. Temko, M. Nedyalkova, E.S. Apostol, C.O. Truică, R. Shigdel,
    J.H. Telalović, E. Bongcam-Rudloff, P. Przymus, N.B. Jordamović, L. Falquet, S.
    Tarazona, A. Sampri, G. Isola, D. Pérez-Serrano, V. Trajkovik, L. Klucar, T. Loncar-Turukalo,
    A.S. Havulinna, C. Jansen, R.J. Bertelsen, M.J. Claesson, Frontiers in Microbiology
    14 (2023).
date_created: 2023-10-22T22:01:16Z
date_published: 2023-09-25T00:00:00Z
date_updated: 2023-12-13T13:07:21Z
day: '25'
ddc:
- '000'
department:
- _id: ScienComp
doi: 10.3389/fmicb.2023.1257002
external_id:
  isi:
  - '001080536000001'
  pmid:
  - '37808321'
file:
- access_level: open_access
  checksum: 6c0acdd8fa111a699826957b8dff19d5
  content_type: application/pdf
  creator: dernst
  date_created: 2023-10-30T13:38:48Z
  date_updated: 2023-10-30T13:38:48Z
  file_id: '14471'
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  file_size: 505078
  relation: main_file
  success: 1
file_date_updated: 2023-10-30T13:38:48Z
has_accepted_license: '1'
intvolume: '        14'
isi: 1
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
publication: Frontiers in Microbiology
publication_identifier:
  eissn:
  - 1664-302X
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Advancing microbiome research with machine learning: Key findings from the
  ML4Microbiome COST action'
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2023'
...
---
_id: '12469'
abstract:
- lang: eng
  text: 'Hosts can carry many viruses in their bodies, but not all of them cause disease.
    We studied ants as a social host to determine both their overall viral repertoire
    and the subset of actively infecting viruses across natural populations of three
    subfamilies: the Argentine ant (Linepithema humile, Dolichoderinae), the invasive
    garden ant (Lasius neglectus, Formicinae) and the red ant (Myrmica rubra, Myrmicinae).
    We used a dual sequencing strategy to reconstruct complete virus genomes by RNA-seq
    and to simultaneously determine the small interfering RNAs (siRNAs) by small RNA
    sequencing (sRNA-seq), which constitute the host antiviral RNAi immune response.
    This approach led to the discovery of 41 novel viruses in ants and revealed a
    host ant-specific RNAi response (21 vs. 22 nt siRNAs) in the different ant species.
    The efficiency of the RNAi response (sRNA/RNA read count ratio) depended on the
    virus and the respective ant species, but not its population. Overall, we found
    the highest virus abundance and diversity per population in Li. humile, followed
    by La. neglectus and M. rubra. Argentine ants also shared a high proportion of
    viruses between populations, whilst overlap was nearly absent in M. rubra. Only
    one of the 59 viruses was found to infect two of the ant species as hosts, revealing
    high host-specificity in active infections. In contrast, six viruses actively
    infected one ant species, but were found as contaminants only in the others. Disentangling
    spillover of disease-causing infection from non-infecting contamination across
    species is providing relevant information for disease ecology and ecosystem management.'
acknowledgement: "We thank D.J. Obbard for sharing the details of the dual RNA-seq/sRNA-seq
  approach, S.\r\nMetzler and R. Ferrigato for the photographs (Figure 1), M. Konrad,
  B. Casillas-Perez, C.D.\r\nPull and X. Espadaler for help with ant collection, and
  the Social Immunity Team at IST\r\nAustria, in particular J. Robb, A. Franschitz,
  E. Naderlinger, E. Dawson and B. Casillas-Perez\r\nfor support and comments on the
  manuscript. The study was funded by the Austrian Science\r\nFund (FWF; M02076-B25
  to MAF) and the Academy of Finland (343022 to LV). "
article_number: '1119002'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Lumi
  full_name: Viljakainen, Lumi
  last_name: Viljakainen
- first_name: Matthias
  full_name: Fürst, Matthias
  id: 393B1196-F248-11E8-B48F-1D18A9856A87
  last_name: Fürst
  orcid: 0000-0002-3712-925X
- first_name: Anna V
  full_name: Grasse, Anna V
  id: 406F989C-F248-11E8-B48F-1D18A9856A87
  last_name: Grasse
- first_name: Jaana
  full_name: Jurvansuu, Jaana
  last_name: Jurvansuu
- first_name: Jinook
  full_name: Oh, Jinook
  id: 403169A4-080F-11EA-9993-BF3F3DDC885E
  last_name: Oh
  orcid: 0000-0001-7425-2372
- first_name: Lassi
  full_name: Tolonen, Lassi
  last_name: Tolonen
- first_name: Thomas
  full_name: Eder, Thomas
  last_name: Eder
- first_name: Thomas
  full_name: Rattei, Thomas
  last_name: Rattei
- first_name: Sylvia
  full_name: Cremer, Sylvia
  id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
  last_name: Cremer
  orcid: 0000-0002-2193-3868
citation:
  ama: Viljakainen L, Fürst M, Grasse AV, et al. Antiviral immune response reveals
    host-specific virus infections in natural ant populations. <i>Frontiers in Microbiology</i>.
