My Europe trip continues, from fruitful visits in Scotland and England to some time off with my family next week. Nonetheless, here’s a summary of some publications that caught my eye in the field of microbiome research, microbial genomics and ecology, and others in the last two weeks (this time as well). Comments in blue are personal and hopefully useful!

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Noteworthy studies and publications

(a) Microbiome(s)

• Tissue-resident bacteria in metabolic diseases: emerging evidence and challenges
  Lucas Massier et al. Nature Metabolism — 19 June 2024.
  Comment: Fascinating review with an original angle, summarizing knowledge on bacterial translocation in metabolically active organs, something they term “tissue-resident bacteria”. Various body sites are well known to have a high biomass of microbes and active functional microbiota, but less is known about microbial colonization of other sites (e.g. liver, adipose tissue, pancreas, kidney) and its impact on metabolic health. Very interesting read., especially with an ecological consideration of holobionts etc.

• Cross-feeding of bifidobacteria promotes intestinal homeostasis: a lifelong perspective on the host health
  Meifang Xiao et al. npj Biofilms and microbiomes — 19 June 2024.
  Comment: I found the angle of this review very interesting and somehow original. The role of Bifidobacterium in health, particularly infant health, is very described and studied, which means that it becomes possible to look at cross-feeding and metabolic interactions between various different species and strains within this genus. A clear summary of what is known!

• Association between gut microbiota and CpG island methylator phenotype in colorectal cancer.
  Pyoung Hwa Park et al. Gut Microbes — 11 June 2024.
  Comment: This interesting study investigates the association between gut microbiota, specifically the enrichment of Bacteroides fragilis, Escherichia coli, Fusobacterium nucleatum, and Klebsiella pneumoniae, and the CpG island methylator phenotype (CIMP) in colorectal cancer (CRC). A few hundred samples from colorectal adenocarcinoma tumors and adjacent normal tissue were analysed which led authors to suggest a potential influence of bacteria on DNA methylation patterns in CRC.

• Longitudinal multi-omics analysis of host microbiome architecture and immune responses during short-term spaceflight
  Braden T. Tierney, JangKeun Kim et al. Nature Microbiology — 11 June 2024.
  Comment: These studies always seem at first to feel as is we are looking too hard for anything meaningful, just because the samples are extremely original and difficult to obtain. Are there really particularities in human-microbes interactions during spaceflight and prolonged life in absence of gravity? If there is anything, this study is the most comprehensive I’ve seen so far (without really following the field). Authors look at time-dependent, multikingdom microbiome changes across 750 samples and 10 body sites before, during and after spaceflight at eight timepoints. They mostly find transient alterations of the skin and oral microbiota and immune cell expression. Very intresting study, most probably impactful for spaceflight management.

• Single-cell transcriptomics across 2,534 microbial species reveals functional heterogeneity in the rumen microbiome.
  Minghui Jia, Senlin Zhu, Ming-Yuan Xue et al. Nature Microbiology — 12 June 2024.
  Comment: Quite an impressive study, using droplet-based single-cell RNA sequencing and pangenome-based computational analysis to characterize the functional heterogeneity of the rumen microbiome. The resulting atlas encompasses 174,531 microbial cells and 2,534 species, of which 172 are core active species grouped into 12 functional clusters, allowing to study the microbiome at unprecedented resolution. On the biological side of things, authors highlight a new potential key role for Basfia succiniciproducens in the carbohydrate metabolic niche of the rumen microbiome, as well as its biofilm abilities.

• Paternal and induced gut microbiota seeding complement mother-to-infant transmission
  Léonard Dubois, Mireia Valles-Colomer et al. Cell Host & Microbe — 12 June 2024.
  Comment: The role of the gut microbiota in early life is of course extensively studied, but this particular study focuses on analysing the HELMi and SECFLOR cohorts and look at the impact of maternal fecal microbiota transplantation (FMT) on cesarean-born infants (something that has been studied and “semi” debated over the years). Authors show that maternal FMT can enhance microbial richness, increase strain sharing with infants, and reduce pathogen colonization. Interestingly, they also underscore the importance of both parents (including paternal) in shaping the infant gut microbiome and suggest that maternal FMT could potentially restore disrupted microbiota transmission in cesarean-born infants.

