The ISME Journal

Collection 15 June 2023

Editors' Choice

Our Editors-in-Chief are delighted to share with you a selection of key papers from each issue that highlight some of the best research published in The ISME Journal. These papers showcase the breadth of scope and coverage the journal consistently delivers to its readers.
Editors Choice articles will be freely accessible for the month of the issue in which they feature.

2023

Targeting Fusobacterium nucleatum through chemical modifications of host-derived transfer RNA fragments
- Mengdi Yang
- Pu-Ting Dong
- Jiahe Li
ArticleOpen Access1 Apr 2023 The ISME Journal
Cuticle supplementation and nitrogen recycling by a dual bacterial symbiosis in a family of xylophagous beetles
- Julian Simon Thilo Kiefer
- Eugen Bauer
- Tobias Engl
ArticleOpen Access21 Apr 2023 The ISME Journal
Collective protection against the type VI secretion system in bacteria
- Elisa T. Granato
- William P. J. Smith
- Kevin R. Foster
ArticleOpen Access24 Apr 2023 The ISME Journal
Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies
- Hugo Doré
- Ulysse Guyet
- Laurence Garczarek
ArticleOpen Access25 Feb 2023 The ISME Journal
Shifts from cooperative to individual-based predation defense determine microbial predator-prey dynamics
- Magali de la Cruz Barron
- Ellen van Velzen
- David Kneis
ArticleOpen Access28 Feb 2023 The ISME Journal
Comparative susceptibility of SARS-CoV-2, SARS-CoV, and MERS-CoV across mammals
- Meng Li
- Juan Du
- Xuming Zhou
ArticleOpen Access23 Jan 2023 The ISME Journal
Life history strategies among soil bacteria—dichotomy for few, continuum for many
- Bram W. G. Stone
- Paul Dijkstra
- Bruce A. Hungate
ArticleOpen Access2 Feb 2023 The ISME Journal
Silent gene clusters encode magnetic organelle biosynthesis in a non-magnetotactic phototrophic bacterium
- M. V. Dziuba
- A. Paulus
- D. Schüler
ArticleOpen Access14 Dec 2022 The ISME Journal
Plant microbiomes harbor potential to promote nutrient turnover in impoverished substrates of a Brazilian biodiversity hotspot
- Antonio P. Camargo
- Rafael S. C. de Souza
- Paulo Arruda
ArticleOpen Access20 Dec 2022 The ISME Journal
Basin-scale biogeography of Prochlorococcus and SAR11 ecotype replication
- Alyse A. Larkin
- George I. Hagstrom
- Adam C. Martiny
ArticleOpen Access22 Oct 2022 The ISME Journal
In situ electrosynthetic bacterial growth using electricity generated by a deep-sea hydrothermal vent
- Masahiro Yamamoto
- Yoshihiro Takaki
- Ken Takai
ArticleOpen Access23 Sep 2022 The ISME Journal
Diazotrophs are overlooked contributors to carbon and nitrogen export to the deep ocean
- Sophie Bonnet
- Mar Benavides
- Francisco M. Cornejo-Castillo
ArticleOpen Access26 Sep 2022 The ISME Journal
Metabolic genes on conjugative plasmids are highly prevalent in Escherichia coli and can protect against antibiotic treatment
- Alana Palomino
- Danya Gewurz
- Allison J. Lopatkin
ArticleOpen Access19 Oct 2022 The ISME Journal
Bacterial ectosymbionts in cuticular organs chemically protect a beetle during molting stages
- Rebekka S. Janke
- Filip Kaftan
- Laura V. Flórez
ArticleOpen Access2 Sep 2022 The ISME Journal
Genomic diversity and biosynthetic capabilities of sponge-associated chlamydiae
- Jennah E. Dharamshi
- Natalia Gaarslev
- Thijs J. G. Ettema
ArticleOpen Access30 Aug 2022 The ISME Journal

