Journal of Microbiology

Editorial

Editorial] Bacterial Regulatory Mechanisms for the Control of Cellular Processes: Simple Organisms’ Complex Regulation: Jin-Won Lee; J. Microbiol. 2023;61(3):273-276. Published online April 3, 2023; DOI: https://doi.org/10.1007/s12275-023-00036-6

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Bacteria employ a diverse array of cellular regulatory mechanisms to successfully adapt and thrive in ever-changing environments, including but not limited to temperature changes, fluctuations in nutrient availability, the presence or absence of electron acceptors such as oxygen, the availability of metal ions crucial for enzyme activity, and the existence of antibiotics. Bacteria can virtually modulate any step of gene expression from transcr!ptional initiation to posttranslational modification of a protein for the control of cellular processes. Furthermore, one gene regulator often controls another in a complex gene regulatory network. Thus, it is not easy to fully understand the intricacies of bacterial regulatory mechanisms in various environments. In this special issue, while acknowledging the challenge of covering all aspects of bacterial regulatory mechanisms across diverse environments, seven review articles are included to provide insight into the recent progress in understanding such mechanisms from different perspectives: positive regulatory mechanisms by secondary messenger (cAMP receptor protein), two-component signal transduction mechanisms (Rcs and Cpx), diverse regulatory mechanisms by a specific environmental factor in specific bacteria (oxygen availability in Mycobacterium and manganese ion availability in Salmonella), diverse regulatory mechanisms by a specific environmental factor (temperature and antibiotics), and regulatory mechanisms by antibiotics in cell wall synthesis. Bacteria, as ubiquitous organisms that can be found in almost every environment, carry out complex cellular processes that allow them to survive and thrive in a variety of different conditions despite their small size and relative simplicity. One of the key factors that allows bacteria to carry out these complex processes is their ability to regulate gene expression through various mechanisms. Gene expression is a fundamental biological process by which the genetic information encoded in a gene is transcribed into an RNA molecule and subsequently translated into a functional gene product, often a protein. Furthermore, the activity levels of proteins may further be altered by posttranslational modification. Regulation of gene expression refers to the control of the amount and timing of gene expression, and thus it can be divided into transcr!ptional, translational, and posttranslational levels.

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The PhoBR two-component system upregulates virulence in Aeromonas dhakensis C4–1
Wei Feng, Xuesong Li, Nuo Yang, Lixia Fan, Guiying Guo, Jun Xie, Xiuqing Cai, Yuqi Meng, Jifeng Zeng, Yu Han, Jiping Zheng
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Molecular mechanisms of cold stress response in cotton: Transcriptional reprogramming and genetic strategies for tolerance
Washu Dev, Fahmida Sultana, Hongge Li, Daowu Hu, Zhen Peng, Shoupu He, Haobo Zhang, Muhammad Waqas, Xiaoli Geng, Xiongming Du
Plant Science.2025; 352: 112390. CrossRef
PhoPQ-mediated lipopolysaccharide modification governs intrinsic resistance to tetracycline and glycylcycline antibiotics in Escherichia coli
Byoung Jun Choi, Umji Choi, Dae-Beom Ryu, Chang-Ro Lee, Mehrad Hamidian, You-Hee Cho
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Navigating the signaling landscape of Ralstonia solanacearum: a study of bacterial two-component systems
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Journal Articles

Characterization of components of a reducing system for SoxR in the cytoplasmic membrane of Escherichia coli: Kang-Lok Lee , Kyung-Chang Lee , Joon-Hee Lee , Jung-Hye Roe; J. Microbiol. 2022;60(4):387-394. Published online March 28, 2022; DOI: https://doi.org/10.1007/s12275-022-1667-1

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Abstract

A reducing system of SoxR, a regulator of redox-active molecules, was identified as rsxABCDGE gene products and RseC in Escherichia coli through genetic studies. We found that ApbE was an additional component of the reducer system. Bacterial two hybrid analysis revealed that these proteins indeed had multiple interactions among themselves. RseC and RsxB formed the core of the complex, interacting with more than five other components. RsxC, the only cytoplasmic component of the system, interacted with SoxR. It might be linked with the rest of the complex via RsxB. Membrane fractions containing the wild type complex but not the mutant complex reduced purified SoxR using NADH as an electron source. These results suggest that Rsx genes, RseC, and ApbE can form a complex using NAD(P)H to reduce SoxR.

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AcrAB-TolC efflux pump overexpression and tet(A) gene mutation increase tigecycline resistance in Klebsiella pneumoniae
Zhaoxin Xia, Jing zhou, Nana Gao, Ge Li, Runde Liu, Guoping Lu, Jilu Shen
World Journal of Microbiology and Biotechnology.2024;[Epub] CrossRef
The Na+-translocating NADH:quinone oxidoreductase (Na+-NQR): Physiological role, structure and function of a redox-driven, molecular machine
Julia Steuber, Günter Fritz
Biochimica et Biophysica Acta (BBA) - Bioenergetics.2024; 1865(4): 149485. CrossRef
Functional analysis of bacterial genes accidentally packaged in rhizospheric phageome of the wild plant species Abutilon fruticosum
Ruba Abdulrahman Ashy
Saudi Journal of Biological Sciences.2023; 30(10): 103789. CrossRef

Meiotic prophase roles of Pds5 in recombination and chromosome condensation in budding yeast: Jeong Hwan Joo , Hyun Ah Kang , Keun Pil Kim , Soogil Hong; J. Microbiol. 2022;60(2):177-186. Published online February 1, 2022; DOI: https://doi.org/10.1007/s12275-022-1635-9

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Abstract

Genetic variation in eukaryotes is mediated during meiosis by the exchange of genetic material between homologous chromosomes to produce recombinant chromosomes. Cohesin is essential to promote proper chromosome segregation, chromosome morphogenesis, and recombination in meiotic cells. Cohesin consists of three main subunits–Smc1, Smc3, and the kleisin subunit Mcd1/Scc1 (Rec8 in meiosis)–and cohesin accessory factors. In Saccharomyces cerevisiae, the cohesin regulatory subunit Pds5 plays a role in homolog pairing, meiotic axis formation, and interhomolog recombination. In this study, we examine the prophase functions of Pds5 by performing physical analysis of recombination and three-dimensional high-resolution microscopy analysis to identify its roles in meiosis-specific recombination and chromosome morphogenesis. To investigate whether Pds5 plays a role in mitoticlike recombination, we inhibited Mek1 kinase activity, which
result
ed in switching to sister template bias by Rad51-dependent recombination. Reductions in double-strand breaks and crossover products and defective interhomolog recombination occurred in the absence of Pds5. Furthermore, recombination intermediates, including single-end invasion and double-Holliday junction, were reduced in the absence of Pds5 with Mek1 kinase inactivation compared to Mek1 kinase inactivation cells. Interestingly, the absence of Pds5
result
ed in increasing numbers of chromosomes with hypercompaction of the chromosome axis. Thus, we suggest that Pds5 plays an essential role in recombination by suppressing the pairing of sister chromatids and abnormal compaction of the chromosome axis.

