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Harnessing Emergent Properties of Microbial Consortia: Assembly of the Xilonen SynCom bioRxiv. Microbiol. Pub Date : 2024-04-24 Gabriela Gastelum, Bruno Gomez-Gil, Gabriela Olmedo-Alvarez, Jorge Rocha
Synthetic communities (SynComs) are valuable tools for addressing fundamental questions in microbial ecology regarding community assembly. They could also potentially aid in successfully manipulating microbial communities for clinical, biotechnological, and agricultural applications. SynCom design is complicated since interactions between microbes cannot be predicted based on their individual properties
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Carbonic anhydrase plays multiple roles in acetotrophic growth of a model marine methanogen from the domain Archaea bioRxiv. Microbiol. Pub Date : 2024-04-24 James G. Ferry, Michel Geovanni Santiago-Martinez, Sabrina Zimmerman, Kevin R Sowers, Ethel Apolinario
Carbonic anhydrase (CA) catalyzes the reversible hydration of CO2 to bicarbonate and a proton. The enzyme is universally distributed in all three domains of life and plays diverse physiological roles in the domains Eukarya and Bacteria. Remarkably, a physiological role has not been identified for any CA from the domain Archaea. Herein are described roles for a gamma class CA (Cam) from the methane-producing
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Growth characteristics of natural microbial populations are skewed towards bacteria with low specific growth rates bioRxiv. Microbiol. Pub Date : 2024-04-24 Ashley N Bulseco, Wenzhou Yang, Julie A. Huber, Joseph J Vallino
Microbes are often functionally characterized by traits that specify their optimum environmental conditions for growth, such as temperature or pH, as well as upper and lower bounds where growth is possible. While any given microbe will have a narrow environmental window where growth can occur, a diverse community can span a much larger range of conditions where growth is possible by at least some members
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Association of diet and inflammation with the vaginal microbiota of pregnant individuals with or without IBD bioRxiv. Microbiol. Pub Date : 2024-04-24 Daniela Vargas Robles, Yap Yan Rou, Biplab Singha, Joyce Tien, Mallika Purandare, Mayra Rojas-Correa, Camilla Madziar, Mellissa Picker, Tina Dumont, Heidi Leftwich, Christine F Frisard, Doyle V Ward, Inga Peter, Barbara Olendzki, Ana Maldonado-Contreras
Background and aims: Vaginal dysbiosis has been associated with adverse pregnancy outcomes. Here, we characterized the vaginal microbiota of pregnant individuals with inflammatory bowel disease (IBD) and investigated whether gut or vaginal inflammation and diet influence the vaginal microbiota diversity of these individuals. Study Design: We recruited 48 individuals in their third trimester of pregnancy
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Quinoxaline-Based Anti-Schistosomal Compounds Have Potent Anti-Malarial Activity bioRxiv. Microbiol. Pub Date : 2024-04-24 Mukul Rawat, Gilda Padalino, Tomas Yeo, Andrea Brancale, David Fidock, Karl Hoffmann, Marcus Lee
The human pathogens Plasmodium and Schistosoma are each responsible for over 200 million infections annually, being particularly problematic in low- and middle-income countries. There is a pressing need for new drug targets for these diseases, driven by emergence of drug-resistance in Plasmodium and the overall dearth of new drug targets for Schistosoma. Here, we explored the opportunity for pathogen-hopping
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A novel micronemal protein, Scot1, is essential for apicoplast biogenesis and liver stage development in Plasmodium berghei bioRxiv. Microbiol. Pub Date : 2024-04-24 Ankit Ghosh, Akancha Mishra, Raksha Devi, Sunil Kumar Narwal, Nirdosh Nirdosh, Pratik Narain Srivastava, Satish Mishra
Plasmodium sporozoites invade hepatocytes, transform into liver stages, and replicate into thousands of merozoites that infect erythrocytes and cause malaria. Proteins secreted from micronemes play an essential role in hepatocyte invasion, and unneeded micronemes are subsequently discarded for replication. The liver-stage parasites are potent immunogens that prevent malarial infection. Late liver stage-arresting
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Vaginal metatranscriptome meta-analysis reveals functional BV subgroups and novel colonisation strategies bioRxiv. Microbiol. Pub Date : 2024-04-24 Scott J Dos Santos, Clara Copeland, Jean M Macklaim, Gregor Reid, Gregory B Gloor
The application of '-omics' technologies to study bacterial vaginosis (BV) has uncovered vast differences in composition and scale between the vaginal microbiomes of healthy and BV patients. Compared to amplicon sequencing and shotgun metagenomic approaches focusing on a single or few species, investigating the transcriptome of the vaginal microbiome at a system-wide level can provide insight into
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Quinolone resistance genes qnr, aac(6′)-Ib-cr, oqxAB, and qepA in environmental Escherichia coli: insights into their genetic contexts from comparative genomics bioRxiv. Microbiol. Pub Date : 2024-04-24 Ryota Gomi, Fumie Adachi
Previous studies have reported the occurrence of transferable quinolone resistance determinants in environmental Escherichia coli. However, little is known about their vectors and genetic contexts. To gain insights into these genetic characteristics, we analyzed the complete genomes of 53 environmental E. coli isolates, including 20 sequenced in this study and 33 sourced from RefSeq. The following
