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Life at the borderlands: microbiomes of interfaces critical to One Health FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2024-02-28 Simon R Law, Falko Mathes, Amy M Paten, Pamela Alexandre, Roshan Regmi, Cameron Reid, Azadeh Safarchi, Shaktivesh Shaktivesh, Yanan Wang, Annaleise Wilson, Scott A Rice, Vadakattu V S R Gupta
Microbiomes are foundational components of the environment that provide essential services relating to food security, carbon sequestration, human health, and the overall well-being of ecosystems. Microbiota exert their effects primarily through complex interactions at interfaces with their plant, animal, and human hosts, as well as within the soil environment. This review aims to explore the ecological
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In vitro modelling of bacterial pneumonia: a comparative analysis of widely applied complex cell culture models FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2024-02-27 Laure Mahieu, Laurence Van Moll, Linda De Vooght, Peter Delputte, Paul Cos
Bacterial pneumonia greatly contributes to the disease burden and mortality of lower respiratory tract infections among all age groups and risk profiles. Therefore, laboratory modelling of bacterial pneumonia remains important for elucidating the complex host-pathogen interactions and to determine drug efficacy and toxicity. In vitro cell culture enables for the creation of high-throughput, specific
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Towards a rational approach to promoter engineering: understanding the complexity of transcription initiation in prokaryotes FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2024-02-20 Cara Deal, Lien De Wannemaeker, Marjan De Mey
Promoter sequences are important genetic control elements. Through their interaction with RNA polymerase they determine transcription strength and specificity, thereby regulating the first step in gene expression. Consequently, they can be targeted as elements to control predictability and tuneability of a genetic circuit, which is essential in applications such as the development of robust microbial
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Evolution and emergence of Mycobacterium tuberculosis FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2024-02-16 Mickael Orgeur, Camille Sous, Jan Madacki, Roland Brosch
Tuberculosis (TB) remains one of the deadliest infectious diseases in human history, prevailing even in the 21st century. The causative agents of TB are represented by a group of closely-related bacteria belonging to the Mycobacterium tuberculosis complex (MTBC), which can be subdivided into several lineages of human- and animal-adapted strains, thought to have shared a last common ancestor emerged
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Anelloviruses versus human immunity: how do we control these viruses? FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2024-02-10 Anne L Timmerman, Antonia L M Schönert, Lia van der Hoek
One continuous companion and one of the major players in the human blood virome are members of the Anelloviridae family. Anelloviruses are probably found in all humans, infection occurs early in life and the composition (anellome) is thought to remain stable and personal during adulthood. The stable anellome implies a great balance between the host immune system and the virus. However, the lack of
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The role of human extracellular matrix proteins in defining Staphylococcus aureus biofilm infections FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2024-02-10 Mohini Bhattacharya, Alexander R Horswill
20–41% of the world's population is either transiently or permanently colonized by the Gram-positive bacterium, Staphylococcus aureus. In 2017, the CDC designated methicillin resistant S. aureus (MRSA) as a serious threat, reporting ∼300 000 cases of MRSA-associated hospitalizations annually, resulting in over 19 000 deaths, surpassing that of HIV in the United States. S. aureus is a proficient biofilm-forming
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Crosstalk between immunity and behavior: insights from entomopathogenic fungi and their insect hosts FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2024-02-09 Wei Zhang, Xuanyu Chen, Ioannis Eleftherianos, Amr Mohamed, Ashley Bastin, Nemat O Keyhani
Insects are one of the most successful animals in nature, and entomopathogenic fungi play a significant role in the natural epizootic control of insect populations in many ecosystems. The interaction between insects and entomopathogenic fungi has continuously co-evolved over hundreds of millions of years. Many components of the insect innate immune responses against fungal infection are conserved across