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RPA interacts with Rad52 to promote meiotic crossover and noncrossover recombination
Jeong H Joo, Soogil Hong, Mika T Higashide, Eui-Hwan Choi, Seobin Yoon, Min-Su Lee, Hyun Ah Kang, Akira Shinohara, Nancy Kleckner, Keun P Kim
Nucleic Acids Research.2024; 52(7): 3794. CrossRef
Cohesin is required for meiotic spindle assembly independent of its role in cohesion in C. elegans
Karen P. McNally, Elizabeth A. Beath, Brennan M. Danlasky, Consuelo Barroso, Ting Gong, Wenzhe Li, Enrique Martinez-Perez, Francis J. McNally, Sarit Smolikove
PLOS Genetics.2022; 18(10): e1010136. CrossRef
Yeast polyubiquitin unit regulates synaptonemal complex formation and recombination during meiosis
Min-Kyung Jo, Kiwon Rhee, Keun Pil Kim, Soogil Hong
Journal of Microbiology.2022; 60(7): 705. CrossRef

Antiviral effects of human placenta hydrolysate (Laennec) against SARS-CoV-2 in vitro and in the ferret model: Eun-Ha Kim , Young-il Kim , Seung-Gyu Jang , Minju Im , Kyeongsoo Jeong , Young Ki Choi , Hae-Jung Han; J. Microbiol. 2021;59(11):1056-1062. Published online October 6, 2021; DOI: https://doi.org/10.1007/s12275-021-1367-2

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Abstract

The COVID-19 pandemic has caused unprecedented health, social, and economic crises worldwide. However, to date, there is an only a limited effective treatment for this disease. Human placenta hydrolysate (hPH) has previously been shown to be safe and to improve the health condition in patients with hyperferritinemia and COVID-19. In this study, we aimed to determine the antiviral effects of hPH against SARS-CoV-2 in vitro and in vivo models and compared with Remdesivir, an FDA-approved drug for COVID-19 treatment. To assess whether hPH inhibited SARS-CoV-2 replication, we determined the CC50, EC50, and selective index (SI) in Vero cells by infection with a SARS-CoV-2 at an MOI of 0.01. Further, groups of ferrets infected with 105.8 TCID50/ml of SARS-CoV-2 and treated with hPH at 2, 4, 6 dpi, and compared their clinical manifestation and virus titers in respiratory tracts with PBS control-treated group. The mRNA expression of immunerelated cytokines was determined by qRT-PCR. hPH treatment attenuated virus replication in a dose-dependent manner in vitro. In a ferret infection study, treatment with hPH resulted in minimal bodyweight loss and attenuated virus replication in the nasal wash, turbinates, and lungs of infected ferrets. In addition, qRT-PCR results revealed that the hPH treatment remarkably upregulated the gene expression of type I (IFN-α and IFN-β) and II (IFN-γ) IFNs in SARS-CoV-2 infected ferrets. Our data collectively suggest that hPH has antiviral efficacy against SARS-CoV-2 and might be a promising therapeutic agent for the treatment of SARS-CoV-2 infection.

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Perinatal Hypoxia and Immune System Activation in Schizophrenia Pathogenesis: Critical Considerations During COVID-19 Pandemic
I Kawikova, K Hakenova, M Lebedeva, L Kleteckova, L Jakob, V Spicka, L Wen, F Spaniel, K Vales
Physiological Research.2024; : S615. CrossRef
Human Placenta Extract (HPH) Suppresses Inflammatory Responses in TNF-α/IFN-γ-Stimulated HaCaT Cells and a DNCB Atopic Dermatitis (AD)-Like Mouse Model
Jung Ok Lee, Youna Jang, A Yeon Park, Jung Min Lee, Kyeongsoo Jeong, So-Hyun Jeon, Hui Jin, Minju Im, Jae-Won Kim, Beom Joon Kim
Journal of Microbiology and Biotechnology.2024; 34(10): 1969. CrossRef
Systematic analysis of the pharmacology of standardized extracts of human placenta
T. E. Bogacheva, I. Yu. Torshin, O. A. Gromova
Pharmacokinetics and Pharmacodynamics.2024; (4): 3. CrossRef
Distinctive Combinations of RBD Mutations Contribute to Antibody Evasion in the Case of the SARS-CoV-2 Beta Variant
Tae-Hun Kim, Sojung Bae, Sunggeun Goo, Jinjong Myoung
Journal of Microbiology and Biotechnology.2023; 33(12): 1587. CrossRef
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Ailong Sha, Yi Liu, Haiyan Hao
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SARS-CoV-2 Aerosol and Intranasal Exposure Models in Ferrets
Elizabeth E. Zumbrun, Samantha E. Zak, Eric D. Lee, Philip A. Bowling, Sara I. Ruiz, Xiankun Zeng, Jeffrey W. Koehler, Korey L. Delp, Russel R. Bakken, Shannon S. Hentschel, Holly A. Bloomfield, Keersten M. Ricks, Tamara L. Clements, April M. Babka, John
Viruses.2023; 15(12): 2341. CrossRef
Human placenta hydrolysates: from V.P. Filatov to the present day: Review
Olga A. Gromova, Ivan Yu. Torshin, Alexander G. Chuchalin, Valeriy А. Maximov
Terapevticheskii arkhiv.2022; 94(3): 434. CrossRef

Effects of mycosubtilin homolog algicides from a marine bacterium, Bacillus sp. SY-1, against the harmful algal bloom species Cochlodinium polykrikoides: Seong-Yun Jeong , Hong-Joo Son; J. Microbiol. 2021;59(4):389-400. Published online March 29, 2021; DOI: https://doi.org/10.1007/s12275-021-1086-8

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Abstract

The marine bacterium, Bacillus sp. SY-1, produced algicidal compounds that are notably active against the bloom-forming alga Cochlodinium polykrikoides. We isolated three algicidal compounds and identified these as mycosubtilins with molecular weights of 1056, 1070, and 1084 (designated MS 1056, 1070, and 1084, respectively), based on amino acid analyses and 1H, 13C, and two-dimensional nuclear magnetic resonance spectroscopy, including 1H-15N heteronuclear multiple bond correlation analysis. MS 1056 contains a β- amino acid residue with an alkyl side chain of C15, which has not previously been seen in known mycosubtilin families. MS 1056, 1070, and 1084 showed algicidal activities against C. polykrikoides with 6-h LC50 values of 2.3 ± 0.4, 0.8 ± 0.2, and 0.6 ± 0.1 μg/ml, respectively. These compounds also showed significant algicidal activities against other harmful algal bloom species. In contrast, MS 1084 showed no significant growth inhibitory effects against other organisms, including bacteria and microalgae, although does inhibit the growth of some fungi and yeasts. These observations imply that the algicidal bacterium Bacillus sp. SY-1 and its algicidal compounds could play an important role in regulating the onset and development of harmful algal blooms in natural environments.