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Expanding the genome information on Bacillales for biosynthetic gene cluster discovery bioRxiv. Microbiol. Pub Date : 2024-04-24 Lijie Song, Lasse Johan Dyrbye Nielsen, Xinming Xu, Omkar Satyavan Mohie, Matin Nuhamunada, Zhihui Xu, Robert Murphy, Kasun Bodawatta, Michael Poulsen, Mohamed Hatha Abdulla, Eva C. Sonnenschein, Tilmann Weber, Akos T. Kovacs
This study showcases 121 new genomes of spore-forming Bacillales from strains collected globally from a variety of habitats, assembled using Oxford Nanopore long-read and MGI short-read sequences. Bacilli are renowned for their capacity to produce diverse secondary metabolites with use in agriculture, biotechnology, and medicine. These secondary metabolites are encoded within biosynthetic gene clusters
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Contrasting dynamics of two incursions of low pathogenicity avian influenza virus into Australia bioRxiv. Microbiol. Pub Date : 2024-04-24 Michelle Wille, Ivano Broz, Allison Crawley, Blaine Farrugia, Mark Ford, Melinda Frost, Joanne Grimsey, Peter Kirkland, Tanya Cherrington, Shaylie Latimore, Stacey Lynch, Sue Martin, Cornelius Matereke, Peter Mee, Matthew Neave, Mark O'Dea, Andrew Read, Kim O'Riley, Vittoria Stevens, Sivapiragasam Tharaparan, Sara Zufan, Silvia Ban de Gouvea Pedroso, Victoria Grillo, Andrew Breed, Ian Barr, Edward
The current panzootic of high pathogenicity avian influenza virus H5N1 demonstrates how viral incursions can have major ramifications for wildlife and domestic animals. Herein, we describe the recent incursion into Australia of two low pathogenicity avian influenza virus subtypes, H4 and H10, that exhibited contrasting evolutionary dynamics. Viruses detected from national surveillance and disease investigations
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Reassortant strains of infectious bursal disease virus (IBDV) belonging to genogroup A3B1 predominate in British broiler chicken flocks. bioRxiv. Microbiol. Pub Date : 2024-04-24 Vishwanatha R. A. P. Reddy, Carlo Bianco, Christopher Poulos, Andrew J. Brodrick, Salik Nazki, Alex Schock, Andrew James Broadbent
As part of ongoing epidemiological surveillance for infectious bursal disease virus (IBDV), the hypervariable region (HVR) of the VP2 capsid gene encoded by segment A, and a region of the VP1 polymerase gene, encoded by segment B, were sequenced from 20 IBDV-positive bursal samples obtained in 2020 and 2021, from 16 commercial British broiler farms. Of the 16 farms, none contained very virulent (vv)
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SUN-domain proteins of the malaria parasite Plasmodium falciparum are essential for proper nuclear division and DNA repair bioRxiv. Microbiol. Pub Date : 2024-04-24 Sofiya Kandelis-Shalev, Manish Goyal, Shany Assaraf, Tal Elam, Noa Dahan, Eduard Berenshtein, Ron Dzikowski
The protozoan parasite Plasmodium falciparum, which is responsible for the deadliest form of human malaria, accounts for over half a million deaths a year. These parasites proliferate in human red blood cells by consecutive rounds of closed mitoses called schizogony. Their virulence is attributed to their ability to modify the infected red cells to adhere to the vascular endothelium and to evade immunity
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The Chlamydia effector IncE employs two short linear motifs to reprogram host vesicle trafficking bioRxiv. Microbiol. Pub Date : 2024-04-24 Khavong Pha, Katherine Mirrashidi, Jessica Sherry, Cuong Joseph Tran, Clara M. Herrera, Eleanor McMahon, Cherilyn Elwell, Joanne Engel
Chlamydia trachomatis, a leading cause of bacteria sexually transmitted infections, creates a specialized intracellular replicative niche by translocation and insertion of a diverse array of effectors (Incs) into the inclusion membrane. Here, we characterize IncE, a multi-functional Inc that encodes two non-overlapping short linear motifs (SLiMs) within its short cytosolic C-terminus. The proximal
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Large circulation of a novel vesiculovirus in bats in the Mediterranean region bioRxiv. Microbiol. Pub Date : 2024-04-24 Dong Sheng Luo, Marketa Harazim, Corinne Maufrais, Simon Bonas, Natalia Martinkova, Aude Lalis, Emmanuel Nakoune, Edgard Valery Adjogoua, Mory Douno, Blaise Kadjo, Marc Lopez-Roig, Jiri Pikula, Zheng Li Shi, Herve Bourhy, Jordi Serra-Cobo, Laurent Dacheux
Bats are the natural reservoirs of a variety of emerging or reemerging viruses. Among them, rabies virus (genus Lyssavirus, family Rhabdoviridae) is of the first and most iconic described in these animals. Since its first description, various new bat lyssaviruses have been regularly described. Apart from lyssaviruses, other bat rhabdoviruses have been also identified, including members of the Vesiculovirus
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SARS-CoV-2 Omicron Envelope T9I adaptation confers resistance to autophagy bioRxiv. Microbiol. Pub Date : 2024-04-24 Susanne Klute, Rayhane Nchioua, Arne Cordsmeier, Jyoti Vishwakarma, Lennart Koepke, Hala Alshammary, Christoph Jung, Maximilian Hirschenberger, Helene Hoenigsperger, Jana-Romana Fischer, Fabian Zech, Steffen Stenger, Ruth Serra-Moreno, Ana S Gonzalez-Reiche, Emilia Mia Sordillo, Harm van Bakel, Viviana Simon, Frank Kirchhoff, Timo Jacob, Dorota Kmiec, Andreas Pichlmair, Armin Ensser, Konstantin MJ