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Radioactive waste microbiology: predicting microbial survival and activity in changing extreme environments FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2024-01-11 Simon P Gregory, Jessica R M Mackie, Megan J Barnett
The potential for microbial activity to occur within the engineered barrier system (EBS) of a geological disposal facility (GDF) for radioactive waste is acknowledged by waste management organisations as it has the potential to affect many aspects of the safety functions of a GDF. Microorganisms within an EBS will be exposed to changing temperature, pH, radiation, salinity, saturation and availability
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Connecting the dots: key insights on ParB for chromosome segregation from single-molecule studies FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-12-24 Miloš Tišma, Jovana Kaljević, Stephan Gruber, Tung B K Le, Cees Dekker
Bacterial cells require DNA segregation machinery to properly distribute a genome to both daughter cells upon division. The most common system involved in chromosome and plasmid segregation in bacteria is the ParABS system. A core protein of this system – partition protein B (ParB) – regulates chromosome organization and chromosome segregation during the bacterial cell cycle. Over the past decades
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Root colonization by beneficial rhizobacteria FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-12-14 Yunpeng Liu, Zhihui Xu, Lin Chen, Weibing Xun, Xia Shu, Yu Chen, Xinli Sun, Zhengqi Wang, Yi Ren, Qirong Shen, Ruifu Zhang
Rhizosphere microbes play critical roles for plant's growth and health. Among them, the beneficial rhizobacteria have the potential to be developed as the biofertilizer or bioinoculants for sustaining the agricultural development. The efficient rhizosphere colonization of these rhizobacteria is a prerequisite for exerting their plant beneficial functions, but the colonizing process and underlying mechanisms
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Processing of stalled replication forks in Bacillus subtilis FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-12-05 Begoña Carrasco, Rubén Torres, María Moreno-del Álamo, Cristina Ramos, Silvia Ayora, Juan C Alonso
Accurate DNA replication and transcription elongation are crucial for preventing the accumulation of unreplicated DNA and genomic instability. Cells have evolved multiple mechanisms to deal with impaired replication fork progression, challenged by both intrinsic and extrinsic impediments. The bacterium Bacillus subtilis, which adopts multiple forms of differentiation and development, serves as an excellent
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Small proteins in gram-positive bacteria FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-12-04 Sabine Brantl, Inam Ul Haq
Small proteins comprising less than 100 amino acids have been often ignored in bacterial genome annotations. About 10 years ago, focused efforts started to investigate whole peptidomes, which resulted in the discovery of a multitude of small proteins, but only a number of them have been characterized in detail. Generally, small proteins can be either membrane or cytosolic proteins. The latter interact
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Exposing the small protein load of bacterial life FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-11-28 Laure Simoens, Igor Fijalkowski, Petra Van Damme
The ever-growing repertoire of genomic techniques continues to expand our understanding of the true diversity and richness of prokaryotic genomes. Riboproteogenomics laid the foundation for dynamic studies of previously overlooked genomic elements. Most strikingly, bacterial genomes were revealed to harbor robust repertoires of small open reading frames (sORFs) encoding a diverse and broadly expressed
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Exploitation of microbial activities at low pH to enhance planetary health FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-11-21 Merve Atasoy, Avelino Álvarez Ordóñez, Adam Cenian, Aleksandra Djukić-Vuković, Peter A Lund, Fatih Ozogul, Janja Trček, Carmit Ziv, Daniela De Biase
Awareness is growing that human health cannot be considered in isolation but is inextricably woven with the health of the environment in which we live. It is however under-recognised that the sustainability of human activities strongly relies on preserving the equilibrium of the microbial communities living in/on/around us. Microbial metabolic activities are instrumental for production, functionalization
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Pseudomonas aeruginosa biofilm exopolysaccharides: Assembly, function, and degradation FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-10-27 Andreea A Gheorghita, Daniel J Wozniak, Matthew R Parsek, P Lynne Howell
