Long COVID: major findings, mechanisms and recommendations
@EricTopol
@ahandvanish
@LisaAMcCorkell
@julialmv
explore key findings, potential mechanisms, overlap with other conditions, potential treatments, and perspectives on long COVID research and care
The gut microbiota and its biogeography
McCallum & Tropini discuss physical and biological factors affecting microbiota biogeography and organization at different scales. They overview the whole gut at the macroscale and zoom in to the scale of host and microbial interactions.
Scientists’ warning to humanity: microorganisms and climate change
A group of leading microbiologists have come together to alert humanity that the central role and global importance of microorganisms in climate change biology must not be underestimated.
Microbiota succession throughout life from the cradle to the grave
The human microbiota can undergo dramatic changes during different phases of life. In this Review, Knight & co discuss the microbiota successions that occur from the cradle to the grave.
Molecular mechanisms of antibiotic resistance revisited
Blair, Webber and colleagues explore our understanding of the mechanisms of antibiotic resistance and how this information can aid in developing the next generation of antimicrobial therapies
Machine learning for microbiologists
In this Review, Segata, Waldron and co discuss key concepts of machine learning that are relevant to microbiologists and provide them with a set of tools to apply machine learning in microbiology research.
Antibiotic perturbations to the gut microbiome
Dantas & co. discuss factors that influence restructuring of the gut microbiome on antibiotic exposure, and explore promising therapeutics to minimize antibiotic-induced damage to the microbiome or restore the community structure.
Coronavirus biology and replication: implications for SARS-CoV-2
In this Review, Thiel and colleagues discuss the key aspects of coronavirus biology and their implications for SARS-CoV-2 infections as well as for treatment and prevention strategies.
SARS-CoV-2 biology and host interactions
In this Review,
@ProfVolkerThiel
& colleagues summarize current knowledge of the SARS-CoV-2 intracellular life cycle and the molecular functions of viral proteins, as well as their interaction with the host cell.
📢SARS-CoV-2 variant biology: immune escape, transmission and fitness
The authors discuss the mutations of SARS-CoV-2 variants, the impact of mutations on virus infectivity and transmissibility, and SARS-CoV-2 evolution in the context of immunity.
Plasmids, a molecular cornerstone of antimicrobial resistance in the One Health era
Castañeda-Barba, Top & Stalder synthesize the recent literature on the ecological and evolutionary factors that determine the successful spread of plasmid-mediated antimicrobial resistance genes.
Life and death in the soil microbiome: how ecological processes influence biogeochemistry
Sokol et al. illustrate how the ecological processes of living and decaying microorganisms can shape soil biogeochemistry
Alternative functions of CRISPR–Cas systems in the evolutionary arms race
Staals, van der Oost and colleagues explore these non-canonical functions of CRISPR–Cas systems with relevant consequences for CRISPR-based genome editing applications
Innovations to culturing the uncultured microbial majority
Ettema and colleagues highlight recent successes in culturing elusive lineages, innovative methods and key targets for future cultivation
@Ettema_lab
Bacterial Biofilms
This Focus issue explores insights into biofilm formation, gradients and consequences of heterogeneity in biofilms, tolerance of biofilms to antibiotics and host responses, and the spatial patterning of biofilms in infections
Bacterial defences: mechanisms, evolution and antimicrobial resistance
Smith, Foster & co. discuss the mechanisms, evolution and clinical implications of bacterial protective strategies, new therapies for treating disease and how to minimize resistance.
Antigenic evolution will lead to new SARS-CoV-2 variants with unpredictable severity
@pvmarkov
,
@ArisKatzourakis
& Stilianakis argue that ongoing rapid antigenic evolution is likely to produce new variants that may escape immunity and be more severe.
📢The highly diverse antiphage defence systems of bacteria
Georjon & Bernheim provide an overview of the molecular diversity of the most recently discovered bacterial antiphage defence systems and discuss their evolution and the ecological impact of their diversity.
Soil microbiomes and climate change
Review: Jansson and Hofmockel explore the impacts of climate change on soil microorganisms and the potential ways that soil microorganisms can be harnessed to help mitigate the negative consequences of climate change.
Trichoderma: a multipurpose, plant-beneficial microorganism for eco-sustainable agriculture
Woo et al. discuss the ecophysiology and diversity of Trichoderma and the complexity of its relationships in the agroecosystem environment
Mass spectrometry-based metabolomics in microbiome investigations
Dorrestein and colleagues review common forms of untargeted mass spectrometry and the types of data that can be obtained in the context of microbiome analysis
📣The oral microbiome: diversity, biogeography and human health
He & co. explore the structure and diversity of the oral microbiota, and they discuss the role of the oral microbiota in the pathology of both oral and systemic diseases.
read it here:
Towards SARS-CoV-2 serotypes?