    2023;14. doi:<a href="https://doi.org/10.3389/fmicb.2023.1119002">10.3389/fmicb.2023.1119002</a>
  apa: Viljakainen, L., Fürst, M., Grasse, A. V., Jurvansuu, J., Oh, J., Tolonen,
    L., … Cremer, S. (2023). Antiviral immune response reveals host-specific virus
    infections in natural ant populations. <i>Frontiers in Microbiology</i>. Frontiers.
    <a href="https://doi.org/10.3389/fmicb.2023.1119002">https://doi.org/10.3389/fmicb.2023.1119002</a>
  chicago: Viljakainen, Lumi, Matthias Fürst, Anna V Grasse, Jaana Jurvansuu, Jinook
    Oh, Lassi Tolonen, Thomas Eder, Thomas Rattei, and Sylvia Cremer. “Antiviral Immune
    Response Reveals Host-Specific Virus Infections in Natural Ant Populations.” <i>Frontiers
    in Microbiology</i>. Frontiers, 2023. <a href="https://doi.org/10.3389/fmicb.2023.1119002">https://doi.org/10.3389/fmicb.2023.1119002</a>.
  ieee: L. Viljakainen <i>et al.</i>, “Antiviral immune response reveals host-specific
    virus infections in natural ant populations,” <i>Frontiers in Microbiology</i>,
    vol. 14. Frontiers, 2023.
  ista: Viljakainen L, Fürst M, Grasse AV, Jurvansuu J, Oh J, Tolonen L, Eder T, Rattei
    T, Cremer S. 2023. Antiviral immune response reveals host-specific virus infections
    in natural ant populations. Frontiers in Microbiology. 14, 1119002.
  mla: Viljakainen, Lumi, et al. “Antiviral Immune Response Reveals Host-Specific
    Virus Infections in Natural Ant Populations.” <i>Frontiers in Microbiology</i>,
    vol. 14, 1119002, Frontiers, 2023, doi:<a href="https://doi.org/10.3389/fmicb.2023.1119002">10.3389/fmicb.2023.1119002</a>.
  short: L. Viljakainen, M. Fürst, A.V. Grasse, J. Jurvansuu, J. Oh, L. Tolonen, T.
    Eder, T. Rattei, S. Cremer, Frontiers in Microbiology 14 (2023).
date_created: 2023-01-31T08:13:40Z
date_published: 2023-03-16T00:00:00Z
date_updated: 2023-08-01T12:39:58Z
day: '16'
ddc:
- '570'
department:
- _id: SyCr
doi: 10.3389/fmicb.2023.1119002
external_id:
  isi:
  - '000961542100001'
  pmid:
  - 'PPR559293 '
file:
- access_level: open_access
  checksum: cd52292963acce1111634d9fac08c699
  content_type: application/pdf
  creator: dernst
  date_created: 2023-04-17T07:49:09Z
  date_updated: 2023-04-17T07:49:09Z
  file_id: '12843'
  file_name: 2023_FrontMicrobiology_Viljakainen.pdf
  file_size: 4866332
  relation: main_file
  success: 1
file_date_updated: 2023-04-17T07:49:09Z
has_accepted_license: '1'
intvolume: '        14'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25DF61D8-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: M02076
  name: Viral pathogens and social immunity in ants
publication: Frontiers in Microbiology
publication_identifier:
  eissn:
  - 1664-302X
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Antiviral immune response reveals host-specific virus infections in natural
  ant populations
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 14
year: '2023'
...