The biofilm matrix is a fortress; sheltering bacteria in a protective and nourishing barrier that allows for growth and adaptation to various surroundings. A variety of different components are found within the matrix including water, lipids, proteins, extracellular DNA, RNA, membrane vesicles, phages, and exopolysaccharides. As part of its biofilm matrix, Pseudomonas aeruginosa is genetically capable
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Mechanisms of Alternaria pathogenesis in animals and plants FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-10-25 Chantal Fernandes, Arturo Casadevall, Teresa Gonçalves
Alternaria species are cosmopolitan fungi darkly pigmented by melanin that infect numerous plant species causing economically important agricultural spoilage of various food crops. Alternaria spp. also infect animals, being described as entomopathogenic fungi but also infecting warm-blooded animals, including humans. Their clinical importance in human health, as infection agents, lay in the growing
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Role of the Extracellular Matrix in Candida Biofilm Antifungal Resistance FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-10-11 Justin Massey, Robert Zarnowski, David Andes
Clinical infection due to Candida species frequently involve growth in biofilm communities. Recalcitrance despite antifungal therapy leads to disease persistence associated with high morbidity and mortality. Candida possesses several tools allowing evasion of antifungal effects. Among these, protection of biofilm cells via encasement by the extracellular matrix is responsible for a majority drug resistance
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Global diversity and inferred ecophysiology of microorganisms with the potential for dissimilatory sulfate/sulfite reduction FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-10-03 Muhe Diao, Stefan Dyksma, Elif Koeksoy, David Kamanda Ngugi, Karthik Anantharaman, Alexander Loy, Michael Pester
Sulfate/sulfite-reducing microorganisms (SRM) are ubiquitous in nature, driving the global sulfur cycle. A hallmark of SRM is the dissimilatory sulfite reductase encoded by the genes dsrAB. Based on analysis of 950 mainly metagenome-derived dsrAB-carrying genomes, we redefine the global diversity of microorganisms with the potential for dissimilatory sulfate/sulfite reduction and uncover genetic repertoires
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Molecular strategies for the utilisation of human milk oligosaccharides by infant gut-associated bacteria FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-10-03 Leonie Jane Kiely, Kizkitza Busca, Jonathan A Lane, Douwe van Sinderen, Rita M Hickey
A number of bacterial species are found in high abundance in the faeces of healthy breast-fed infants, an occurrence that is understood to be, at least in part, due to the ability of these bacteria to metabolize human milk oligosaccharides (HMOs). HMOs are the third most abundant component of human milk after lactose and lipids, and represent complex sugars which possess unique structural diversity
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Chromosome Structure and DNA Replication Dynamics During the Life Cycle of the Predatory Bacterium Bdellovibrio bacteriovorus FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-10-02 Karolina Pląskowska, Jolanta Zakrzewska-Czerwińska
Bdellovibrio bacteriovorus, an obligate predatory Gram-negative bacterium that proliferates inside and kills other Gram-negative bacteria, was discovered more than 60 years ago. However, we have only recently begun to understand the detailed cell biology of this proficient bacterial killer. B. bacteriovorus exhibits a peculiar life cycle and bimodal proliferation, and thus represents an attractive
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Structural analysis of novel drug targets for mitigation of Pseudomonas aeruginosa biofilms FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-09-27 Moumita Ghosh, Shikha Raghav, Puja Ghosh, Swagatam Maity, Kavery Mohela, Deepti Jain
Pseudomonas aeruginosa is an opportunistic human pathogen responsible for acute and chronic, hard to treat infections. Persistence of P. aeruginosa is due to its ability to develop into biofilms which are sessile bacterial communities adhered to substratum and encapsulated in layers of self-produced exopolysaccharides. These biofilms provide enhanced protection from the host immune system and resilience
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Virologs, viral mimicry, and virocell metabolism: The expanding scale of cellular functions encoded in the complex genomes of giant viruses FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-09-21 Mohammad Moniruzzaman, Paula Maria Erazo-Garcia, Roxanna Farzad, Anh D Ha, Abdeali Jivaji, Sangita Karki, Uri Sheyn, Joshua Stanton, Benjamin Minch, Danae Stephens, Dustin C Hancks, Rodrigo A L Rodrigues, Jonatas S Abrahao, Assaf Vardi, Frank O Aylward