To date, five variants of concern (VOCs) of SARS-CoV-2 have emerged that show increased fitness and/or immune evasion. While the continuously evolving escape from humoral immune responses has been analyzed in detail, adaptation of SARS-CoV-2 to human innate immune defenses such as autophagy is less understood. Here, we demonstrate that mutation T9I in the structural envelope (E) protein confers autophagy
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RNA-Seq reveals that Pseudomonas aeruginosa mounts growth medium-dependent competitive responses when sensing diffusible cues from Burkholderia cenocepacia bioRxiv. Microbiol. Pub Date : 2024-04-24 Anne Leinweber, Clémentine Laffont, Martina Lardi, Leo Eberl, Gabriella Pessi, Rolf Kümmerli
Most habitats host diverse bacterial communities, offering opportunities for inter-species interactions. While competition might often dominate such interactions, little is known about whether bacteria can sense competitors and mount adequate responses. The competition-sensing hypothesis proposes that bacteria can use cues such as nutrient stress and cell damage to prepare for battle. Here, we tested
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Antimicrobial effects, and selection for AMR by non-antibiotic drugs on bacterial communities bioRxiv. Microbiol. Pub Date : 2024-04-23 April Hayes, Lihong Zhang, Ed Feil, Barbara Kasprzyk-Hordern, Jason Snape, William H Gaze, Aimee K Murray
Antimicrobial resistance (AMR) is a major threat to human, veterinary, and agricultural health. AMR can be directly selected for by antibiotics, and indirectly co-selected for by biocides and metals. Some evidence suggests that non-antibiotic drugs (NADs) can co-select for AMR, but previous work focused on exposing single model bacterial species to predominately high concentrations of NADs. Here, we
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Harnessing defective interfering particles and lipid nanoparticles for effective delivery of an anti-dengue virus RNA therapy bioRxiv. Microbiol. Pub Date : 2024-04-23 Min-Hsuan Lin, Pramila Maniam, Dongsheng Li, Bing Tang, Cameron Bishop, Andreas Suhrbier, Lucy Wales-Earl, Yaman Tayyar, Nigel A. J. McMillan, Li Li, David Harrich
Presently, no approved antiviral drug targets dengue virus (DENV) infection. Treatment mainly relies on supportive measures, while the efficacy of DENV vaccines varies based on factors like vaccine type, circulating DENV serotypes, and the vaccinated population. This study explores using defective interfering particles (DIPs) and lipid nanoparticles (LNPs) to deliver an anti-DENV defective interfering
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First application of digital-PCR in oenology for the specific detection of intact cells of Brettanomyces bruxellensis in the winemaking process bioRxiv. Microbiol. Pub Date : 2024-04-23 Cecile Gruet, Jeremy Di Mattia, Magali Hiaumet, Dylan Pestel, Caroline Araiz, Sarah Saadi, Marie Ducousso, Olivier Courot
Wine is a complex matrix resulting from a fermentation process carried out by specific microbial communities. These communities can be in competition and the development of some microorganisms, as the yeast Brettanomyces bruxellensis, can impact the fermentation process and lead to organoleptic alterations of wine. To manage this risk, microbiological diagnostic methods as microscopic observations
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Capsular Polysaccharide Restrains Type VI Secretion in Acinetobacter baumannii bioRxiv. Microbiol. Pub Date : 2024-04-23 Nicolas Flaugnatti, Loriane Bader, Mary Croisier-Coeytaux, Melanie Blokesch
The type VI secretion system (T6SS) is a sophisticated, contact-dependent nanomachine involved in interbacterial competition. To function effectively, the T6SS must penetrate the membranes of both attacker and target bacteria. Structures associated with the cell envelope, like polysaccharides chains, can therefore introduce spatial separation and steric hindrance, potentially affecting the efficacy
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Production, analysis, and safety assessment of a soil and plant-based natural material with microbiome- and immune-modulatory effects bioRxiv. Microbiol. Pub Date : 2024-04-23 Anirudra Parajuli, Iida Makela, Marja I Roslund, Emma Ringqvist, Juulia Manninen, Yan Sun, Noora Nurminen, Sami Oikarinen, Oll H Laitinen, Heikki Hyoty, Malin Flodstrom-Tullberg, Aki Sinkkonen
Reduced contact with the microbiota from the natural environment has been suggested to contribute to the rising incidence of immune-mediated inflammatory disorders (IMIDs) in the western, highly urbanized societies. In line with this, we have previously shown that exposure to environmental microbiota in the form of a blend comprising of soil and plant-based material (biodiversity blend; BDB) enhances
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Phages indirectly maintain plant pathogen defense through regulation of the commensal microbiome bioRxiv. Microbiol. Pub Date : 2024-04-23 Reena Reed Debray, Asa Conover, Britt Koskella
Many infectious diseases are associated with altered communities of bacteriophage viruses (phages). As parasites of bacteria, phages can regulate microbiome diversity and composition and may therefore affect disease susceptibility. Yet observational studies alone do not allow us to determine whether altered phage profiles are a contributor to disease risk, a response to infection, or simply an indicator
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Hackflex library preparation enables low-cost metagenomic profiling bioRxiv. Microbiol. Pub Date : 2024-04-23 Samantha L Goldman, Jon G Sanders, Daniel D Sprockett, Abigail Landers, Weiwei Yan, Andrew H Moeller