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Biological and Chemical Approaches for Controlling Harmful Microcystis Blooms
Wonjae Kim, Yerim Park, Jaejoon Jung, Che Ok Jeon, Masanori Toyofuku, Jiyoung Lee, Woojun Park
Journal of Microbiology.2024; 62(3): 249. CrossRef
A Bacillus subtilis strain with efficient algaecide of Microcystis aeruginosa and degradation of microcystins
Yuanyuan Chen, Fei Xiong, Ying Zhu, Dongdong Zhai, Hongyan Liu, Lin Zhang, Ming Xia
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Kristy S. Syhapanha, David A. Russo, Yun Deng, Nils Meyer, Remington X. Poulin, Georg Pohnert
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Algicidal Potential of the Endosymbiont Bacterial Consortium of the Seagrasses Enhalus acoroides and Thalassia hemprichii
G I Setiabudi, I N D Prasetia, K L Antara, G S br. Sitepu, J M Amelia, M D K Maharani
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Algicidal substances of Brevibacillus laterosporus and their effect on red tide organisms
Shanshan Liu, Zhiming Yu, Zaixing Wu, Xihua Cao, Ruihong Cheng, Xiuxian Song
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So-Ra Ko, Ve Van Le, Ankita Srivastava, Mingyeong Kang, Hee-Mock Oh, Chi-Yong Ahn
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Algicidal Bacteria: A Review of Current Knowledge and Applications to Control Harmful Algal Blooms
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Transcriptomic and proteomic profiling revealed global changes in Streptococcus thermophilus during pH-controlled batch fermentations: Yali Qiao , Cong Leng , Gefei Liu , Yanjiao Zhang , Xuepeng Lv , Hongyu Chen , Jiahui Sun , Zhen Feng; J. Microbiol. 2019;57(9):769-780. Published online June 14, 2019; DOI: https://doi.org/10.1007/s12275-019-8604-y

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Abstract

Understanding global changes of physiological processes at the molecular level during the growth of Streptococcus thermophilus is essential for the rational design of cultivation media and the optimization of bioprocesses. Transcriptomics and proteomics were combined to investigate the global changes at the transcript and protein level during the growth of S. thermophilus. The expression of 1396 genes (FDR ≤ 0.001) and 876 proteins (P < 0.05) changed significantly over time. The most remarkable growth phase dependent changes occurred in the late-lag phase and were related to heterofermentation, glycolysis, peptidoglycan biosynthesis, conversion between amino acids and stress response. The present
results
could provide theoretical guidance for high-cell-density culture, help design cultivation media, and help attain a high biomass of S. thermophilus.

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The contribution of microorganisms to sustainable development: towards a green future through synthetic biology and systems biology
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Chemical Engineering Journal.2024; 497: 154410. CrossRef
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Chandraprakash Yamini, Govindasamy Sharmila, Chandrasekaran Muthukumaran, Kumar Pavithran, Narasimhan Manojkumar
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Martin H. Rau, Paula Gaspar, Maiken Lund Jensen, Asger Geppel, Ana Rute Neves, Ahmad A. Zeidan, Danilo Ercolini
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Metabolic Pathway Profiling in Intracellular and Extracellular Environments of Streptococcus thermophilus During pH-Controlled Batch Fermentations
Yali Qiao, Gefei Liu, Xuepeng Lv, Xuejing Fan, Yanjiao Zhang, Li Meng, Mingzhi Ai, Zhen Feng
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De novo transcriptome assembly and characterization of the 10-hydroxycamptothecin-producing Xylaria sp. M71 following salicylic acid treatment: Xiaowei Ding , Kaihui Liu , Yonggui Zhang , Feihu Liu; J. Microbiol. 2017;55(11):871-876. Published online October 27, 2017; DOI: https://doi.org/10.1007/s12275-017-7173-1

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Abstract

In the present study, we identified genes that are putatively involved in the production of fungal 10-hydroxycamptothecin via transcriptome sequencing and characterization of the Xylaria sp. M71 treated with salicylic acid (SA). A total of 60,664,200 raw reads were assembled into 26,044 unigenes. BLAST assigned 8,767 (33.7%) and 10,840 (41.6%) unigenes to 40 Gene Ontology (GO) annotations and 108 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, respectively. A total of 3,713 unigenes comprising 1,504 upregulated and 2,209 downregulated unigenes were found to be differentially expressed between SA-induced and control fungi. Based on the camptothecin biosynthesis pathway in plants, 13 functional genes of Xylaria sp. M71 were mapped to the mevalonate (MVA) pathway, suggesting that the fungal 10-hydroxycamptothecin is produced via the MVA pathway. In summary, analysis of the Xylaria sp. M71 transcriptome allowed the identification of unigenes that are putatively involved in 10-hydroxycamptothecin biosynthesis in fungi.

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Review

REVIEW] Mechanisms of Synergy in Polymicrobial Infections: Justine L. Murray , Jodi L. Connell , Apollo Stacy , Keith H. Turner , Marvin Whiteley; J. Microbiol. 2014;52(3):188-199. Published online March 1, 2014; DOI: https://doi.org/10.1007/s12275-014-4067-3

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Abstract

Communities of microbes can live almost anywhere and contain many different species. Interactions between members of these communities often determine the state of the habitat in which they live. When these habitats include sites on the human body, these interactions can affect health and disease. Polymicrobial synergy can occur during infection, in which the combined effect of two or more microbes on disease is worse than seen with any of the individuals alone. Powerful genomic methods are increasingly used to study microbial communities, including metagenomics to reveal the members and genetic content of a community and metatranscriptomics to describe the activities of community members. Recent efforts focused toward a mechanistic understanding of these interactions have led to a better appreciation of the precise bases of polymicrobial synergy in communities containing bacteria, eukaryotic microbes, and/or viruses. These studies have benefited from advances in the development of in vivo models of polymicrobial infection and modern techniques to profile the spatial and chemical bases of intermicrobial communication. This review describes the breadth of mechanisms microbes use to interact in ways that impact pathogenesis and techniques to study polymicrobial communities.