The phylum Nucleocytoviricota includes the largest and most complex viruses known. These “giant viruses” have a long evolutionary history that dates back to the early diversification of eukaryotes, and over time they have evolved elaborate strategies for manipulating the physiology of their hosts during infection. One of the most captivating of these mechanisms involves the use of genes acquired from
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Correction to: Exploring probiotic effector molecules and their mode of action in gut-immune interactions. FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-09-05
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Type II bacterial toxin-antitoxins: hypotheses, facts, and the newfound plethora of the PezAT system. FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-09-05 Wai Ting Chan,Maria Pilar Garcillán-Barcia,Chew Chieng Yeo,Manuel Espinosa
Toxin-antitoxin (TA) systems are entities found in the prokaryotic genomes, with eight reported types. Type II, the best characterized, is comprised of two genes organized as an operon. Whereas toxins impair growth, the cognate antitoxin neutralizes its activity. TAs appeared to be involved in plasmid maintenance, persistence, virulence, and defence against bacteriophages. Most Type II toxins target
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Methodologies for bacterial ribonuclease characterization using RNA-seq. FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-09-05 Laura Broglia,Anaïs Le Rhun,Emmanuelle Charpentier
Bacteria adjust gene expression at the post-transcriptional level through an intricate network of small regulatory RNAs and RNA-binding proteins, including ribonucleases (RNases). RNases play an essential role in RNA metabolism, regulating RNA stability, decay, and activation. These enzymes exhibit species-specific effects on gene expression, bacterial physiology, and different strategies of target
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Illuminating the oral microbiome and its host interactions: recent Advancements in omics and bioinformatics technologies in the context of oral microbiome research FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-09-05 Jonathon L Baker
The oral microbiota has an enormous impact on human health, with oral dysbiosis now linked to many oral and systemic diseases. Recent advancements in sequencing, mass spectrometry, bioinformatics, computational biology, and machine learning are revolutionizing oral microbiome research, enabling analysis at an unprecedented scale and level of resolution using omics approaches. This review contains a
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What's in a name? Characteristics of clinical biofilms FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-08-30 Mads Lichtenberg, Tom Coenye, Matthew R Parsek, Thomas Bjarnsholt, Tim Holm Jakobsen
In vitro biofilms are communities of microbes with unique features compared to individual cells. Biofilms are commonly characterized by physical traits like size, adhesion, and a matrix made of extracellular substances. They display distinct phenotypic features, such as metabolic activity and antibiotic tolerance. However, the relative importance of these traits depends on the environment and bacterial
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Praemonitus praemunitus: can we forecast and prepare for future viral disease outbreaks? FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-08-19 Zoe Sessions, Tesia Bobrowski, Holli-Joi Martin, Jon-Michael T Beasley, Aneri Kothari, Trevor Phares, Michael Li, Vinicius M Alves, Marcus T Scotti, Nathaniel J Moorman, Ralph Baric, Alexander Tropsha, Eugene N Muratov
Understanding the origins of past and present viral epidemics is critical in preparing for future outbreaks. Many viruses, including SARS-CoV-2, have led to significant consequences not only due to their virulence, but also because we were unprepared for their emergence. We need to learn from large amounts of data accumulated from well-studied, past pandemics and employ modern informatics and therapeutic
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Bacteria and microalgae associations in periphyton – mechanisms and biotechnological opportunities FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-08-17 Francisca Vale, Cátia A Sousa, Henrique Sousa, Lúcia C Simões, Andrew J McBain, Manuel Simões
Phototrophic and heterotrophic microorganisms coexist in complex and dynamic structures called periphyton. These structures shape the biogeochemistry and biodiversity of aquatic ecosystems. In particular, microalgae-bacteria interactions are a prominent focus of study by microbial ecologists and can provide biotechnological opportunities for numerous applications (i.e. microalgal bloom control, aquaculture