Shotgun metagenomic sequencing provides valuable insights into microbial communities, but the high cost of library preparation with standard kits and protocols is a barrier for many. New methods such as Hackflex use diluted commercially available reagents to greatly reduce library preparation costs. However, these methods have not been systematically validated for metagenomic sequencing. Here, we evaluate
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A conserved lysine/arginine-rich motif in potyviral 6K1 protein is key in engaging autophagy-mediated self-degradation for completing pepper veinal mottle virus infection bioRxiv. Microbiol. Pub Date : 2024-04-23 Weiyao Hu, Changhui Deng, Li Qin, Peilan Liu, Linxi Wang, Xaioqin Wang, Wei Shi, Asma Aziz, Fangfang Li, Xiaofei Cheng, Aiming Wang, Zhaoji Dai, Xiaohua Xiang, Hongguang Cui
Potyviruses possess one positive-sense single-stranded RNA genome mainly with polyprotein processing as their gene expression strategy. The resulting polyproteins are proteolytically processed by three virus-encoded proteases into 11 or 12 mature proteins. One of such, 6-kDa peptide 1 (6K1), is an understudied viral factor. Its function in viral infection remains largely mysterious. This study is to
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Mitochondrial ATP synthesis is essential for efficient gametogenesis in Plasmodium falciparum bioRxiv. Microbiol. Pub Date : 2024-04-23 Penny C Sparkes, Mufuliat Toyin Famodimu, Eduardo Alves, Eric Springer, Jude Marek Przyborski, Michael J Delves
Interrupting parasite transmission from humans to mosquitoes is vital for malaria elimination and eradication. Plasmodium male and female gametocytes are the gatekeepers of human to mosquito transmission. Whilst dormant in the human host, their divergent roles during transmission become visually apparent soon after ingestion by the mosquito after rapid transformation into gametes - the males forming
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Dimalis: A complete standalone pipeline to analyse prokaryotic cell growth from time-lapse imaging bioRxiv. Microbiol. Pub Date : 2024-04-23 Jan Roelof van der Meer, Helena Todorov, Bouke Bentvelsen, Stefano Ugolini, Alan R. Pacheco, Anthony Convers, Tania Miguel Trabajo
Real-time imaging of bacterial cell division, population growth and behaviour is essential for our understanding of microbial-catalyzed processes at the microscale. However, despite the relative ease by which high resolution imaging data can be acquired, the extraction of relevant cell features from images remains cumbersome. Here we present a versatile pipeline for automated extraction of bacterial
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Identification of distinct genotypes in circulating RSV A strains based on variants on the virus replication-associated genes bioRxiv. Microbiol. Pub Date : 2024-04-23 Abdulafiz Musa, Sydney Faber, Kaitlyn Forrest, Kenneth Smith, Shaon Sengupta, Carolina B. Lopez
Respiratory syncytial virus is a common cause of respiratory infection that often leads to hospitalization of infected younger children and older adults. RSV is classified into two strains, A and B, each with several subgroups or genotypes. One issue with the definition of these subgroups is the lack of a unified method of identification or genotyping. We propose that genotyping strategies based on
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Cell-free assays reveal the HIV-1 capsid protects reverse transcripts from cGAS bioRxiv. Microbiol. Pub Date : 2024-04-23 Tiana M. Scott, Lydia M. Arnold, Jordan A. Powers, Delaney A. McCann, Devin E. Christensen, Wen Zhou, Rachel M. Torrez, Janet H. Iwasa, Philip J. Kranzusch, Wesley I. Sundquist, Jarrod S. Johnson
Retroviruses can be detected by the innate immune sensor cyclic GMP-AMP synthase (cGAS), which recognizes reverse-transcribed DNA and activates an antiviral response. However, the extent to which HIV-1 shields its genome from cGAS recognition remains unclear. To study this process in mechanistic detail, we reconstituted reverse transcription, genome release, and innate immune sensing of HIV-1 in a
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Asymptomatic neonatal herpes simplex virus infection in mice leads to long-term cognitive impairment bioRxiv. Microbiol. Pub Date : 2024-04-23 Abigail J Dutton, Chaya D Patel, Sean A Taylor, Callaghan R Garland, Evelyn Turnbaugh, Roberto Alers-Velazquez, Jesse Mehrbach, Katherine M Nautiyal, David A Leib
Neonatal herpes simplex virus (nHSV) is a devastating infection impacting approximately 14,000 newborns globally each year. Infection is associated with high neurologic morbidity and mortality, making early intervention and treatment critical. Clinical outcomes of symptomatic nHSV infections are well-studied, but little is known about the frequency of, or outcomes following, sub-clinical or asymptomatic
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Silversol (a colloidal nanosilver formulation) inhibits growth of antibiotic-resistant Staphylococcus aureus by disrupting its physiology in multiple ways bioRxiv. Microbiol. Pub Date : 2024-04-23 Nidhi Thakkar, Gemini Gajera, Chhaya Godse, Anselm DeSouza, Dilip Mehta, Vijay Kothari
Antibacterial effect of a colloidal nanosilver formulation Silversol was investigated against an antibioticresistant strain of Staphylococcus aureus. Lower concentrations of the test formulation exerted bacteriostatic and, its higher concentrations exerted bactericidal effect against this pathogen. Silversol at sub-lethal concentration was found to disturb multiple physiological traits of S. aureus