In this Comment article Simon-Loriere & Schwartz discuss lines of evidence in support or against the concept of SARS-CoV-2 serotypes, and the implications of this classification.
Structural and functional diversity of type IV secretion systems
Costa et al. review type IV secretion systems in Gram-negative bacteria, exploring their structures, specialized functions, biogenesis and localization.
Biology and evolution of bacterial toxin–antitoxin systems
Van Melderen & colleagues review the biology and evolution of these small genetic elements, and discuss how genomic conflicts could shape the diversification of toxin–antitoxin systems
Bacterial adhesion at the single-cell level
In this Review, Brun and colleagues summarize our understanding of the mechanisms governing bacterial adhesion at the single-cell level.
📢Disinfectants and antiseptics: mechanisms of action and resistance
Maillard & Pascoe examine the mechanisms of action of biocides, as well as the bacterial intrinsic and acquired resistance to these biocides and its implications in environmental and clinical settings.
Best practices for analysing microbiomes
Knight et al. discuss best practices for performing a
#microbiome
study, including experimental design, molecular analysis technology, methods for data analysis and the integration of omics data sets
@KnightLabNews
Soil microbiomes and one health
Banerjee and van der Heijden outline the central role of the soil microbiome for one health and its detrimental or beneficial effects.
SARS-CoV-2 variants, spike mutations and immune escape
Members of
@CovidGenomicsUK
(COG-UK) & co summarize SARS-CoV-2 spike mutations, their structural context and impacts on antigenicity, and discuss variants of interest or concern and vaccine efficacy.
The pan-immune system of bacteria: antiviral defence as a community resource
Bernheim and Sorek present the ‘pan-immune system’ model in which bacteria employ horizontal gene transfer to access immune defence mechanisms encoded by closely related strains
Carbohydrate-active enzymes (CAZymes) in the gut microbiome
Withers and colleagues discuss the vast diversity and activities of CAZymes and their potential applications.
Utilization of the microbiome in personalized medicine
In this Review, Elinav and colleagues examine the advantages, challenges and future perspectives of utilizing microbiome data in personalized medicine for optimal patient care.
The rapid emergence of antifungal-resistant human-pathogenic fungi
Lockhart & co. discuss the global emergence & spread of Candida auris, azole-resistant Aspergillus fumigatus & Trichophyton indotineae, all three emerging with a high rate of acquired resistance.
A brief guide to scientific writing
If you missed my talk at
#ECCMID19
but would like to get tips for how to write a review well (many points also apply to primary papers):
1. Tell a story
2. ABC of good writing style: accurate, brief, clear
1/3
Conservation and similarity of bacterial and eukaryotic innate immunity
@aaronwhiteley
and
@hannahledvina
review the similarities between eukaryotic and bacterial innate immunity, exploring conserved components, signalling and restriction mechanisms.
SARS-CoV-2 viral load and shedding kinetics
Puhach, Meyer and Eckerle explore insights into what influences SARS-CoV-2 shedding, how this drives transmission and the tools available to measure this and determine infectiousness.
In this Review, Martens and colleagues discuss the complex interactions of commensal and pathogenic microorganisms with the intestinal mucosal barrier.
Alternative therapeutic strategies to treat antibiotic-resistant pathogens
In this Review, MacNair, Rutherford & Tan explore the potential of non-conventional therapeutic strategies in the fight against antibiotic resistance.
Interactions between bacterial and phage communities in natural environments
Chevallereau et al. review the roles of phage communities in controlling the population and evolutionary dynamics of bacterial communities
Proximate and ultimate causes of the bactericidal action of antibiotics
How antibiotics actually kill bacteria is not entirely clear. Baquero & Levin reflect on this ultimate action of antibiotics, considering different mechanisms and modulating factors
Characteristics of SARS-CoV-2 and COVID-19
Zheng-Li Shi et al. summarize the exceptional amount of research that has characterized SARS-CoV-2 and COVID-19, discussing the emergence and virology of SARS-CoV-2 and the pathogenesis and treatment of COVID-19
Influenza virus and SARS-CoV-2: pathogenesis and host responses in the respiratory tract
Schultz-Cherry, Thomas & co discuss influenza virus and SARS-CoV-2 pathogenesis, the host response in severe disease, epithelial repair and therapeutic interventions
Bacteria and archaea on Earth and their abundance in biofilms
Flemming and Wuertz propose that biofilms are the most prominent and influential type of microbial life.