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Exploring probiotic effector molecules and their mode of action in gut-immune interactions FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-08-05 Choong-Gu Lee, Kwang Hyun Cha, Gi-Cheon Kim, Sin-Hyeog Im, Ho-Keun Kwon
Probiotics, live microorganisms that confer health benefits when consumed in adequate amounts, have gained significant attention for their potential therapeutic applications. The beneficial effects of probiotics are believed to stem from their ability to enhance intestinal barrier function, inhibit pathogens, increase beneficial gut microbes, and modulate immune responses. However, clinical studies
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Illuminating the Oral Microbiome: Cellular Microbiology FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-08-03 Richard J Lamont, Daniel P Miller, Juhi Bagaitkar
Epithelial cells line mucosal surfaces such as in the gingival crevice and provide a barrier to the ingress of colonizing microorganisms. However, epithelial cells are more than a passive barrier to microbial intrusion, and rather constitute an interactive interface with colonizing organisms which senses the composition of the microbiome and communicates this information to the underlying cells of
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Giving a signal: How protein phosphorylation helps Bacillus navigate through different life stages FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-08-01 Aakriti Gangwal, Nishant Kumar, Nitika Sangwan, Neha Dhasmana, Uma Dhawan, Andaleeb Sajid, Gunjan Arora, Yogendra Singh
Protein phosphorylation is a universal mechanism regulating a wide range of cellular responses across all domains of life. The antagonistic activities of kinases and phosphatases can orchestrate the life cycle of an organism. The availability of bacterial genome sequences, particularly Bacillus species, followed by proteomics and functional studies have aided in the identification of putative protein
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Protozoan predation as a driver of diversity and virulence in bacterial biofilms FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-07-17 M Mozammel Hoque, Gustavo Espinoza-Vergara, Diane McDougald
Protozoa are eukaryotic organisms that play a crucial role in nutrient cycling and maintaining balance in the food web. Predation, symbiosis and parasitism are three types of interactions between protozoa and bacteria. However, not all bacterial species are equally susceptible to protozoan predation as many are capable of defending against predation in numerous ways and may even establish either a
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Faecalibacterium: a bacterial genus with promising human health applications FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-07-15 Rebeca Martín, David Rios-Covian, Eugénie Huillet, Sandrine Auger, Sara Khazal, Luis G Bermúdez-Humarán, Harry Sokol, Jean-Marc Chatel, Philippe Langella
In humans, many diseases are associated with alterations in gut microbiota, namely increases or decreases in the abundance of specific bacterial groups. One example is the genus Faecalibacterium. Numerous studies have underscored that low levels of Faecalibacterium are correlated with inflammatory conditions, with inflammatory bowel disease (IBD) in the forefront. Its representation is also diminished
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Improving the safety and efficacy of phage therapy from the perspective of phage-mammal interactions FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-07-14 Geng Zou, Lijun He, Jing Rao, Zhiyong Song, Hu Du, Runze Li, Wenjing Wang, Yang Zhou, Lu Liang, Huanchun Chen, Jinquan Li
Phage therapy has re-emerged as a promising solution for combating antimicrobial-resistant bacterial infections. Increasingly, studies have revealed that phages possess therapeutic potential beyond their antimicrobial properties, including regulating the gut microbiome and maintain intestinal homeostasis, as a novel nanocarrier for targeted drug delivery. However, the complexity and unpredictability
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Anti-infective activities of long-chain fatty acids against foodborne pathogens FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-07-13 Caroline Borreby, Eva Maria Sternkopf Lillebæk, Birgitte H Kallipolitis
Free fatty acids (FFAs) have long been acknowledged for their antimicrobial activity. More recently, long-chain FFAs (>12 carbon atoms) are receiving increased attention for their potent anti-virulence activity against pathogenic bacteria. In the gastrointestinal tract, foodborne pathogens encounter a variety of long-chain FFAs derived from the diet, metabolic activities of the gut microbiota, or the