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An efficient plasmid-based system for the recovery of recombinant vesicular stomatitis virus encoding foreign glycoproteins bioRxiv. Microbiol. Pub Date : 2024-04-23 Maria-Carmen Marques, Ivan Andreu-Moreno, Rafael Sanjuan, Santiago F. Elena, Ron Geller
Viral glycoproteins mediate entry into host cells, thereby dictating host range and pathogenesis. In addition, they constitute the principal target of neutralizing antibody responses, making them important antigens in vaccine development. Recombinant vesicular stomatitis virus (VSV) encoding foreign glycoproteins can provide a convenient and safe surrogate system to interrogate the function, evolution
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The role of endospore appendages in spore-spore contacts in pathogenic bacilli bioRxiv. Microbiol. Pub Date : 2024-04-22 Unni Lise Jonsmoen, Dmitry Malyshev, Mike Sleutel, Elise Egeli Kristensen, Ephrem Debebe Zegeye, Han Remaut, Magnus Andersson, Marina Elisabeth Aspholm
Species within the spore-forming Bacillus cereus sensu lato group are recognized for their role in food spoilage and food poisoning. B. cereus spores are decorated with numerous pilus-like appendages, called S-ENAs and L-ENAs. These appendages are believed to play crucial roles in self-aggregation, adhesion, and biofilm formation. By using both bulk and single-cell approaches, we investigate the role
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Species-Specific ribosomal RNA-FISH identifies interspecies cellular-material exchange, active-cell population dynamics and cellular localization of translation machinery in clostridial cultures and co-cultures bioRxiv. Microbiol. Pub Date : 2024-04-22 John D Hill, Eleftherios T Papoutsakis
The development of synthetic microbial consortia in recent years has revealed that complex interspecies interactions, notably, the exchange of cytoplasmic material, exist even among organisms that originate from different ecological niches. Although morphogenetic characteristics, viable RNA and protein dyes and fluorescent reporter proteins have played an essential role in exploring such interactions
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Molecular architecture of glideosome and nuclear F-actin in Plasmodium falciparum bioRxiv. Microbiol. Pub Date : 2024-04-22 Vojtech Prazak, Daven Vasishtan, Kay Grunewald, Ross Gavin Douglas, Josie Liane Ferreira
Actin-based motility is required for the transmission of malaria sporozoites. However, direct structural data for this process is lacking. We used FIB-milling and electron cryo-tomography to study untreated actin in situ and dissect the path of actin filaments during parasite gliding. This revealed unexpected structures, including currently unknown filaments reinforcing the pellicle and actin bundles
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Heterogeneous efflux pump expression underpins phenotypic resistance to antimicrobial peptides bioRxiv. Microbiol. Pub Date : 2024-04-22 Ka Kiu Lee, Urszula Lapinska, Giulia Tolle, Wanida Phetsang, Anthony Verderosa, Brandon M. Invergo, Joseph Westley, Attila Bebes, Raif Yuecel, Paul A. ONeill, Audrey Farbos, Aaron R. Jeffries, Stineke van Houte, Pierluigi Caboni, Mark Blaskovich, Benjamin Housden, Krasimira Tsaneva-Atanasova, Stefano Pagliara
Antimicrobial resistance threatens the viability of modern medical interventions. There is a dire need of developing novel approaches to counter resistance mechanisms employed by starved or slow-growing pathogens that are refractory to conventional antimicrobial therapies. Antimicrobial peptides have been advocated as potential therapeutic solutions due to low levels of genetic resistance observed
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Microbiota from young mice counteracts susceptibility to age-related gout through modulating butyric acid levels in aged mice bioRxiv. Microbiol. Pub Date : 2024-04-22 Ning Song, Hang Gao, Jianhao Li, Yi Liu, Mingze Wang, Zhiming Ma, Naisheng Zhang, Wenlong Zhang
Gout is a prevalent form of inflammatory arthritis that occurs due to high levels of uric acid in the blood leading to the formation of urate crystals in and around the joints, particularly affecting the elderly. Recent research has provided evidence of distinct differences in the gut microbiota of patients with gout and hyperuricemia when compared to healthy individuals. However, the link between
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Deep sequencing of 16 Ixodes ricinus ticks unveils insights into their interactions with endosymbionts. bioRxiv. Microbiol. Pub Date : 2024-04-22 Paulina M. Lesiczka, Tal Azagi, Aleksandra I. Krawczyk, William T. Scott, Ron P. Dirks, Ladislav Simo, Gerhard Dobler, Bart Nijsse, Peter J. Schaap, Hein Sprong, Jasper J. Koehorst
Background: Ixodes ricinus ticks act as vectors for numerous pathogens that present substantial health threats. Additionally, they harbor vertically transmitted symbionts, some of which have been linked to diseases. The difficulty of isolating and cultivating these symbionts has has hampered our understanding of their biological role, their potential to cause disease, and their modes of transmission
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The gatekeeper to gastric cancer; gastric microbiota invade the lamina propria in Helicobacter pylori-associated gastric carcinogenesis bioRxiv. Microbiol. Pub Date : 2024-04-22 Harriet J. Giddings, Ana Teodósio, Jack L. McMurray, Kelly Hunter, Zainab Abdawn, Jeffrey A. Cole, Claire D. Shannon-Lowe, Amanda E. Rossiter-Pearson