2022

Ecological memory of prior nutrient exposure in the human gut microbiome
- Jeffrey Letourneau
- Zachary C. Holmes
- Lawrence A. David
Article23 Jul 2022 The ISME Journal
Flavonoid-attracted Aeromonas sp. from the Arabidopsis root microbiome enhances plant dehydration resistance
- Danxia He
- Sunil K. Singh
- Huiming Zhang
ArticleOpen Access16 Jul 2022 The ISME Journal
Novel form of collective movement by soil bacteria
- I. C. Engelhardt
- D. Patko
- L. X. Dupuy
Article7 Jul 2022 The ISME Journal
Pathogenic fungus uses volatiles to entice male flies into fatal matings with infected female cadavers
- Andreas Naundrup
- Björn Bohman
- Henrik H. De Fine Licht
Article13 Jul 2022 The ISME Journal
Endosymbiont population genomics sheds light on transmission mode, partner specificity, and stability of the scaly-foot snail holobiont
- Yi Lan
- Jin Sun
- Pei-Yuan Qian
ArticleOpen Access17 Jun 2022 The ISME Journal
Honey bee symbiont buffers larvae against nutritional stress and supplements lysine
- Audrey J. Parish
- Danny W. Rice
- Irene L. G. Newton
Article20 Jun 2022 The ISME Journal
Photophysiological response of Symbiodiniaceae single cells to temperature stress
- Linhong Xiao
- Sofia Johansson
- Lars Behrendt
Brief CommunicationOpen Access26 Apr 2022 The ISME Journal
Ecological dynamics of the gut microbiome in response to dietary fiber
- Hongbin Liu
- Chen Liao
- Lei Dai
Article21 May 2022 The ISME Journal
Decreased efficacy of antimicrobial agents in a polymicrobial environment
- Thomas James O’Brien
- Wendy Figueroa
- Martin Welch
ArticleOpen Access19 Mar 2022 The ISME Journal
Microbial communities of Auka hydrothermal sediments shed light on vent biogeography and the evolutionary history of thermophily
- Daan R. Speth
- Feiqiao B. Yu
- Victoria J. Orphan
ArticleOpen Access28 Mar 2022 The ISME Journal
Abiotic factors modulate interspecies competition mediated by the type VI secretion system effectors in Vibrio cholerae
- Ming-Xuan Tang
- Tong-Tong Pei
- Tao Dong
Article30 Mar 2022 The ISME Journal
Experimental evaluation of ecological principles to understand and modulate the outcome of bacterial strain competition in gut microbiomes
- Rafael R. Segura Munoz
- Sara Mantz
- Amanda E. Ramer-Tait
ArticleOpen Access24 Feb 2022 The ISME Journal
Diversity and origins of bacterial and archaeal viruses on sinking particles reaching the abyssal ocean
- Elaine Luo
- Andy O. Leu
- Edward F. DeLong
ArticleOpen Access2 Mar 2022 The ISME Journal
Infection strategy and biogeography distinguish cosmopolitan groups of marine jumbo bacteriophages
- Alaina R. Weinheimer
- Frank O. Aylward
ArticleOpen Access8 Mar 2022 The ISME Journal
Quantification of archaea-driven freshwater nitrification from single cell to ecosystem levels
- Franziska Klotz
- Katharina Kitzinger
- Michael Pester
ArticleOpen Access8 Mar 2022 The ISME Journal
Mammalian gut metabolomes mirror microbiome composition and host phylogeny
- Rachel Gregor