Origin of viruses: primordial replicators recruiting capsids from hosts
In this Opinion article, Krupovic, Dolja and Koonin propose a new scenario for the origin of viruses based on primordial, selfish replicators acquiring structural proteins from cells
The ancestral and industrialized gut microbiota and implications for human health
Sonnenburg and Sonnenburg explore whether individuals in the industrialized world may be harbouring a microbial community that is now incompatible with human biology.
The gut microbiota–brain axis in behaviour and brain disorders
@liviahmorais
,
@HelixIV
& Mazmanian discuss intricate and potentially important connections between the gut microbiota and brain, and possible contributions by the gut microbiota to behaviour
Bacterial motility: machinery and mechanisms
Wadhwa & Berg review bacterial motility mechanisms and the current understanding of the molecular machines that enable bacteria to swim in aqueous media and move on solid surfaces
@NavishWadhwa
@MCB_Harvard
The human virome: assembly, composition and host interactions
Liang and Bushman review research on the human virome and highlight studies that explore the assembly and composition of the virome as well as host–virome interactions in health and disease.
NEW Review🙌Forest microbiome and global change🌲
Baldrian & co. discuss the effects of global change on the forest ecosystem and its microbiome across different climatic zones, and present different strategies to reduce global change impact on forests.
Our December issue is now live!
Read it here:
The cover is inspired by two Reviews on the disruptive effects of antibiotic-induced damage to the gut microbiota.
Pseudomonas aeruginosa adaptation and evolution in patients with cystic fibrosis
In this Review, Johansen and colleagues highlight genomic and phenotypic adaptation of Pseudomonas aeruginosa and the implications for infection management.
The host-associated archaeome
Moissl-Eichinger & colleagues discuss the diversity and potential roles of the archaea associated with protists, plants and animals, highlighting their potential roles in human health & disease
@chmoei
@SGribaldo
Revisiting the rules of life for viruses of microorganisms
Correa et al advance a conceptual framework that recognizes virus–host interactions across a continuum of infection modalities
Microbiome-based therapeutics
Sorbara & Pamer review the major bacterial phyla associated with health benefits and the potential of microbiome-based therapeutics, and the challenges confronting therapeutic development as well as the regulatory hurdles
Examining horizontal gene transfer in microbial communities
Brito discusses methods to study how HGT shapes the function of natural microbial communities and explores questions to which some of these tools can be applied
@ilanabrito123
Protein post-translational modifications in bacteria
In this Review, Macek and colleagues introduce the major types of protein post-translational modifications in bacteria and discuss their roles in various aspects of bacterial cell biology.
Playing dead during phage infection
#ResearchHighlight
: A recent study reports that Cas13 induces a state of dormancy in bacteria, which inhibits viral replication and the rise of CRISPR-resistant phages.
@alexjmeeske
Gut microbiota in human metabolic health and disease
Fan & Pedersen discuss how the gut microbiota and derived microbial compounds may contribute to human metabolic health and to the pathogenesis of common metabolic diseases
@Metabolcenter
Physical properties of the bacterial outer membrane
Huang and colleagues discuss key molecular factors and interactions that give rise to the spatial organization, limited diffusivity and stress-bearing capacity of the outer membrane
Microbial diversity in extreme environments
Shu and Huang explore the diversity, functions and evolution of bacteria and archaea inhabiting Earth’s major extreme environments
Effects of climate change and human activities on vector-borne diseases
de Souza & Weaver examine various factors, such as climate change, human activities, and mobility, impacting the redistribution of vectors and vector-borne disease spread
@wmarciels
🐝 The honeybee microbiota and its impact on health and disease
Motta and Moran discuss how the gut microbiota influences honeybee biology and health, and explore environmental factors that can disrupt it and strategies for restoration.
@ErickMotta19
Tolerance and resistance of microbial biofilms
Ciofu and colleagues discuss our current understanding of the mechanisms of tolerance of biofilms to the immune system as well as tolerance and resistance to antimicrobials
Giant virus biology and diversity in the era of genome-resolved metagenomics
In this Review, Schulz, Abergel and Woyke explore insights into the diversity, biology, biogeography and ecology of giant viruses provided by culture and genomic technologies.