Stomach cancer is the fourth leading cause of cancer-related deaths worldwide. Helicobacter pylori is the main risk factor for gastric adenocarcinoma (GAC), yet the mechanism underpinning this association remains uncharacterised. Gastric intestinal metaplasia (GIM) represents the pre-cancerous stage and follows H. pylori-associated chronic gastritis (CG). Sequencing studies have revealed fewer H. pylori
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Ultra-sensitive metaproteomics (uMetaP) redefines the dark field of metaproteome, enables single-bacterium resolution, and discovers hidden functions in the gut microbiome bioRxiv. Microbiol. Pub Date : 2024-04-22 Feng Xian, Malena Brenek, Christoph Krisp, Ranjith Kumar Ravi Kumar, Manuela Schmidt, David Gomez Varela
Metaproteomics uniquely characterizes host-microbiome interactions. However, most species detected by metagenomics remain hidden to metaproteomics due to sensitivity limits. We present a novel ultra-sensitive metaproteomic solution (uMetaP) that, for the first time, reaches full-length 16S rRNA taxonomic depth and can simultaneously decipher functional features. Querying the mouse gut microbiome, uMetaP
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Re-examination of the taxonomic status of the Antarctic Pseudomonas syringae Lz4W isolate and proposal to rename it as a novel species Pseudomonas cryophila sp. nov. bioRxiv. Microbiol. Pub Date : 2024-04-22 Malay Kumar Ray, Apuratha Pandiyan, Bhubanananda Sahu
A taxonomic re-evaluation of the Antarctic psychrotrophic bacterium Pseudomonas syringae Lz4W was performed in the light of its available genome sequence and due to a revision in the key phenotypic characteristics that are in conflict with the syringae group of Pseudomonads. A 16S rRNA gene sequence based phylogenetic analysis suggested that Lz4WT strain belongs to fragi cluster of Pseudomonas species
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Beyond membrane permeability: A role for the small RNA MicF in regulation of chromosome replication and partitioning bioRxiv. Microbiol. Pub Date : 2024-04-22 Aaron Y Stibelman, Amy Y Sariles, Melissa K Takahashi
Small regulatory RNAs (sRNA) have been shown to play a large role in the management of stress responses in Escherichia coli and other bacteria. sRNAs act post-transcriptionally on target mRNA through an imperfect base pairing mechanism to regulate downstream protein expression. The imperfect base pairing allows a single sRNA to bind and regulate a variety mRNA targets which can form intricate regulatory
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Conservation of C4BP-binding Sequence Patterns in Streptococcus pyogenes M and Enn Proteins bioRxiv. Microbiol. Pub Date : 2024-04-22 Piotr Kolesinski, Matthew McGowan, Anne Botteaux, Pierre R Smeesters, Partho Ghosh
Antigenically sequence variable M proteins of the major bacterial pathogen Streptococcus pyogenes (Strep A) are responsible for recruiting human C4b-binding protein (C4BP) to the bacterial surface, which enables Strep A to evade destruction by the immune system. The most sequence divergent portion of M proteins, the hypervariable region (HVR), is responsible for binding C4BP. Structural evidence points
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A phage satellite manipulates the viral DNA packaging motor to inhibit phage and promote satellite spread bioRxiv. Microbiol. Pub Date : 2024-04-22 Caroline Boyd, Kimberley Seed
ICP1, a lytic bacteriophage of Vibrio cholerae, is parasitized by phage satellites, PLEs, which hijack ICP1 proteins for their own horizontal spread. PLEs dependence on ICP1s DNA replication machinery, and virion components results in inhibition of ICP1s lifecycle. PLEs are expected to depend on ICP1 factors for genome packaging, but the mechanism(s) PLEs use to inhibit ICP1 genome packaging is currently
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Antiviral and Antibacterial Efficacy of Nanocomposite Amorphous Carbon Films with Copper Nanoparticles bioRxiv. Microbiol. Pub Date : 2024-04-22 Shah Bakhet, Asta Tamuleviciene, Andrius Vasiliauskas, Mindaugas Andrulevicius, Sarunas Meskinis, Sigitas Tamulevicius, Neringa Kasetiene, Mindaugas Malakauskas, Raimundas Lelesius, Dainius Zienius, Algirdas Salomskas, Krisjanis Smits, Tomas Tamulevicius
Copper compound-rich films and coatings are effective against widespread viruses and bacteria. Even though the killing mechanisms are still debated it is agreed that the metal ion, nanoparticle release, and surface effects are of paramount importance in the antiviral and antibacterial efficacy of the surfaces. In this work we have investigated the behaviour of the reactive magnetron sputtered nanocomposite
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Interspecies surfactants serve as public goods enabling surface motility in Pseudomonas aeruginosa bioRxiv. Microbiol. Pub Date : 2024-04-22 Delayna L. Warrell, Tiffany M. Zarrella, Christopher Machalek, Anupama Khare
In most natural environments, bacteria live in polymicrobial communities where secreted molecules from neighboring species alter bacterial behaviors including motility, but such interactions are understudied. Pseudomonas aeruginosa is a motile opportunistic pathogen that exists in diverse multispecies environments such as the soil and is frequently found in human wound and respiratory tract co-infections