- Maraike Probst
- Itzhak Mizrahi
ArticleOpen Access13 Dec 2021 The ISME Journal
Phage co-transport with hyphal-riding bacteria fuels bacterial invasion in a water-unsaturated microbial model system
- Xin You
- René Kallies
- Lukas Y. Wick
ArticleOpen Access13 Dec 2021 The ISME Journal
Forest tree growth is linked to mycorrhizal fungal composition and function across Europe
- Mark A. Anthony
- Thomas W. Crowther
- Colin Averill
ArticleOpen Access10 Jan 2022 The ISME Journal
Activity-based, genome-resolved metagenomics uncovers key populations and pathways involved in subsurface conversions of coal to methane
- Luke J. McKay
- Heidi J. Smith
- Matthew W. Fields
Article23 Oct 2021 The ISME Journal
Bacterial response to spatial gradients of algal-derived nutrients in a porous microplate
- Hyungseok Kim
- Jeffrey A. Kimbrel
- Cullen R. Buie
ArticleOpen Access17 Nov 2021 The ISME Journal
In vitro interaction network of a synthetic gut bacterial community
- Anna S. Weiss
- Anna G. Burrichter
- Bärbel Stecher
ArticleOpen Access2 Dec 2021 The ISME Journal
Fecal filtrate transplantation protects against necrotizing enterocolitis
- Anders Brunse
- Ling Deng
- Thomas Thymann
ArticleOpen Access22 Sep 2021 The ISME Journal
Incomplete tricarboxylic acid cycle and proton gradient in Pandoravirus massiliensis: is it still a virus?
- Sarah Aherfi
- Djamal Brahim Belhaouari
- Bernard La Scola
ArticleOpen Access23 Sep 2021 The ISME Journal
Inter-species interactions alter antibiotic efficacy in bacterial communities
- Michael J. Bottery
- Jessica L. Matthews
- Ville-Petri Friman
ArticleOpen Access9 Oct 2021 The ISME Journal
T6SS secretes an LPS-binding effector to recruit OMVs for exploitative competition and horizontal gene transfer
- Changfu Li
- Lingfang Zhu
- Xihui Shen
ArticleOpen Access25 Aug 2021 The ISME Journal
Spatial separation of ribosomes and DNA in Asgard archaeal cells
- Burak Avcı
- Jakob Brandt
- Kasper Urup Kjeldsen
Brief CommunicationOpen Access31 Aug 2021 The ISME Journal
Artificial sweeteners stimulate horizontal transfer of extracellular antibiotic resistance genes through natural transformation
- Zhigang Yu
- Yue Wang
- Jianhua Guo
ArticleOpen Access1 Sep 2021 The ISME Journal
Highly diverse flavobacterial phages isolated from North Sea spring blooms
- Nina Bartlau
- Antje Wichels
- Cristina Moraru
ArticleOpen Access2 Sep 2021 The ISME Journal
Microbiome diversity and host immune functions influence survivorship of sponge holobionts under future ocean conditions
- Niño Posadas
- Jake Ivan P. Baquiran
- Cecilia Conaco
Article3 Jul 2021 The ISME Journal
Sulfate differentially stimulates but is not respired by diverse anaerobic methanotrophic archaea
- Hang Yu
- Connor T. Skennerton
- Victoria J. Orphan
Article20 Jul 2021 The ISME Journal
Large-scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups
- Marguerite V. Langwig
- Valerie De Anda
- Brett J. Baker
Article30 Jul 2021 The ISME Journal