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Microbiologically Influenced Corrosion - More than just Microorganisms FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-07-11 J Knisz, R Eckert, L M Gieg, A Koerdt, J S Lee, E R Silva, T L Skovhus, B A An Stepec, S A Wade
Microbiologically influenced corrosion (MIC) is a phenomenon of increasing concern which affects various materials and sectors of society. MIC describes the effects, often negative, that a material can experience due to the presence of microorganisms. Unfortunately, although several research groups and industrial actors worldwide have already addressed MIC, discussions are fragmented, while information
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Drivers and consequences of bacteriophage host range FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-07-07 D Holtappels, Poliane Alfenas-Zerbini, B Koskella
Bacteriophages are obligate parasites of bacteria characterized by the breadth of hosts that they can infect. This ‘host range’ depends on the genotypes and morphologies of the phage and the bacterial host, but also on the environment in which they are interacting. Understanding phage host range is critical to predicting the impacts of these parasites in their natural host communities and their utility
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Crosstalk between gut microbiota and RNA N6-methyladenosine modification in cancer FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-07-06 Hao Su, Henley Cheung, Harry Cheuk-Hay Lau, Hongyan Chen, Xiaoting Zhang, Na Qin, Yifei Wang, Matthew Tak Vai Chan, William Ka Kei Wu, Huarong Chen
The gut microbiota plays a crucial role in regulating various host metabolic, immune, and neuroendocrine functions, and has a significant impact on human health. Several lines of evidence suggest that gut dysbiosis is associated with a variety of diseases, including cancer. The gut microbiota can impact the development and progression of cancer through a range of mechanisms, such as regulating cell
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Editorial 14th international symposium on lactic acid bacteria (LAB14). FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-07-05 Eddy J Smid,Sarah Lebeer,Egon B Hansen
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Correction to: four billion years of microbial terpenome evolution. FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-07-05
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Correction to: RTX proteins: A highly diverse family secreted by a common mechanism. FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-07-05
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The never-ending battle between lactic acid bacteria and their phages FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-06-24 Cécile Philippe, Jeffrey K Cornuault, Alessandra G de Melo, Rachel Morin-Pelchat, Alice P Jolicoeur, Sylvain Moineau
Over the past few decades, the interest in lactic acid bacteria (LAB) has been steadily growing. This is mainly due to their industrial use, their health benefits as probiotic bacteria and their ecological importance in host-related microbiota. Phage infection represents a significant risk for the production and industrial use of LAB. This created the need to study the various means of defense put
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Gas and light: triggers of c-di-GMP-mediated regulation FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-06-21 Zhaoqing Yu, Wei Zhang, He Yang, Shan-Ho Chou, Michael Y Galperin, Jin He
The widespread bacterial second messenger c-di-GMP is responsible for regulating many important physiological functions such as biofilm formation, motility, cell differentiation, and virulence. The synthesis and degradation of c-di-GMP in bacterial cells depend, respectively, on diguanylate cyclases and c-di-GMP-specific phosphodiesterases. Since c-di-GMP metabolic enzymes (CMEs) are often fused to
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Bacteriophage-host interactions in Streptococcus thermophilus and their impact on co-evolutionary processes FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-06-21 Katherine Lavelle, Brian McDonnell, Gerald Fitzgerald, Douwe van Sinderen, Jennifer Mahony
Bacteriophages (or phages) represent a persistent threat to the success and reliability of food fermentation processes. Recent reports of phages that infect Streptococcus thermophilus have highlighted the diversification of phages of this species. Phages of S. thermophilus typically exhibit a narrow range, a feature that is suggestive of diverse receptor moieties being presented on the cell surface
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Physicochemical homeostasis in bacteria FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-06-20 Bert Poolman