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How Mycobacterium tuberculosis builds a home: Single-cell analysis reveals M. tuberculosis ESX-1-mediated accumulation of anti-inflammatory macrophages in infected mouse lungs. bioRxiv. Microbiol. Pub Date : 2024-04-22 Weihao Zheng, Michael Borja, Leah Dorman, Jonathan Liu, Andy Zhou, Amanda Seng, Ritwicq Arjyal, Sara Sunshine, Alina Nalyvayko, Angela Oliveira Pisco, Oren Rosenberg, Norma Neff, Beth Shoshana Zha
Mycobacterium tuberculosis (MTB) infects and replicates in lung mononuclear phagocytes (MNPs) with astounding ability to evade elimination. ESX-1, a type VII secretion system, acts as a virulence determinant that contributes to MTB's ability to survive within MNPs, but its effect on MNP recruitment and/or differentiation remains unknown. Here, using single-cell RNA sequencing, we studied the role of
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CyAbrB2 in Synechocystis sp. PCC6803 is a cyanobacterial nucleoid-associated protein controlling the expression of hydrogenase under the fermentative condition bioRxiv. Microbiol. Pub Date : 2024-04-22 Ryo Kariyazono, Takashi Osanai
The hox operon in Synechocystis sp. PCC 6803, encoding bidirectional hydrogenase responsible for H2 production, is transcriptionally upregulated under microoxic conditions. Although several regulators for hox transcription have been identified, their dynamics and higher-order DNA structure of hox region in microoxic conditions remain elusive. We focused on key regulators for the hox operon: cyAbrB2
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Limnospira (Cyanobacteria) chemical fingerprint reveals local molecular adaptation bioRxiv. Microbiol. Pub Date : 2024-04-22 Benjamin Marie, Théotime Roussel, Cédric Hubas, Sébastien Halary, Mathias Chynel, Charlotte Duval, Jean-Paul Cadoret, Tarik Meziane, Léa Vernes, Claude Yéprémian, Cécile Bernard
Limnospira can colonize a wide variety of environments (e.g. freshwater, brackish, alkaline or alkaline-saline water) and develop permanent blooms that limit overshadowed adjacent phototrophs diversity, especially in alkaline and saline environments. Previous phylogenomic analysis of Limnospira allowed us to distinguish two major phylogenetic clades (I and II) but failed to clearly segregate strains
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Discovery of anti-infective compounds against Mycobacterium marinum after biotransformation of simple natural stilbene scaffolds by a fungal secretome bioRxiv. Microbiol. Pub Date : 2024-04-22 Nabil Hanna, Thierry Soldati, Jahn Nitschke, Robin Huber, Stefania Vossio, Dimitri Moreau, Laurence Marcourt, Katia Gindro, Emerson F. Queiroz
This study evaluated the efficacy of a high-throughput Dictyostelium discoideum – Mycobacterium marinum Dd-Mm infection system by first benchmarking it against a set of antibiotics and second in screening a library of natural product (NP) derivatives for anti-infective activity against intracellular Mycobacterium marinum (Mm). The study observed no activity of pyrazinamide against Mm, consistent with
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Rhizosphere bacterial colonization of beet occurs in discrete phases regardless of bioinoculation with the wild sea beet root community bioRxiv. Microbiol. Pub Date : 2024-04-22 Marcin Golebiewski, Marcin Sikora, Justyna Mazur, Sonia Szymanska, Jaroslaw Tyburski, Katarzyna Hrynkiewicz, Werner Ulrich
Bioinoculation can increase crop yields under environmental stress. Plant colonization by microbes is an example of succession, with its distinct phases differing in community structure and diversity. This process needs to be studied to determine the optimal timing for bioinoculation and its effects. Here, we show that, regardless of bio-inoculation, soil type and plant genotype, bacteria colonize
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Nanocluster-antibody-drug conjugates (NADC) as an intravesical precision theranostic agent for interstitial cystitis bioRxiv. Microbiol. Pub Date : 2024-04-21 Zhijun Lin, Wanyan Wang, Dingxin Liu, Zhifeng Xu, Zhiming Wu, Xiangfu Zhou, Xiaodong Zhang, Yong Huang, Qi Zhao, Jiang Yang
Interstitial cystitis (IC) is a chronic inflammatory disorder characterized by recurring severe pain in the bladder and surrounding pelvic areas, lacking timely diagnostic and therapeutic options. Here, we propose a unitary theranostic nanocluster-antibody-drug conjugate (NADC) by covalently placing dihydroorotate dehydrogenase inhibitors (DHODHi) and ultrasmall gold quantum clusters (AuQCs) on a nerve
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A Novel Pan-Proteome Array for High-Throughput Profiling of the Humoral Response to Treponema pallidum subsp. pallidum: a Pre-Clinical Study bioRxiv. Microbiol. Pub Date : 2024-04-21 Joseph J Campo, Emily Romeis, Amit Oberai, Jozelyn Pablo, Christopher Hung, Andy Teng, Adam D Shandling, Amber Phan, Austin Haynes, Lorenzo Giacani
Background: Given the resurgence of syphilis, research endeavors to improve current assays for serological diagnosis and management of this disease are a priority. A proteome-scale platform for high-throughput profiling of the humoral response to Treponema pallidum (T. pallidum) proteins during infection could identify antigens suitable to ameliorate the performance and capabilities of treponemal tests
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The SPFH complex HflK-HflC regulates aerobic respiration in bacteria bioRxiv. Microbiol. Pub Date : 2024-04-21 Maria Isabel Perez-Lopez, Paul Lubrano, Georgia Angelidou, Timo Glatter, Nicole Paczia, Hannes Link, Victor Sourjik