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Meina Hu, Xiaojing Liu, Shidi Liu, Tao Ya, Minglu Zhang, Tingting Zhang, Xiaoping Gao, Xiaohui Wang
Journal of Environmental Management.2023; 348: 119408. CrossRef
The interactions of SARS-CoV-2 with cocirculating pathogens: Epidemiological implications and current knowledge gaps
Anabelle Wong, Laura Andrea Barrero Guevara, Elizabeth Goult, Michael Briga, Sarah C. Kramer, Aleksandra Kovacevic, Lulla Opatowski, Matthieu Domenech de Cellès, Tom C. Hobman
PLOS Pathogens.2023; 19(3): e1011167. CrossRef
Effect of extracellular levanase SacC from Bacillus subtillis on two–species Staphylococcus aureus – Pseudomonas aeruginosa biofilms
Guzel Mutallapova, Daria Zhuravleva, Airat Kayumov, Elena Trizna, I. Abdullayev, V. Kukhar, E. Akhmetshin, D. Bekjanov, A. Carballo-Penela
E3S Web of Conferences.2023; 449: 07016. CrossRef
Cross-protection and cross-feeding between Klebsiella pneumoniae and Acinetobacter baumannii promotes their co-existence
Lucie Semenec, Amy K. Cain, Catherine J. Dawson, Qi Liu, Hue Dinh, Hannah Lott, Anahit Penesyan, Ram Maharjan, Francesca L. Short, Karl A. Hassan, Ian T. Paulsen
Nature Communications.2023;[Epub] CrossRef
Microbiota and fungal-bacterial interactions in the cystic fibrosis lung
Eneko Santos-Fernandez, Leire Martin-Souto, Aitziber Antoran, Maialen Areitio, Leire Aparicio-Fernandez, Jean-Philippe Bouchara, Carsten Schwarz, Aitor Rementeria, Idoia Buldain, Andoni Ramirez-Garcia
FEMS Microbiology Reviews.2023;[Epub] CrossRef
Defining microbial community functions in chronic human infection with metatranscriptomics
Aanuoluwa E. Adekoya, Hoody A. Kargbo, Carolyn B. Ibberson, Rachel Poretsky
mSystems.2023;[Epub] CrossRef
Illuminating the oral microbiome and its host interactions: tools and approaches for molecular microbiology studies
Justin Merritt, Jens Kreth
FEMS Microbiology Reviews.2023;[Epub] CrossRef
Cooperation and cheating orchestrate Vibrio assemblages and polymicrobial synergy in oysters infected with OsHV-1 virus
Daniel Oyanedel, Arnaud Lagorce, Maxime Bruto, Philippe Haffner, Amandine Morot, Yannick Labreuche, Yann Dorant, Sébastien de La Forest Divonne, François Delavat, Nicolas Inguimbert, Caroline Montagnani, Benjamin Morga, Eve Toulza, Cristian Chaparro, Jean
Proceedings of the National Academy of Sciences.2023;[Epub] CrossRef
Influence of the Type of Bone Cement Used in Two-Stage Exchange Arthroplasty for Chronic Periarticular Joint Infection on the Spacer Replacement and Reinfection Rate
Meng-Wei Chang, Cheng-Ta Wu, Shih-Hsiang Yen, Timothy L. Tan, Po-Chun Lin, Feng-Chih Kuo
Journal of Clinical Medicine.2023; 12(2): 600. CrossRef
Fusobacterium nucleatum Metabolically Integrates Commensals and Pathogens in Oral Biofilms
Akito Sakanaka, Masae Kuboniwa, Shuichi Shimma, Samar A. Alghamdi, Shota Mayumi, Richard J. Lamont, Eiichiro Fukusaki, Atsuo Amano, Heather D. Bean
mSystems.2022;[Epub] CrossRef
Suppurative Thrombosis of the Portal Vein (Pylephlebits): A Systematic Review of Literature
Dorde Jevtic, Tatjana Gavrancic, Ivana Pantic, Terri Nordin, Charles W. Nordstrom, Marina Antic, Nikola Pantic, Marija Kaljevic, Bojan Joksimovic, Milan Jovanovic, Emilia Petcu, Mladen Jecmenica, Tamara Milovanovic, Lawrence Sprecher, Igor Dumic
Journal of Clinical Medicine.2022; 11(17): 4992. CrossRef
Effect of Polymicrobial Interactions on Antimicrobial Resistance: An in vitro Analysis in Human Ocular Infections
Sanchita Mitra, Aparajita Mallick, Shilpa Priyadarshini
Future Microbiology.2022; 17(7): 491. CrossRef
Precise spatial structure impacts antimicrobial susceptibility of S. aureus in polymicrobial wound infections
Carolyn B. Ibberson, Juan P. Barraza, Avery L. Holmes, Pengbo Cao, Marvin Whiteley
Proceedings of the National Academy of Sciences.2022;[Epub] CrossRef
PECULIARITIES OF DISTRIBUTION OF ANTIBIOTIC RESISTANT STRAINS OF E. COLI - E. FAECALIS ASSOCIATION IN THE UROGENITAL TRACT OF PREGNANT WOMEN
Olha S. Voronkova, Maksym V. Lusta, Yuliia S. Voronkova, Yelyzaveta S. Fawzy, Tetiana H. Ostanina
Wiadomości Lekarskie.2022; 75(2): 462. CrossRef
Corncob structures in dental plaque reveal microhabitat taxon specificity
Viviana Morillo-Lopez, Alexandra Sjaarda, Imon Islam, Gary G. Borisy, Jessica L. Mark Welch
Microbiome.2022;[Epub] CrossRef
Polymicrobial Infections and Biofilms: Clinical Significance and Eradication Strategies
V T Anju, Siddhardha Busi, Madangchanok Imchen, Ranjith Kumavath, Mahima S. Mohan, Simi Asma Salim, Pattnaik Subhaswaraj, Madhu Dyavaiah
Antibiotics.2022; 11(12): 1731. CrossRef
Potential Facilitation Between a Commensal and a Pathogenic Microbe in a Wildlife Disease
Franziska C. Sandmeier, Kendra L. Leonard, Chava L. Weitzman, C. Richard Tracy
EcoHealth.2022; 19(3): 427. CrossRef
Increasing the Efficacy of Treatment of Staphylococcus aureus–Candida albicans Mixed Infections with Myrtenol
Ruba Y. Mahmoud, Elena Y. Trizna, Rand K. Sulaiman, Roman S. Pavelyev, Ilmir R. Gilfanov, Svetlana A. Lisovskaya, Olga V. Ostolopovskaya, Larisa L. Frolova, Alexander V. Kutchin, Galina B. Guseva, Elena V. Antina, Mikhail B. Berezin, Liliya E. Nikitina, A
Antibiotics.2022; 11(12): 1743. CrossRef
Bacteriological Studies of Venomous Snakebite Wounds in Hangzhou, Southeast China
Sipin Hu, Zhengqing Lou, Yuchen Shen, Mengyun Tu
The American Journal of Tropical Medicine and Hygiene.2022; 107(4): 925. CrossRef
Environment Constrains Fitness Advantages of Division of Labor in Microbial Consortia Engineered for Metabolite Push or Pull Interactions
Ashley E. Beck, Kathryn Pintar, Diana Schepens, Ashley Schrammeck, Timothy Johnson, Alissa Bleem, Martina Du, William R. Harcombe, Hans C. Bernstein, Jeffrey J. Heys, Tomas Gedeon, Ross P. Carlson, Alejandra Rodríguez-Verdugo, Davide Ciccarese
mSystems.2022;[Epub] CrossRef
Porphyromonas gingivalis Tyrosine Kinase Is a Fitness Determinant in Polymicrobial Infections
John D. Perpich, Lan Yakoumatos, Kendall S. Stocke, Gina R. Lewin, Anayancy Ramos, Deborah R. Yoder-Himes, Marvin Whiteley, Richard J. Lamont, Andreas J. Bäumler
Infection and Immunity.2022;[Epub] CrossRef
Priority effects dictate community structure and alter virulence of fungal-bacterial biofilms
J Z Alex Cheong, Chad J Johnson, Hanxiao Wan, Aiping Liu, John F Kernien, Angela L F Gibson, Jeniel E Nett, Lindsay R Kalan
The ISME Journal.2021; 15(7): 2012. CrossRef
A Pseudomonas aeruginosa Antimicrobial Affects the Biogeography but Not Fitness of Staphylococcus aureus during Coculture
Juan P. Barraza, Marvin Whiteley, Dominique H. Limoli, Michael S. Gilmore
mBio.2021;[Epub] CrossRef
Pseudomonas aeruginosa biofilms and their partners in crime