---
_id: '12478'
abstract:
- lang: eng
  text: In Gram negative bacteria, the multiple antibiotic resistance or mar operon,
    is known to control the expression of multi-drug efflux genes that protect bacteria
    from a wide range of drugs. As many different chemical compounds can induce this
    operon, identifying the parameters that govern the dynamics of its induction is
    crucial to better characterize the processes of tolerance and resistance. Most
    experiments have assumed that the properties of the mar transcriptional network
    can be inferred from population measurements. However, measurements from an asynchronous
    population of cells can mask underlying phenotypic variations of single cells.
    We monitored the activity of the mar promoter in single Escherichia coli cells
    in linear micro-colonies and established that the response to a steady level of
    inducer was most heterogeneous within individual colonies for an intermediate
    value of inducer. Specifically, sub-lineages defined by contiguous daughter-cells
    exhibited similar promoter activity, whereas activity was greatly variable between
    different sub-lineages. Specific sub-trees of uniform promoter activity persisted
    over several generations. Statistical analyses of the lineages suggest that the
    presence of these sub-trees is the signature of an inducible memory of the promoter
    state that is transmitted from mother to daughter cells. This single-cell study
    reveals that the degree of epigenetic inheritance changes as a function of inducer
    concentration, suggesting that phenotypic inheritance may be an inducible phenotype.
acknowledgement: This work was supported by NIH P50 award P50GM081892-02 to the University
  of Chicago, a catalyst grant from the Chicago Biomedical Consortium with support
  from The Searle Funds at The Chicago Community Trust to PC, and a Yen Fellowship
  to CCG. MA was partially supported by PAPIIT-UNAM grant IN-11322.
article_number: '1049255'
article_processing_charge: Yes
article_type: original
author:
- first_name: Calin C
  full_name: Guet, Calin C
  id: 47F8433E-F248-11E8-B48F-1D18A9856A87
  last_name: Guet
  orcid: 0000-0001-6220-2052
- first_name: L
  full_name: Bruneaux, L
  last_name: Bruneaux
- first_name: P
  full_name: Oikonomou, P
  last_name: Oikonomou
- first_name: M
  full_name: Aldana, M
  last_name: Aldana
- first_name: P
  full_name: Cluzel, P
  last_name: Cluzel
citation:
  ama: Guet CC, Bruneaux L, Oikonomou P, Aldana M, Cluzel P. Monitoring lineages of
    growing and dividing bacteria reveals an inducible memory of <i>mar</i> operon
    expression. <i>Frontiers in Microbiology</i>. 2023;14. doi:<a href="https://doi.org/10.3389/fmicb.2023.1049255">10.3389/fmicb.2023.1049255</a>
  apa: Guet, C. C., Bruneaux, L., Oikonomou, P., Aldana, M., &#38; Cluzel, P. (2023).
    Monitoring lineages of growing and dividing bacteria reveals an inducible memory
    of <i>mar</i> operon expression. <i>Frontiers in Microbiology</i>. Frontiers.
    <a href="https://doi.org/10.3389/fmicb.2023.1049255">https://doi.org/10.3389/fmicb.2023.1049255</a>
  chicago: Guet, Calin C, L Bruneaux, P Oikonomou, M Aldana, and P Cluzel. “Monitoring
    Lineages of Growing and Dividing Bacteria Reveals an Inducible Memory of <i>Mar</i>
    Operon Expression.” <i>Frontiers in Microbiology</i>. Frontiers, 2023. <a href="https://doi.org/10.3389/fmicb.2023.1049255">https://doi.org/10.3389/fmicb.2023.1049255</a>.
  ieee: C. C. Guet, L. Bruneaux, P. Oikonomou, M. Aldana, and P. Cluzel, “Monitoring
    lineages of growing and dividing bacteria reveals an inducible memory of <i>mar</i>
    operon expression,” <i>Frontiers in Microbiology</i>, vol. 14. Frontiers, 2023.
  ista: Guet CC, Bruneaux L, Oikonomou P, Aldana M, Cluzel P. 2023. Monitoring lineages
    of growing and dividing bacteria reveals an inducible memory of <i>mar</i> operon
    expression. Frontiers in Microbiology. 14, 1049255.
  mla: Guet, Calin C., et al. “Monitoring Lineages of Growing and Dividing Bacteria
    Reveals an Inducible Memory of <i>Mar</i> Operon Expression.” <i>Frontiers in
    Microbiology</i>, vol. 14, 1049255, Frontiers, 2023, doi:<a href="https://doi.org/10.3389/fmicb.2023.1049255">10.3389/fmicb.2023.1049255</a>.