In living cells the biochemical processes such as energy provision, molecule synthesis, gene expression and cell division take place in a confined space where the internal chemical and physical conditions are different from those in dilute solutions. The concentrations of specific molecules and the specific reactions and interactions vary for different types of cells, but a number of factors are universal
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Quorum sensing architecture network in Escherichia coli virulence and pathogenesis FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-06-13 Celia Mayer, Anabela Borges, Saskia-Camille Flament-Simon, Manuel Simões
Escherichia coli is a Gram-negative commensal bacterium of the normal microbiota of humans and animals. However, several E. coli strains are opportunistic pathogens responsible for severe bacterial infections including gastrointestinal and urinary tract infections. Due to the emergence of multidrug-resistant serotypes that can cause a wide spectrum of diseases, E. coli is considered one of the most
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The Role of Glycoconjugates as Receptors for Insecticidal Proteins FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-06-09 Hannah L Best, Lainey J Williamson, Emily A Heath, Helen Waller-Evans, Emyr Lloyd-Evans, Colin Berry
Bacillus thuringiensis (Bt) proteins are an environmentally safe and effective alternative to chemical pesticides and have been used as biopesticides, with great commercial success, for over 50 years. Global agricultural production is predicted to require a 70% increase until 2050 to provide for an increasing population. In addition to agriculture, Bt proteins are utilised to control human vectors
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Microbiota and fungal-bacterial interactions in the Cystic Fibrosis lung FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-06-08 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
The most common genetic hereditary disease affecting Caucasians is Cystic Fibrosis (CF), which is caused by autosomal recessive mutations in the CFTR gene. The most serious consequence is the production of a thick and sticky mucus in the respiratory tract, which entraps airborne microorganisms and facilitates colonization, inflammation, and infection. Therefore, the present article compiles the information
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From genotype to phenotype: computational approaches for inferring microbial traits relevant to the food industry FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-06-08 Signe T Karlsen, Martin H Rau, Benjamín J Sánchez, Kristian Jensen, Ahmad A Zeidan
When selecting microbial strains for the production of fermented foods, various microbial phenotypes need to be taken into account to achieve target product characteristics, such as biosafety, flavor, texture, and health-promoting effects. Through continuous advances in sequencing technologies, microbial whole-genome sequences of increasing quality can now be obtained both cheaper and faster, which
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Have genetic targets for faecal pollution diagnostics and source tracking revolutionised water quality analysis yet? FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-06-08 Katalin Demeter, Rita Linke, Elisenda Ballesté, Georg Reischer, René E Mayer, Julia Vierheilig, Claudia Kolm, Margaret E Stevenson, Julia Derx, Alexander K T Kirschner, Regina Sommer, Orin C Shanks, Anicet R Blanch, Joan Rose, Warish Ahmed, Andreas H Farnleitner
The impacts on faecal pollution analysis using nucleic acid-based methods, such as PCR and sequencing, in health-related water quality research were assessed by rigorous literature analysis. A wide range of application areas and study designs has been identified since the first application more than 30 years ago (>1,100 publications). Given the consistency of methods and assessment types, we suggest
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Cyclic-di-AMP signalling in lactic acid bacteria FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-05-24 Mark S Turner, Yuwei Xiang, Zhao-Xun Liang, Esteban Marcellin, Huong Thi Pham
Cyclic-di-AMP is a nucleotide second messenger present in Gram-positive bacteria and some Gram-negative bacteria and Archaea. The intracellular concentration of cyclic-di-AMP is adjusted in response to environmental and cellular cues, primarily through the activities of synthesis and degradation enzymes. It performs its role by binding to protein and riboswitch receptors, many of which contribute to
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Nuclear genome organization in fungi: From gene folding to Rabl chromosomes FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-05-18 David E Torres, Andrew T Reckard, Andrew D Klocko, Michael F Seidl