Maria del Mar Cendra, Eduard Torrents
Biotechnology Advances.2021; 49: 107734. CrossRef
Pseudomonas aeruginosa reverse diauxie is a multidimensional, optimized, resource utilization strategy
S. Lee McGill, Yeni Yung, Kristopher A. Hunt, Michael A. Henson, Luke Hanley, Ross P. Carlson
Scientific Reports.2021;[Epub] CrossRef
Effect of co-positivity for brucellosis and tuberculosis on milk yield and fertility of Holstein cows
M. Mellado, N. Treviño, F. G. Véliz, U. Macías-Cruz, L. Avendaño-Reyes, A. de Santiago, J. E. García
Tropical Animal Health and Production.2021;[Epub] CrossRef
Detection of bacterial fluorescence from in vivo wound biofilms using a point‐of‐care fluorescence imaging device
Andrea J. Lopez, Laura M. Jones, Landrye Reynolds, Rachel C. Diaz, Isaiah K. George, William Little, Derek Fleming, Anna D'souza, Monique Y. Rennie, Kendra P. Rumbaugh, Allie Clinton Smith
International Wound Journal.2021; 18(5): 626. CrossRef
Ditylenchus dipsaci and Fusarium oxysporum on garlic: one plus one does not equal two
Mary Ruth McDonald, Lilieth Ives, Kwasi Adusei-Fosu, Katerina S. Jordan
Canadian Journal of Plant Pathology.2021; 43(5): 749. CrossRef
Effects of inflammatory stimuli on responses of macrophages to Mycoplasma bovis infection
Monica Baquero, Ksenia Vulikh, Cassidy Wong, Meghan Domony, DeLenn Burrows, David Marom, Jose Perez-Casal, Hugh Y. Cai, Jeff L. Caswell
Veterinary Microbiology.2021; 262: 109235. CrossRef
Polymicrobial Interactions in the Urinary Tract: Is the Enemy of My Enemy My Friend?
Jordan R. Gaston, Alexandra O. Johnson, Kirsten L. Bair, Ashley N. White, Chelsie E. Armbruster, Karen M. Ottemann
Infection and Immunity.2021;[Epub] CrossRef
Clinical Implications of Polymicrobial Synergism Effects on Antimicrobial Susceptibility
William Little, Caroline Black, Allie Clinton Smith
Pathogens.2021; 10(2): 144. CrossRef
Bacterial Interactions with Aspergillus fumigatus in the Immunocompromised Lung
Anatte Margalit, James C. Carolan, Kevin Kavanagh
Microorganisms.2021; 9(2): 435. CrossRef
Characterization of Polybacterial versus Monobacterial Conjunctivitis Infections in Pediatric Subjects Across Multiple Studies and Microbiological Outcomes with Besifloxacin Ophthalmic Suspension 0.6%
Joseph M Blondeau, Howard M Proskin, Christine M Sanfilippo, Heleen H DeCory
Clinical Ophthalmology.2021; Volume 15: 4419. CrossRef
Prospective assessment of catheter-associated bacteriuria clinical presentation, epidemiology, and colonization dynamics in nursing home residents
Chelsie E. Armbruster, Aimee L. Brauer, Monica S. Humby, Jiahui Shao, Saptarshi Chakraborty
JCI Insight.2021;[Epub] CrossRef
Burns and biofilms: priority pathogens and in vivo models
Evgenia Maslova, Lara Eisaiankhongi, Folke Sjöberg, Ronan R. McCarthy
npj Biofilms and Microbiomes.2021;[Epub] CrossRef
Genetically Programmable Microbial Assembly
Mark T. Kozlowski, Bradley R. Silverman, Christopher P. Johnstone, David A. Tirrell
ACS Synthetic Biology.2021; 10(6): 1351. CrossRef
Hormones Can Influence Antibiotic Susceptibilities Even in Mono- and Co-Culture Conditions
Fatma Kalaycı-Yüksek, Defne Gümüş, Mine Anğ-Küçüker
Acta Biologica Marisiensis.2021; 4(2): 39. CrossRef
Synergistic Cues from Diverse Bacteria Enhance Multicellular Development in a Choanoflagellate
Ella V. Ireland, Arielle Woznica, Nicole King, Eric V. Stabb
Applied and Environmental Microbiology.2020;[Epub] CrossRef
Cooperation and Conflict Within the Microbiota and Their Effects On Animal Hosts
Alexandre R. T. Figueiredo, Jos Kramer
Frontiers in Ecology and Evolution.2020;[Epub] CrossRef
Weakest-Link Dynamics Predict Apparent Antibiotic Interactions in a Model Cross-Feeding Community
Elizabeth M. Adamowicz, William R. Harcombe
Antimicrobial Agents and Chemotherapy.2020;[Epub] CrossRef
Pseudomonad reverse carbon catabolite repression, interspecies metabolite exchange, and consortial division of labor
Heejoon Park, S. Lee McGill, Adrienne D. Arnold, Ross P. Carlson
Cellular and Molecular Life Sciences.2020; 77(3): 395. CrossRef
Strain Background, Species Frequency, and Environmental Conditions Are Important in Determining Pseudomonas aeruginosa and Staphylococcus aureus Population Dynamics and Species Coexistence
Selina Niggli, Rolf Kümmerli, Donald W. Schaffner
Applied and Environmental Microbiology.2020;[Epub] CrossRef
Molecular characteristics and risk factors associated with linezolid-resistant Enterococcus faecalis infection in Southwest China
Jiaqi Zou, Yun Xia
Journal of Global Antimicrobial Resistance.2020; 22: 504. CrossRef
From Nursery to Nursing Home: Emerging Concepts in Clostridioides difficile Pathogenesis
Alexander B. Smith, Joshua Soto Ocana, Joseph P. Zackular, Anthony R. Richardson
Infection and Immunity.2020;[Epub] CrossRef
Successful treatment of a unique chronic multi-bacterial scalp infection with N-chlorotaurine, N-bromotaurine and bromamine T
Anthony M. Kyriakopoulos, Markus Nagl, Dorothea Orth-Höller, Janusz Marcinkiewicz, Stella Baliou, Vassilis Zoumbourlis
Access Microbiology .2020;[Epub] CrossRef
The social life of microbes in chronic infection
Carolyn B Ibberson, Marvin Whiteley
Current Opinion in Microbiology.2020; 53: 44. CrossRef
Polymicrobial Biofilm Interaction Between Histophilus somni and Pasteurella multocida
Briana Petruzzi, Allan Dickerman, Kevin Lahmers, William K. Scarratt, Thomas J. Inzana
Frontiers in Microbiology.2020;[Epub] CrossRef
Quantitative Framework for Model Evaluation in Microbiology Research Using Pseudomonas aeruginosa and Cystic Fibrosis Infection as a Test Case
Daniel M. Cornforth, Frances L. Diggle, Jeffrey A. Melvin, Jennifer M. Bomberger, Marvin Whiteley, Arturo Casadevall
mBio.2020;[Epub] CrossRef
Harnessing bacterial interactions to manage infections: a review on the opportunistic pathogen Pseudomonas aeruginosa as a case example
Chiara Rezzoagli, Elisa T. Granato, Rolf Kümmerli
Journal of Medical Microbiology.2020; 69(2): 147. CrossRef
Comparison of sTREM‐1 and associated periodontal and bacterial factors before/after periodontal therapy, and impact of psychosocial factors
Marie Dubar, Jean‐Pol Frippiat, Thomas Remen, Amir Boufenzer, Corentine Alauzet, Cedric Baumann, Sebastien Gibot, Catherine Bisson
Journal of Clinical Periodontology.2020; 47(9): 1064. CrossRef
Cooperative Interactions between Trichomonas vaginalis and Associated Bacteria Enhance Paracellular Permeability of the Cervicovaginal Epithelium by Dysregulating Tight Junctions
Annabel S. Hinderfeld, Niha Phukan, Ann-Katrein Bär, Anthony M. Roberton, Augusto Simoes-Barbosa, De'Broski R. Herbert
Infection and Immunity.2019;[Epub] CrossRef