2021

Degradation of biological macromolecules supports uncultured microbial populations in Guaymas Basin hydrothermal sediments
- Sherlynette Pérez Castro
- Mikayla A. Borton
- S. Emil Ruff
ArticleOpen Access10 Jun 2021 The ISME Journal
Fungal phytopathogen modulates plant and insect responses to promote its dissemination
- Flávia P. Franco
- Amanda C. Túler
- Marcio C. Silva-Filho
ArticleOpen Access14 Jun 2021 The ISME Journal
Methanogenic archaea use a bacteria-like methyltransferase system to demethoxylate aromatic compounds
- Julia M. Kurth
- Masaru K. Nobu
- Cornelia U. Welte
ArticleOpen Access18 Jun 2021 The ISME Journal
Open challenges for microbial network construction and analysis
- Karoline Faust
PerspectiveOpen Access9 Jun 2021 The ISME Journal
Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling
- Mathias Flieder
- Joy Buongiorno
- Kenneth Wasmund
ArticleOpen Access12 May 2021 The ISME Journal
Mutualistic microalgae co-diversify with reef corals that acquire symbionts during egg development
- Kira E. Turnham
- Drew C. Wham
- Todd C. LaJeunesse
Article19 May 2021 The ISME Journal
Photoferrotrophy and phototrophic extracellular electron uptake is common in the marine anoxygenic phototroph Rhodovulum sulfidophilum
- Dinesh Gupta
- Michael S. Guzman
- Arpita Bose
Article30 May 2021 The ISME Journal
Evolutionary stasis of a deep subsurface microbial lineage
- Eric D. Becraft
- Maggie C. Y. Lau Vetter
- Ramunas Stepanauskas
ArticleOpen Access6 Apr 2021 The ISME Journal
Archaeal extracellular vesicles are produced in an ESCRT-dependent manner and promote gene transfer and nutrient cycling in extreme environments
- Junfeng Liu
- Virginija Cvirkaite-Krupovic
- Mart Krupovic
Article26 Apr 2021 The ISME Journal
Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem
- Ya-Jou Chen
- Pok Man Leung
- Chris Greening
ArticleOpen Access3 May 2021 The ISME Journal
Population dynamics of microbial cross-feeding are determined by co-localization probabilities and cooperation-independent cheater growth
- Rinke J. van Tatenhove-Pel
- Daan H. de Groot
- Herwig Bachmann
ArticleOpen Access5 May 2021 The ISME Journal
Microbial hitchhiking: how Streptomyces spores are transported by motile soil bacteria
- Alise R. Muok
- Dennis Claessen
- Ariane Briegel
ArticleOpen Access15 Mar 2021 The ISME Journal
Social networks strongly predict the gut microbiota of wild mice
- Aura Raulo
- Bryony E. Allen
- Sarah C. L. Knowles
ArticleOpen Access17 Mar 2021 The ISME Journal
Sulfoquinovose is a select nutrient of prominent bacteria and a source of hydrogen sulfide in the human gut
- Buck T. Hanson
- K. Dimitri Kits
- Alexander Loy
ArticleOpen Access31 Mar 2021 The ISME Journal
Climate change alters temporal dynamics of alpine soil microbial functioning and biogeochemical cycling via earlier snowmelt
- Arthur A. D. Broadbent
- Helen S. K. Snell
- Richard D. Bardgett
Article22 Feb 2021 The ISME Journal
Conserved and reproducible bacterial communities associate with extraradical hyphae of arbuscular mycorrhizal fungi
- Bryan D. Emmett
- Véronique Lévesque-Tremblay
- Maria J. Harrison
ArticleOpen Access1 Mar 2021 The ISME Journal
Systematic discovery of pseudomonad genetic factors involved in sensitivity to tailocins
- Sean Carim
- Ashley L. Azadeh
- Adam P. Arkin
ArticleOpen Access1 Mar 2021 The ISME Journal
Nonnutritive sweeteners can promote the dissemination of antibiotic resistance through conjugative gene transfer
- Zhigang Yu
- Yue Wang
- Jianhua Guo
ArticleOpen Access15 Feb 2021 The ISME Journal
Soil microbial diversity–biomass relationships are driven by soil carbon content across global biomes
- Felipe Bastida
- David J. Eldridge
- Manuel Delgado-Baquerizo
ArticleOpen Access9 Feb 2021 The ISME Journal
Sulfur bacteria promote dissolution of authigenic carbonates at marine methane seeps