Comparative genomics has recently provided unprecedented insights into the biology and evolution of the fungal lineage. In the post-genomics era, a major research interest focuses now on detailing the functions of fungal genomes, i.e. how genomic information manifests into complex phenotypes. Emerging evidence across diverse eukaryotes has revealed that the organization of DNA within the nucleus is
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The small intestine: dining table of host-microbiota meetings FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-05-17 Karen Delbaere, Inez Roegiers, Auriane Bron, Claude Durif, Tom Van de Wiele, Stephanie Blanquet-Diot, Ludovica Marinelli
Growing evidence suggests the importance of the small intestinal bacteria in the diet-host-microbiota dialogue in various facets of health and disease. Yet, this body site is still poorly explored and its ecology and mechanisms of interaction with the host are just starting to be unraveled. In this review, we describe the current knowledge on the small intestinal ecology, its composition and diversity
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Bacterial extracellular electron transfer in plant and animal ecosystems FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-05-16 Eric Stevens, Maria Marco
Extracellular electron transfer (EET) is a bioelectrochemical process performed by electrochemically active bacteria (EAB) found in host-associated environments, including plant and animal ecosystems and fermenting plant- and animal-derived foods. Through direct or mediated electron transfer pathways, certain bacteria use EET to enhance ecological fitness with host-impacting effects. In the plant rhizosphere
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After a century of nisin research, where are we now and where are we going? FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-05-12 Des Field, Miguel Fernandez de Ullivarri, R Paul Ross, Colin Hill
It is almost a century since nisin was discovered in fermented milk cultures, coincidentally in the same year that penicillin was first described. Over the last 100 years this small, highly modified pentacyclic peptide has not only found success in the food industry as a preservative but has also served as the paradigm for our understanding of the genetic organization, expression and regulation of
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Targeting the nucleotide metabolism of Trypanosoma brucei and other trypanosomatids FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-05-08 Anders Hofer
African sleeping sickness, Chagas disease, and leishmaniasis are life-threatening diseases that together affect millions of people around the world and are caused by different members of the protozoan family Trypanosomatidae. The most-studied member of the family is Trypanosoma brucei, which is spread by tsetse flies and causes African sleeping sickness. Nucleotide metabolism in T. brucei and other
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Illuminating the Oral Microbiome and its Host Interactions: Animal models of disease FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-04-28 George Hajishengallis
Periodontitis and caries are driven by complex interactions between the oral microbiome and host factors, i.e., inflammation and dietary sugars, respectively. Animal models have been instrumental in our mechanistic understanding of these oral diseases, although no single model can faithfully reproduce all aspects of a given human disease. This review discusses evidence that the utility of an animal
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Engineering lanthipeptides by introducing a large variety of RiPP modifications to obtain new-to-nature bioactive peptides FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-04-25 Yuxin Fu, Yanli Xu, Fleur Ruijne, Oscar P Kuipers
Natural bioactive peptide discovery is a challenging and time-consuming process. However, advances in synthetic biology are providing promising new avenues in peptide engineering that allow for the design and production of a large variety of new-to-nature peptides with enhanced or new bioactivities, using known peptides as templates. Lanthipeptides are ribosomally synthesized and post-translationally
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Meat fermentation at a crossroads: where the age-old interplay of human, animal, and microbial diversity and contemporary markets meet FEMS Microbiol. Rev. (IF 11.3) Pub Date : 2023-04-20 Frédéric Leroy, Christina Charmpi, Luc De Vuyst
Despite being part of the now often unfavourably perceived category of processed meats, fermented meats remain of substantial nutritional, economic, and cultural importance in today's foodscapes. This translates into a vast assortment of different products. Fermentation is driven by microorganisms (e.g. in fermented sausages), although the terminology is sometimes used to also designate products in