The Structure of Dental Plaque Microbial Communities in the Transition from Health to Dental Caries and Periodontal Disease
Alex M. Valm
Journal of Molecular Biology.2019; 431(16): 2957. CrossRef
2018 international consensus meeting on musculoskeletal infection: Summary from the biofilm workgroup and consensus on biofilm related musculoskeletal infections
Kordo Saeed, Alex C. McLaren, Edward M. Schwarz, Valentin Antoci, William V. Arnold, Antonia F. Chen, Martin Clauss, Jaime Esteban, Vanya Gant, Edward Hendershot, Noreen Hickok, Carlos A. Higuera, Débora C. Coraça‐Huber, Hyonmin Choe, Jessica A. Jennings,
Journal of Orthopaedic Research.2019; 37(5): 1007. CrossRef
Antimicrobial resistance three ways: healthcare crisis, major concepts and the relevance of biofilms
Paula Jorge, Andreia Patrícia Magalhães, Tânia Grainha, Diana Alves, Ana Margarida Sousa, Susana Patrícia Lopes, Maria Olívia Pereira
FEMS Microbiology Ecology.2019;[Epub] CrossRef
Optimal environmental and culture conditions allow the in vitro coexistence of Pseudomonas aeruginosa and Staphylococcus aureus in stable biofilms
Maria del Mar Cendra, Núria Blanco-Cabra, Lucas Pedraz, Eduard Torrents
Scientific Reports.2019;[Epub] CrossRef
In vitro and ex vivo systems at the forefront of infection modeling and drug discovery
Di Shi, Gujie Mi, Mian Wang, Thomas J. Webster
Biomaterials.2019; 198: 228. CrossRef
Microbiome Dependent Regulation of Tregs and Th17 Cells in Mucosa
Pushpa Pandiyan, Natarajan Bhaskaran, Mangge Zou, Elizabeth Schneider, Sangeetha Jayaraman, Jochen Huehn
Frontiers in Immunology.2019;[Epub] CrossRef
Porphyromonas gingivalis Tyrosine Phosphatase Php1 Promotes Community Development and Pathogenicity
Young-Jung Jung, Daniel P. Miller, John D. Perpich, Zackary R. Fitzsimonds, Daonan Shen, Jun Ohshima, Richard J. Lamont, Indranil Biswas
mBio.2019;[Epub] CrossRef
Coinfection with Leishmania major and Staphylococcus aureus enhances the pathologic responses to both microbes through a pathway involving IL-17A
Tiffany Y. Borbón, Breanna M. Scorza, Gwendolyn M. Clay, Fellipe Lima Nobre de Queiroz, Alan J. Sariol, Jayden L. Bowen, Yani Chen, Bayan Zhanbolat, Corey P. Parlet, Diogo G. Valadares, Suzanne L. Cassel, William M. Nauseef, Alexander R. Horswill, Fayyaz
PLOS Neglected Tropical Diseases.2019; 13(5): e0007247. CrossRef
A Rare Opportunist, Morganella morganii , Decreases Severity of Polymicrobial Catheter-Associated Urinary Tract Infection
Brian S. Learman, Aimee L. Brauer, Kathryn A. Eaton, Chelsie E. Armbruster, Marvin Whiteley
Infection and Immunity.2019;[Epub] CrossRef
Streptococcus gordonii programs epithelial cells to resist ZEB2 induction by Porphyromonas gingivalis
Jun Ohshima, Qian Wang, Zackary R. Fitzsimonds, Daniel P. Miller, Maryta N. Sztukowska, Young-Jung Jung, Mikako Hayashi, Marvin Whiteley, Richard J. Lamont
Proceedings of the National Academy of Sciences.2019; 116(17): 8544. CrossRef
The oral microbiota: dynamic communities and host interactions
Richard J. Lamont, Hyun Koo, George Hajishengallis
Nature Reviews Microbiology.2018; 16(12): 745. CrossRef
Role of Short Chain Fatty Acids in Controlling Tregs and Immunopathology During Mucosal Infection
Natarajan Bhaskaran, Cheriese Quigley, Clarissa Paw, Shivani Butala, Elizabeth Schneider, Pushpa Pandiyan
Frontiers in Microbiology.2018;[Epub] CrossRef
Cross-feeding modulates antibiotic tolerance in bacterial communities
Elizabeth M Adamowicz, Jeffrey Flynn, Ryan C Hunter, William R Harcombe
The ISME Journal.2018; 12(11): 2723. CrossRef
Molecular Identification of Bacteria in Intra-abdominal Abscesses Using Deep Sequencing
Andrew Kozlov, Lorenzo Bean, Emilie V Hill, Lisa Zhao, Eric Li, Gary P Wang
Open Forum Infectious Diseases.2018;[Epub] CrossRef
Options and Limitations in Clinical Investigation of Bacterial Biofilms
Maria Magana, Christina Sereti, Anastasios Ioannidis, Courtney A. Mitchell, Anthony R. Ball, Emmanouil Magiorkinis, Stylianos Chatzipanagiotou, Michael R. Hamblin, Maria Hadjifrangiskou, George P. Tegos
Clinical Microbiology Reviews.2018;[Epub] CrossRef
Mutations in bacterial genes induce unanticipated changes in the relationship between bacterial pathogens in experimental otitis media
Vinal Lakhani, Li Tan, Sayak Mukherjee, William C. L. Stewart, W. Edward Swords, Jayajit Das
Royal Society Open Science.2018; 5(11): 180810. CrossRef
Acclimation of Culturable Bacterial Communities under the Stresses of Different Organic Compounds
Hui Wang, Shuangfei Zhang, Amit Pratush, Xueying Ye, Jinli Xie, Huan Wei, Chongran Sun, Zhong Hu
Frontiers in Microbiology.2018;[Epub] CrossRef
Effects of Growth Surface Topography on Bacterial Signaling in Coculture Biofilms
Arunima Bhattacharjee, Mughees Khan, Maya Kleiman, Allon I. Hochbaum
ACS Applied Materials & Interfaces.2017; 9(22): 18531. CrossRef
In vitro microbicidal, anti‐biofilm and cytotoxic effects of different commercial antiseptics
Silvestre Ortega‐Peña, Christian Hidalgo‐González, Martin C Robson, Edgar Krötzsch
International Wound Journal.2017; 14(3): 470. CrossRef
Pseudomonas aeruginosa Contact-Dependent Growth Inhibition Plays Dual Role in Host-Pathogen Interactions
Jeffrey A. Melvin, Jordan R. Gaston, Shawn N. Phillips, Michael J. Springer, Christopher W. Marshall, Robert M. Q. Shanks, Jennifer M. Bomberger, Sarah E. F. D'Orazio
mSphere.2017;[Epub] CrossRef
Fungal Biofilms and Polymicrobial Diseases
Caroline Costa-Orlandi, Janaina Sardi, Nayla Pitangui, Haroldo De Oliveira, Liliana Scorzoni, Mariana Galeane, Kaila Medina-Alarcón, Wanessa Melo, Mônica Marcelino, Jaqueline Braz, Ana Fusco-Almeida, Maria Mendes-Giannini
Journal of Fungi.2017; 3(2): 22. CrossRef
Discovery of Small Molecules as Multi-Toll-like Receptor Agonists with Proinflammatory and Anticancer Activities
Lei Zhang, Varun Dewan, Hang Yin
Journal of Medicinal Chemistry.2017; 60(12): 5029. CrossRef
Potentiation and tolerance of toll-like receptor priming in human endothelial cells
Stephen R. Koch, Fred S. Lamb, Judith Hellman, Edward R. Sherwood, Ryan J. Stark
Translational Research.2017; 180: 53. CrossRef
Albumin Inhibits Pseudomonas aeruginosa Quorum Sensing and Alters Polymicrobial Interactions
Allie Clinton Smith, Anne Rice, Bryan Sutton, Rebecca Gabrilska, Aimee K. Wessel, Marvin Whiteley, Kendra P. Rumbaugh, Beth McCormick
Infection and Immunity.2017;[Epub] CrossRef
Microbiota Analysis of Biofilms on Experimental Abutments Mimicking Dental Implants: An In Vivo Model
Berta Cortés‐Acha, Rui Figueiredo, Ramón Seminago, Francisco J. Roig, Carlos Llorens, Eduard Valmaseda‐Castellón
Journal of Periodontology.2017; 88(10): 1090. CrossRef