  short: C.C. Guet, L. Bruneaux, P. Oikonomou, M. Aldana, P. Cluzel, Frontiers in
    Microbiology 14 (2023).
date_created: 2023-02-02T08:13:28Z
date_published: 2023-06-20T00:00:00Z
date_updated: 2023-08-02T06:25:04Z
day: '20'
ddc:
- '570'
department:
- _id: CaGu
doi: 10.3389/fmicb.2023.1049255
external_id:
  isi:
  - '001030002600001'
  pmid:
  - '37485524'
file:
- access_level: open_access
  checksum: 7dd322347512afaa5daf72a0154f2f07
  content_type: application/pdf
  creator: dernst
  date_created: 2023-07-31T07:16:34Z
  date_updated: 2023-07-31T07:16:34Z
  file_id: '13322'
  file_name: 2023_FrontiersMicrobiology_Guet.pdf
  file_size: 6452841
  relation: main_file
  success: 1
file_date_updated: 2023-07-31T07:16:34Z
has_accepted_license: '1'
intvolume: '        14'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Frontiers in Microbiology
publication_identifier:
  eissn:
  - 1664-302X
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Monitoring lineages of growing and dividing bacteria reveals an inducible memory
  of <i>mar</i> operon expression
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2023'
...
---
_id: '9380'
abstract:
- lang: eng
  text: Shigella are pathogens originating within the Escherichia lineage but frequently
    classified as a separate genus. Shigella genomes contain numerous insertion sequences
    (ISs) that lead to pseudogenisation of affected genes and an increase of non-homologous
    recombination. Here, we study 414 genomes of E. coli and Shigella strains to assess
    the contribution of genomic rearrangements to Shigella evolution. We found that
    Shigella experienced exceptionally high rates of intragenomic rearrangements and
    had a decreased rate of homologous recombination compared to pathogenic and non-pathogenic
    E. coli. The high rearrangement rate resulted in independent disruption of syntenic
    regions and parallel rearrangements in different Shigella lineages. Specifically,
    we identified two types of chromosomally encoded E3 ubiquitin-protein ligases
    acquired independently by all Shigella strains that also showed a high level of
    sequence conservation in the promoter and further in the 5′-intergenic region.
    In the only available enteroinvasive E. coli (EIEC) strain, which is a pathogenic
    E. coli with a phenotype intermediate between Shigella and non-pathogenic E. coli,
    we found a rate of genome rearrangements comparable to those in other E. coli
    and no functional copies of the two Shigella-specific E3 ubiquitin ligases. These
    data indicate that the accumulation of ISs influenced many aspects of genome evolution
    and played an important role in the evolution of intracellular pathogens. Our
    research demonstrates the power of comparative genomics-based on synteny block
    composition and an important role of non-coding regions in the evolution of genomic
    islands.
acknowledgement: We thank Fyodor Kondrashov for valuable advice and manuscript proofreading.
  We also thank Alla Mikheenko for assistance with Circos.
article_number: '628622'
article_processing_charge: No
article_type: original
author:
- first_name: Zaira
  full_name: Seferbekova, Zaira
  last_name: Seferbekova
- first_name: Alexey
  full_name: Zabelkin, Alexey
  last_name: Zabelkin
- first_name: Yulia
  full_name: Yakovleva, Yulia
  last_name: Yakovleva
- first_name: Robert
  full_name: Afasizhev, Robert
  last_name: Afasizhev
- first_name: Natalia O.
  full_name: Dranenko, Natalia O.
  last_name: Dranenko
- first_name: Nikita
  full_name: Alexeev, Nikita
  last_name: Alexeev
- first_name: Mikhail S.
  full_name: Gelfand, Mikhail S.
  last_name: Gelfand
- first_name: Olga
  full_name: Bochkareva, Olga
  id: C4558D3C-6102-11E9-A62E-F418E6697425
  last_name: Bochkareva
  orcid: 0000-0003-1006-6639
citation:
  ama: Seferbekova Z, Zabelkin A, Yakovleva Y, et al. High rates of genome rearrangements
    and pathogenicity of Shigella spp. <i>Frontiers in Microbiology</i>. 2021;12.