Microbial murmurs — decoding hidden conversations between bacteria
This Genome Watch highlights how genomic analyses revealed the widespread presence of a new class of bacterial signalling peptides that lack conventional characteristics.
📣Insights into the assembly and regulation of the bacterial divisome
Margolin & Cameron explore how the divisome of Escherichia coli is assembled and activated to modulate the division process, and discuss how the divisome machinery can be targeted for therapeutic purposes.
Gut microbial metabolites as multi-kingdom intermediates
Bäckhed et al. discuss major microbial metabolites, highlight how they affect host health & provide a framework for integrating discovery-based metabolite studies with mechanistic work
@BackhedLab
Why does the
#microbiome
affect behaviour?
In this Opinion, Johnson and Foster explore the evolution of this relationship and propose that adaptations of competing gut microorganisms may affect behaviour as a by‑product, leading to host dependence.
Multidrug efflux pumps: structure, function and regulation
This Review describes recent insights into the structure, function and regulation of efflux pumps.
Total synthesis of Escherichia coli with a recoded genome 🧬
@nature
High-fidelity convergent total synthesis is used to produce Escherichia coli with a 61-codon synthetic genome that uses 59 codons to encode all of the canonical amino acids.
Targeting mechanisms of tailed bacteriophages
In this Review,
@StanBrouns
and colleagues explore recent structural and mechanistic insights into the interaction of phage tails with receptors on the bacterial surface.
Beneficial applications of biofilms
Biofilms have diverse applications, from producing compounds to roles in agriculture and bioremediation. Gescher and colleagues provide an overview of the applications, challenges and future of beneficial biofilms.
Archaeal biofilm formation
In this Review, Albers
@Archaellum
and colleagues explore the different stages of archaeal
#biofilm
development and highlight the similarities and differences between archaea and bacteria.
Horizontal gene transfer and adaptive evolution in bacteria
Arnold, Huang & Hanage discuss underlying theory used to infer the selective forces acting on transferred DNA and how they shape patterns of genomic variation
Burkholderia pseudomallei and melioidosis
Meumann et al. discuss B. pseudomallei virulence and interaction with the host, and examine the epidemiology of melioidosis, offering insights into diagnosis, treatment and prevention strategies for this disease.
Co-evolution of immunity and seasonal influenza viruses
Russell & colleagues explore the interplay between immunity evolution from previous infections or vaccination and the evolution of seasonal influenza viruses.
Microorganisms in the reproductive tissues of arthropods
Perlmutter & Bordenstein discuss microbial symbionts in reproductive tissues of arthropods, their transmission modes, and physiological and evolutionary outcomes of their symbiotic relationships
Host–microbiota interactions in immune-mediated diseases
Review: Kriegel & co discuss mechanisms through which the microbiota contributes to the predisposition, initiation and perpetuation of immune-mediated diseases, and explore therapeutic avenues.
Types and origins of bacterial membrane vesicles
This Review provides an overview of different bacterial vesicle types, including classic outer-membrane vesicles and newly identified types that are induced by phage-derived autolysins.
Drug-resistant tuberculosis: a persistent global health concern
Ahead of
#WorldTBDay
this weekend, Pai (
@paimadhu
) & co review the global landscape of drug-resistant TB, its causes, risk factors, impact, latest diagnostics, treatments, and more.
Evolutionary causes and consequences of bacterial antibiotic persistence
Bakkeren, Diard & Hardt review evolutionary forces that favoured the development of persisters in populations & the consequences for spread of resistance & virulence determinants
📢Commensal bacteria fight colorectal cancer
This study reports that some bacterial species of the Lachnospiraceae family can suppress colorectal cancer progression by modulating CD8+ T cell immune surveillance activity.
Featured article in the February issue:
Gut microbial metabolites as multi-kingdom intermediates
In this Review, Bäckhed and colleagues discuss the major classes of microbial metabolites
Diet, microbiome and immune homeostasis
A Collection of Reviews from
@NatureRevMicro
,
@NatRevGastroHep
and
@NatRevImmunol
that explore the relationship between diet, the microbiome and immunity.
Reviews are FREE to read for a limited time!
Non-tuberculous mycobacteria and the rise of Mycobacterium abscessus
In this Review, Johansen, Herrmann and Kremer discuss the infection process, host interactions, mechanisms of drug resistance and drug development
Phages get snappy
#ResearchHighlight
This study shows that a single-stranded RNA phage binds to the Pseudomonas aeruginosa type IV pilus, leading to phage entry into the cell and the detachment of the pilus, which impairs bacterial motility.