Identification by highly sensitive 16S metagenomic sequencing of an unusual case of polymicrobial bacteremia
Benjamin Lelouvier, Florence Servant, Pierre Delobel, Michael Courtney, Meyer Elbaz, Jacques Amar
Journal of Infection.2017; 75(3): 278. CrossRef
Metabolic crosstalk regulates Porphyromonas gingivalis colonization and virulence during oral polymicrobial infection
Masae Kuboniwa, John R. Houser, Erik L. Hendrickson, Qian Wang, Samar A. Alghamdi, Akito Sakanaka, Daniel P. Miller, Justin A. Hutcherson, Tiansong Wang, David A. C. Beck, Marvin Whiteley, Atsuo Amano, Huizhi Wang, Edward M. Marcotte, Murray Hackett, Rich
Nature Microbiology.2017; 2(11): 1493. CrossRef
Rapid susceptibility profiling of carbapenem-resistant Klebsiella pneumoniae
K. T. Mulroney, J. M. Hall, X. Huang, E. Turnbull, N. M. Bzdyl, A. Chakera, U. Naseer, E. M. Corea, M. J. Ellington, K. L. Hopkins, A. L. Wester, O. Ekelund, N. Woodford, T. J. J. Inglis
Scientific Reports.2017;[Epub] CrossRef
Dancing with the Stars: How Choreographed Bacterial Interactions Dictate Nososymbiocity and Give Rise to Keystone Pathogens, Accessory Pathogens, and Pathobionts
George Hajishengallis, Richard J. Lamont
Trends in Microbiology.2016; 24(6): 477. CrossRef
Resource limitation drives spatial organization in microbial groups
Sara Mitri, Ellen Clarke, Kevin R Foster
The ISME Journal.2016; 10(6): 1471. CrossRef
Hydrogen peroxide is a central determinant of oral polymicrobial synergy
Richard J. Lamont
Environmental Microbiology.2016; 18(11): 3609. CrossRef
Interactions between Pseudomonas aeruginosa and Staphylococcus aureus during co-cultivations and polymicrobial infections
Angela T. Nguyen, Amanda G. Oglesby-Sherrouse
Applied Microbiology and Biotechnology.2016; 100(14): 6141. CrossRef
Cyanide Toxicity to Burkholderia cenocepacia Is Modulated by Polymicrobial Communities and Environmental Factors
Steve P. Bernier, Matthew L. Workentine, Xiang Li, Nathan A. Magarvey, George A. O'Toole, Michael G. Surette
Frontiers in Microbiology.2016;[Epub] CrossRef
16S rRNA analysis provides evidence of biofilms on all components of three infected periprosthetic knees including permanent braided suture
Matthew C. Swearingen, Alex C. DiBartola, Devendra Dusane, Jeffrey Granger, Paul Stoodley, Thomas Bjarnsholt
Pathogens and Disease.2016; 74(7): ftw083. CrossRef
A Commensal Bacterium Promotes Virulence of an Opportunistic Pathogen via Cross-Respiration
Apollo Stacy, Derek Fleming, Richard J. Lamont, Kendra P. Rumbaugh, Marvin Whiteley, Michael S. Gilmore, Vanessa Sperandio, Donald Demuth
mBio.2016;[Epub] CrossRef
Fusobacterium nucleatum infections: clinical spectrum and bacteriological features of 78 cases
E. Denes, O. Barraud
Infection.2016; 44(4): 475. CrossRef
The biogeography of polymicrobial infection
Apollo Stacy, Luke McNally, Sophie E. Darch, Sam P. Brown, Marvin Whiteley
Nature Reviews Microbiology.2016; 14(2): 93. CrossRef
Do Polymicrobial Intra-Abdominal Infections Have Worse Outcomes than Monomicrobial Intra-Abdominal Infections?
Puja M. Shah, Brandy L. Edwards, Zachary C. Dietch, Christopher A. Guidry, Stephen W. Davies, Sara A. Hennessy, Therese M. Duane, Patrick J. O'Neill, Raul Coimbra, Charles H. Cook, Reza Askari, Kimberly Popovsky, Robert G. Sawyer
Surgical Infections.2016; 17(1): 27. CrossRef
Stochastic Assembly of Bacteria in Microwell Arrays Reveals the Importance of Confinement in Community Development
Ryan H. Hansen, Andrea C. Timm, Collin M. Timm, Amber N. Bible, Jennifer L. Morrell-Falvey, Dale A. Pelletier, Michael L. Simpson, Mitchel J. Doktycz, Scott T. Retterer, Xiangzhen Li
PLOS ONE.2016; 11(5): e0155080. CrossRef
Study of the growth of Enterococcus faecalis, Escherichia coli and their mixtures by microcalorimetry
C. Vazquez, N. Lago, M. M. Mato, L. Esarte, J. L. Legido
Journal of Thermal Analysis and Calorimetry.2016; 125(2): 739. CrossRef
Let there be bioluminescence: development of a biophotonic imaging platform for in situ analyses of oral biofilms in animal models
Justin Merritt, Hidenobu Senpuku, Jens Kreth
Environmental Microbiology.2016; 18(1): 174. CrossRef
The cystic fibrosis microbiome in an ecological perspective and its impact in antibiotic therapy
Andreia P. Magalhães, Nuno F. Azevedo, Maria O. Pereira, Susana P. Lopes
Applied Microbiology and Biotechnology.2016; 100(3): 1163. CrossRef
Individuality, phenotypic differentiation, dormancy and ‘persistence’ in culturable bacterial systems: commonalities shared by environmental, laboratory, and clinical microbiology
Douglas Kell, Marnie Potgieter, Etheresia Pretorius
F1000Research.2015; 4: 179. CrossRef
Iron-Mediated Control of Pseudomonas aeruginosa-Staphylococcus aureus Interactions in the Cystic Fibrosis Lung
Patricia M. Barnabie, Marvin Whiteley, V. J. DiRita
Journal of Bacteriology.2015; 197(14): 2250. CrossRef
Polymicrobial Infective Endocarditis
Pablo Elpidio García-Granja, Javier López, Isidre Vilacosta, Carlos Ortiz-Bautista, Teresa Sevilla, Carmen Olmos, Cristina Sarriá, Carlos Ferrera, Itziar Gómez, José Alberto San Román
Medicine.2015; 94(49): e2000. CrossRef
Mass spectrometry tools and workflows for revealing microbial chemistry
Tal Luzzatto-Knaan, Alexey V. Melnik, Pieter C. Dorrestein
The Analyst.2015; 140(15): 4949. CrossRef
Solving the etiology of dental caries
Aurea Simón-Soro, Alex Mira
Trends in Microbiology.2015; 23(2): 76. CrossRef
Individuality, phenotypic differentiation, dormancy and ‘persistence’ in culturable bacterial systems: commonalities shared by environmental, laboratory, and clinical microbiology
Douglas Kell, Marnie Potgieter, Etheresia Pretorius
F1000Research.2015; 4: 179. CrossRef
Pseudomonas aeruginosa adaptation to human hosts
Evan S Snitkin, Julia A Segre
Nature Genetics.2015; 47(1): 2. CrossRef
Biofilm Models of Polymicrobial Infection
Rebecca A Gabrilska, Kendra P Rumbaugh
Future Microbiology.2015; 10(12): 1997. CrossRef
The Limitations of In Vitro Experimentation in Understanding Biofilms and Chronic Infection
Aled E.L. Roberts, Kasper N. Kragh, Thomas Bjarnsholt, Stephen P. Diggle
Journal of Molecular Biology.2015; 427(23): 3646. CrossRef
Mass spectrometric metabolomic imaging of biofilms on corroding steel surfaces using laser ablation and solvent capture by aspiration
Jonathan I. Brauer, Zakari Makama, Vincent Bonifay, Egemen Aydin, Eric D. Kaufman, Iwona B. Beech, Jan Sunner
Biointerphases.2015;[Epub] CrossRef
Spoils of war: iron at the crux of clinical and ecological fitness of Pseudomonas aeruginosa
Angela T. Nguyen, Amanda G. Oglesby-Sherrouse
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Research Support, Non-U.S. Gov't