    doi:<a href="https://doi.org/10.3389/fmicb.2021.628622">10.3389/fmicb.2021.628622</a>
  apa: Seferbekova, Z., Zabelkin, A., Yakovleva, Y., Afasizhev, R., Dranenko, N. O.,
    Alexeev, N., … Bochkareva, O. (2021). High rates of genome rearrangements and
    pathogenicity of Shigella spp. <i>Frontiers in Microbiology</i>. Frontiers. <a
    href="https://doi.org/10.3389/fmicb.2021.628622">https://doi.org/10.3389/fmicb.2021.628622</a>
  chicago: Seferbekova, Zaira, Alexey Zabelkin, Yulia Yakovleva, Robert Afasizhev,
    Natalia O. Dranenko, Nikita Alexeev, Mikhail S. Gelfand, and Olga Bochkareva.
    “High Rates of Genome Rearrangements and Pathogenicity of Shigella Spp.” <i>Frontiers
    in Microbiology</i>. Frontiers, 2021. <a href="https://doi.org/10.3389/fmicb.2021.628622">https://doi.org/10.3389/fmicb.2021.628622</a>.
  ieee: Z. Seferbekova <i>et al.</i>, “High rates of genome rearrangements and pathogenicity
    of Shigella spp,” <i>Frontiers in Microbiology</i>, vol. 12. Frontiers, 2021.
  ista: Seferbekova Z, Zabelkin A, Yakovleva Y, Afasizhev R, Dranenko NO, Alexeev
    N, Gelfand MS, Bochkareva O. 2021. High rates of genome rearrangements and pathogenicity
    of Shigella spp. Frontiers in Microbiology. 12, 628622.
  mla: Seferbekova, Zaira, et al. “High Rates of Genome Rearrangements and Pathogenicity
    of Shigella Spp.” <i>Frontiers in Microbiology</i>, vol. 12, 628622, Frontiers,
    2021, doi:<a href="https://doi.org/10.3389/fmicb.2021.628622">10.3389/fmicb.2021.628622</a>.
  short: Z. Seferbekova, A. Zabelkin, Y. Yakovleva, R. Afasizhev, N.O. Dranenko, N.
    Alexeev, M.S. Gelfand, O. Bochkareva, Frontiers in Microbiology 12 (2021).
date_created: 2021-05-09T22:01:38Z
date_published: 2021-04-12T00:00:00Z
date_updated: 2023-08-08T13:30:39Z
day: '12'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.3389/fmicb.2021.628622
ec_funded: 1
external_id:
  isi:
  - '000643713300001'
file:
- access_level: open_access
  checksum: 2f856543add59273a482a7f326fc0400
  content_type: application/pdf
  creator: kschuh
  date_created: 2021-05-11T13:05:52Z
  date_updated: 2021-05-11T13:05:52Z
  file_id: '9384'
  file_name: 2021_Frontiers_Microbiology_Seferbekova.pdf
  file_size: 14362316
  relation: main_file
  success: 1
file_date_updated: 2021-05-11T13:05:52Z
has_accepted_license: '1'
intvolume: '        12'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '754411'
  name: ISTplus - Postdoctoral Fellowships
publication: Frontiers in Microbiology
publication_identifier:
  eissn:
  - 1664-302X
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: High rates of genome rearrangements and pathogenicity of Shigella spp
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...
---
_id: '10271'
abstract:
- lang: eng
  text: Understanding interactions between antibiotics used in combination is an important
    theme in microbiology. Using the interactions between the antifolate drug trimethoprim
    and the ribosome-targeting antibiotic erythromycin in Escherichia coli as a model,
    we applied a transcriptomic approach for dissecting interactions between two antibiotics
    with different modes of action. When trimethoprim and erythromycin were combined,
    the transcriptional response of genes from the sulfate reduction pathway deviated
    from the dominant effect of trimethoprim on the transcriptome. We successfully
    altered the drug interaction from additivity to suppression by increasing the
    sulfate level in the growth environment and identified sulfate reduction as an
    important metabolic determinant that shapes the interaction between the two drugs.
    Our work highlights the potential of using prioritization of gene expression patterns
    as a tool for identifying key metabolic determinants that shape drug-drug interactions.