- Dalton J. Leprich
- Beverly E. Flood
- Jake V. Bailey
ArticleOpen Access11 Feb 2021 The ISME Journal
Experimental identification and in silico prediction of bacterivory in green algae
- Nicholas A. Bock
- Sophie Charvet
- Eunsoo Kim
ArticleOpen Access2 Mar 2021 The ISME Journal
The amphibian microbiome exhibits poor resilience following pathogen-induced disturbance
- Andrea J. Jani
- Jessie Bushell
- Roland A. Knapp
ArticleOpen Access9 Feb 2021 The ISME Journal
A genomic view of the microbiome of coral reef demosponges
- S. J. Robbins
- W. Song
- N. S. Webster
ArticleOpen Access19 Jan 2021 The ISME Journal
Fungal foraging behaviour and hyphal space exploration in micro-structured Soil Chips
- Kristin Aleklett
- Pelle Ohlsson
- Edith C. Hammer
ArticleOpen Access19 Jan 2021 The ISME Journal
Symbiotic associations of the deepest recorded photosynthetic scleractinian coral (172 m depth)
- Héloïse Rouzé
- Pierre E. Galand
- Laetitia Hédouin
Brief Communication15 Jan 2021 The ISME Journal
CRISPR-Cas systems restrict horizontal gene transfer in Pseudomonas aeruginosa
- Rachel M. Wheatley
- R. Craig MacLean
ArticleOpen Access21 Dec 2020 The ISME Journal
A cross-species interaction with a symbiotic commensal enables cell-density-dependent growth and in vivo virulence of an oral pathogen
- Anilei Hoare
- Hui Wang
- Patricia I. Diaz
Article28 Dec 2020 The ISME Journal
Ecology and evolution of antimicrobial resistance in bacterial communities
- Michael J. Bottery
- Jonathan W. Pitchford
- Ville-Petri Friman
PerspectiveOpen Access20 Nov 2020 The ISME Journal
Enrichment and physiological characterization of a novel comammox Nitrospira indicates ammonium inhibition of complete nitrification
- Dimitra Sakoula
- Hanna Koch
- Sebastian Lücker
ArticleOpen Access13 Nov 2020 The ISME Journal
Discovery and quantification of anaerobic nitrogen metabolisms among oxygenated tropical Cuban stony corals
- Andrew R. Babbin
- Tyler Tamasi
- Amy Apprill
ArticleOpen Access20 Dec 2020 The ISME Journal
Food or just a free ride? A meta-analysis reveals the global diversity of the Plastisphere
- Robyn J. Wright
- Morgan G. I. Langille
- Tony R. Walker
ArticleOpen Access2 Nov 2020 The ISME Journal
Microbial competition reduces metabolic interaction distances to the low µm-range
- Rinke J. van Tatenhove-Pel
- Tomaž Rijavec
- Herwig Bachmann
ArticleOpen Access19 Oct 2020 The ISME Journal
Plasmid- and strain-specific factors drive variation in ESBL-plasmid spread in vitro and in vivo
- Fabienne Benz
- Jana S. Huisman
- Sebastian Bonhoeffer
ArticleOpen Access4 Nov 2020 The ISME Journal
Achieving similar root microbiota composition in neighbouring plants through airborne signalling
- Hyun Gi Kong
- Geun Cheol Song
- Choong-Min Ryu
ArticleOpen Access24 Sep 2020 The ISME Journal
Mucin-derived O-glycans supplemented to diet mitigate diverse microbiota perturbations
- K. M. Pruss
- A. Marcobal
- J. L. Sonnenburg
ArticleOpen Access21 Oct 2020 The ISME Journal
Biodiversity of key-stone phylotypes determines crop production in a 4-decade fertilization experiment
- Kunkun Fan
- Manuel Delgado-Baquerizo
- Haiyan Chu
Article7 Oct 2020 The ISME Journal
Bridging the membrane lipid divide: bacteria of the FCB group superphylum have the potential to synthesize archaeal ether lipids
- Laura Villanueva
- F. A. Bastiaan von Meijenfeldt
- Jaap S. Sinninghe Damsté
ArticleOpen Access14 Sep 2020 The ISME Journal
Benchmarking microbial growth rate predictions from metagenomes
- Andrew M. Long
- Shengwei Hou
- Jed A. Fuhrman
ArticleOpen Access16 Sep 2020 The ISME Journal
Disruption of Firmicutes and Actinobacteria abundance in tomato rhizosphere causes the incidence of bacterial wilt disease
- Sang-Moo Lee
- Hyun Gi Kong
- Choong-Min Ryu
ArticleOpen Access7 Oct 2020 The ISME Journal

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