NOTE] rRNASelector: A Computer Program for Selecting Ribosomal RNA Encoding Sequences from Metagenomic and Metatranscriptomic Shotgun Libraries: Jae-Hak Lee , Hana Yi , Jongsik Chun; J. Microbiol. 2011;49(4):689-691. Published online September 2, 2011; DOI: https://doi.org/10.1007/s12275-011-1213-z

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Abstract: Metagenomic and metatranscriptomic shotgun sequencing techniques are gaining popularity as more cost-effective next-generation sequencing technologies become commercially available. The initial stage of bioinformatic analysis generally involves the identification of phylogenetic markers such as ribosomal RNA genes. The sequencing reads that do not code for rRNA can then be used for protein-based analysis. Hidden Markov model is a well-known method for pattern recognition. Hidden Markov models that are trained on well-curated rRNA sequence databases have been successfully used to identify DNA sequence coding for rRNAs in prokaryotes. Here, we introduce rRNASelector, which is a computer program for selecting rRNA genes from massive metagenomic and metatranscriptomic sequences using hidden Markov models. The program successfully identified prokaryotic 5S, 26S, and 23S rRNA genes from Roche 454 FLX Titanium-based metagenomic and metatranscriptomic libraries. The rRNASelector program is available at http://sw.ezbiocloud.net/rrnaselector.

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