    We further demonstrated that the sigma factor-binding protein gene crl shapes
    the interactions between the two antibiotics, which provides a rare example of
    how naturally occurring variations between strains of the same bacterial species
    can sometimes generate very different drug interactions.
acknowledgement: High-throughput sequencing data were generated by the Vienna BioCenter
  Core Facilities. The authors would like to thank Karin Mitosch, Bor Kavcic, and
  Nadine Kraupner for their constructive feedback. The authors would also like to
  thank Gertraud Stift, Julia Flor, Renate Srsek, Agnieszka Wiktor, and Booshini Fernando
  for technical support.
article_number: '760017'
article_processing_charge: No
article_type: original
author:
- first_name: Qin
  full_name: Qi, Qin
  id: 3B22D412-F248-11E8-B48F-1D18A9856A87
  last_name: Qi
  orcid: 0000-0002-6148-2416
- first_name: S. Andreas
  full_name: Angermayr, S. Andreas
  last_name: Angermayr
- first_name: Mark Tobias
  full_name: Bollenbach, Mark Tobias
  id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
  last_name: Bollenbach
  orcid: 0000-0003-4398-476X
citation:
  ama: Qi Q, Angermayr SA, Bollenbach MT. Uncovering Key Metabolic Determinants of
    the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli.
    <i>Frontiers in Microbiology</i>. 2021;12. doi:<a href="https://doi.org/10.3389/fmicb.2021.760017">10.3389/fmicb.2021.760017</a>
  apa: Qi, Q., Angermayr, S. A., &#38; Bollenbach, M. T. (2021). Uncovering Key Metabolic
    Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in
    Escherichia coli. <i>Frontiers in Microbiology</i>. Frontiers. <a href="https://doi.org/10.3389/fmicb.2021.760017">https://doi.org/10.3389/fmicb.2021.760017</a>
  chicago: Qi, Qin, S. Andreas Angermayr, and Mark Tobias Bollenbach. “Uncovering
    Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin
    in Escherichia Coli.” <i>Frontiers in Microbiology</i>. Frontiers, 2021. <a href="https://doi.org/10.3389/fmicb.2021.760017">https://doi.org/10.3389/fmicb.2021.760017</a>.
  ieee: Q. Qi, S. A. Angermayr, and M. T. Bollenbach, “Uncovering Key Metabolic Determinants
    of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia
    coli,” <i>Frontiers in Microbiology</i>, vol. 12. Frontiers, 2021.
  ista: Qi Q, Angermayr SA, Bollenbach MT. 2021. Uncovering Key Metabolic Determinants
    of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia
    coli. Frontiers in Microbiology. 12, 760017.
  mla: Qi, Qin, et al. “Uncovering Key Metabolic Determinants of the Drug Interactions
    Between Trimethoprim and Erythromycin in Escherichia Coli.” <i>Frontiers in Microbiology</i>,
    vol. 12, 760017, Frontiers, 2021, doi:<a href="https://doi.org/10.3389/fmicb.2021.760017">10.3389/fmicb.2021.760017</a>.
  short: Q. Qi, S.A. Angermayr, M.T. Bollenbach, Frontiers in Microbiology 12 (2021).
date_created: 2021-11-11T10:39:37Z
date_published: 2021-10-20T00:00:00Z
date_updated: 2023-08-14T11:43:23Z
day: '20'
ddc:
- '610'
doi: 10.3389/fmicb.2021.760017
ec_funded: 1
external_id:
  isi:
  - '000715997300001'
  pmid:
  - '34745067'
file:
- access_level: open_access
  checksum: d41321748e9588dd3cf03e9a7222127f
  content_type: application/pdf
  creator: cchlebak
  date_created: 2021-11-11T10:54:40Z
  date_updated: 2021-11-11T10:54:40Z
  file_id: '10272'
  file_name: 2021_FrontiersMicrob_Qi.pdf
  file_size: 2397203
  relation: main_file
  success: 1
file_date_updated: 2021-11-11T10:54:40Z
has_accepted_license: '1'
intvolume: '        12'
isi: 1
keyword:
- microbiology
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: P27201-B22
  name: Revealing the mechanisms underlying drug interactions
- _id: 25E83C2C-B435-11E9-9278-68D0E5697425
  call_identifier: FP7
  grant_number: '303507'
  name: Optimality principles in responses to antibiotics
publication: Frontiers in Microbiology
publication_identifier:
  eissn:
  - 1664-302X
publication_status: published
publisher: Frontiers
quality_controlled: '1'
scopus_import: '1'
status: public
title: Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim
  and Erythromycin in Escherichia coli
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2021'
...