The bacterial HflK-HflC membrane complex is a member of the highly conserved SPFH protein family, which is found throughout all domains of life and includes eukaryotic stomatins, flotillins, and prohibitins. These proteins organize cell membranes and are involved in various processes. However, the exact physiological functions of most bacterial SPFH proteins remain unclear. Here, we report that the
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Liming enhances the abundance and stability of nitrogen-cycling microbes: The buffering effect of long-term lime application bioRxiv. Microbiol. Pub Date : 2024-04-21 Akari Mitsuta, Kesia Silva Lourenco, Jingjing Chang, Mart Ros, Rene Schils, Yoshitaka Uchida, Eiko Eurya Kuramae
Lime application (liming) has historically been used to ameliorate soil acidity in grasslands. Liming effectively improves soil pH, plant productivity, and soil physicochemical properties, but the long-term impact of acidity control by liming on key microbial nitrogen (N)-cycling genes in semi-natural grasslands is unknown. We investigated the effect of 65 years of liming on N-cycling processes in
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Accelerating antimalarial drug discovery with a new high-throughput screen for fast-killing compounds bioRxiv. Microbiol. Pub Date : 2024-04-21 Takaya Sakura, Ryuta Ishii, Eri Yoshida, Kiyoshi Kita, Teruhisa Kato, Daniel Ken Inaoka
The urgent need for rapidly acting compounds in the development of antimalarial drugs underscores the significance of such compounds in overcoming resistance issues and improving patient adherence to antimalarial treatments. The present study introduces a high-throughput screening (HTS) approach using 1536-well plates, employing Plasmodium falciparum lactate dehydrogenase (PfLDH) combined with nitroreductase
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Component specific responses of the microbiomes to common chemical stressors in the human food chain bioRxiv. Microbiol. Pub Date : 2024-04-21 Wasimuddin Wasimuddin, Aurea Chiaia-Hernandez, Céline Terrettaz, Lisa Thoenen, Veronica Caggìa, Pierre Matteo, Miquel Coll-Crespi, Matheus Notter, Mohana Mukherjee, Teresa Chavez-Capilla, Francesca Ronchi, Stephanie C. Ganal-Vonarburg, Martin Grosjean, Moritz Bigalke, Sandra Spielvogel, Andrew Macpherson, Adrien Mestrot, Siegfried Hapfelmeier, Matthias Erb, Klaus Schlaeppi, Alban Ramette
Along a food chain, microbiomes occur in each component and often contribute to the functioning or the health of their host or environment. "One Health" emphasizes the connectivity of each component's health. Chemical stress typically causes dysbiotic microbiomes, but it remains unclear whether chemical stressors consistently affect the microbiomes along food chain components. Here, we systematically
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Commensal bacteria inhibit viral infections via a tryptophan metabolite bioRxiv. Microbiol. Pub Date : 2024-04-21 Danting Jiang, Nicole Soo, Chin Yee Tan, Sedem Dankwa, Hsuan-Yuan Wang, Barbara S. Theriot, Amir Ardeshir, Nazema Y. Siddiqui, Koen K. A. Van Rompay, Kristina De Paris, Sallie R Permar, Ria Goswami, Neeraj K. Surana
There is growing appreciation that commensal bacteria impact the outcome of viral infections, though the specific bacteria and their underlying mechanisms remain poorly understood. Studying a simian-human immunodeficiency virus (SHIV)-challenged cohort of pediatric nonhuman primates, we bioinformatically associated Lactobacillus gasseri and the bacterial family Lachnospiraceae with enhanced resistance
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A Blueprint for Broadly Effective Bacteriophage Therapy Against Bacterial Infections bioRxiv. Microbiol. Pub Date : 2024-04-21 Kevin Minyoung Kim, Qingquan Chen, Arne Echterhof, Robert C McBride, Nina Pennetzdorfer, Niaz Banaei, Elizabeth B Burgener, Carlos E Milla, Paul Bollyky
Bacteriophage therapy is a tantalizing therapeutic option for anti-microbial resistant bacterial infections but is currently limited to personalized therapy due to the narrow host range of individual phages. Theoretically, cocktails incorporating numerous phages targeting all possible bacterial receptor specificities could confer broad host range. Practically, however, extensive bacterial diversity
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Engineering, structure, and immunogenicity of a Crimean-Congo hemorrhagic fever virus pre-fusion heterotrimeric glycoprotein complex bioRxiv. Microbiol. Pub Date : 2024-04-21 Elizabeth McFadden, Stephanie Monticelli, Albert Wang, Ajit Ramamohan, Thomas Batchelor, Ana Kuehne, Russell Bakken, Alexandra Tse, Kartik Chandran, Andrew Herbert, Jason McLellan
Crimean-Congo hemorrhagic fever virus (CCHFV) is a tick-borne virus that can cause severe disease in humans with case fatality rates of 10-40%. Although structures of CCHFV glycoproteins GP38 and Gc have provided insights into viral entry and defined epitopes of neutralizing and protective antibodies, the structure of glycoprotein Gn and its interactions with GP38 and Gc have remained elusive. Here
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Molecular basis for dual functions in pilus assembly modulated by the lid of a pilus-specific sortase bioRxiv. Microbiol. Pub Date : 2024-04-21 Chungyu Chang, HyLam Ton-That, Jerzy Osipiuk, Andrzej Joachimiak, Asis Das, Hung Ton-That
The biphasic assembly of Gram-positive pili begins with the covalent polymerization of distinct pilins catalyzed by a pilus-specific sortase, followed by the cell wall anchoring of the resulting polymers mediated by the housekeeping sortase. In Actinomyces oris, the pilus-specific sortase SrtC2 not only polymerizes FimA pilins to assemble type 2 fimbriae with CafA at the tip, but it can also act as