(b) Microbial genetics, ecology, evolution and AMR

• Phollow: Visualizing Gut Bacteriophage Transmission within Microbial Communities and Living Animals
  Lizett Ortiz de Ora et al. bioRxiv — 13 June 2024.
  Comment: I hadn’t come across such a study before, this is very cool! In this preprint, authors fluorescently tagged bacteriophages to follow their transmission and infection routes. Extremely cleverly, they designed a tagging system consisting of multiple fluorescent proteins called “SpyCatcher” which tags the virion differently after each infection of a new bacterial host. The combination of colours can then help visualise the succession of infections. They test their method with in vitro communities of multiple species, as well as in vivo in the gut of zebrafish! Using this tool, they observe that virions can be rapidly taken up by intestinal tissues, including by enteroendocrine cells, and can quickly disseminate to extraintestinal sites, including the liver and brain. Additionally, antibiotics can trigger waves of interbacterial transmission leading to sudden shifts in spatial organization and composition of defined gut communities. Very elegant and impressive!

• Prevalence of errors in lab-made plasmids across the globe
  Xingjian Bai et al. bioRxiv — 18 June 2024.
  Comment: On the importance of sanity checks and careful validation when designing vectors and plasmids in the lab! This will not surprise a lot of “wet lab” plasmid-cloning scientists, I’m sure. This preprint presents a large survey of plasmids from hundreds of academic and industrial labs worldwide and shows that nearly half of them contain design and/or sequence errors. More usefully, authors report what type of errors they encounters, hopefully helpful information for future engineering.

• Applying rearrangement distances to enable plasmid epidemiology with pling
  Daria Frolova et al. bioRxiv — 12 June 2024.
  Comment: New preprint from Zamin Iqbal’s group that will appeal to everyone who has ever worked with plasmid sequences and epidemiology. Plasmids evolve very rapidly and can restructure their genome quite substentially, adding and removing genes and sequences extremely rapidly. Given that, how can we call two plasmids the “same” epidemiologically speaking? This was a central (and tricky) question during our 2018 Bacillus cereus plasmid diversity study, and the fact that this genus harbours “megaplasmids” combining multiple other ones. Here, authors tackle the problem far more elegantly, by incorporating genetic distance, and precise accounting of the possible changes that can occur in plasmid sequences. Their proposed tool (called “pling”, not to be confused with plink!) builds sequence similarity networks (i.e. connect 2 plasmids if 50% of their sequences is alignable). More details on Zamin’s great and clear Twitter thread about it!

• Lytic and temperate phage naturally coexist in a dynamic population model
  Ofer Kimchi et al. The ISME Journal — 31 May 2024.
  Comment: In this modelling (only) study, authors challenge the assumption that one phage strategy (lytic vs. lysogenic) is universally superior, proposing instead that the coexistence of lytic and temperate phages is a natural outcome of complex population dynamics.

• Convergence and horizontal gene transfer drive the evolution of anaerobic methanotrophy in archaea.
  Philip H. Woods et al. bioRxiv — 28 May 2024.
  Comment: In this preprint, authors examine the evolution of anaerobic methanotrophic archaea in the genus Methanovorans. Their analyses of genomes from 10 isolates from various locations suggest an importance of key metabolic genes for methane oxidation and energy conservation, with a role of HGT in local adaptation. They interestingly characterize a gradual loss of genes involved in methylotrophic methanogenesis during the transition to methanotrophy.

• Pan-drug resistance and hypervirulence in a human fungal pathogen are enabled by mutagenesis induced by mammalian body temperature
  Jingjing Huang et al. Nature Microbiology — 19 June 2024.
  Comment: Rhodosporidiobolus fluvialis is a human fungal pathogen, from a genus that is highly resistant to antifungals. In this paper, authors demonstrate that the species can undergo a yeast-to-pseudohyphal transition in, which is considered a key determinant of its increased virulence. Interestingly, human body temperature-induced mutagenesis is highlighted as a driving force behind the development of drug resistance (notably except to polymyxin B) and hypervirulence, also in fungal pathogens in general.

• Deep-learning-enabled antibiotic discovery through molecular de-extinction
  Fangping Wan, Marcelo D. T. Torres et al. Nature Biomedical Engineering — 11 June 2024.
  Comment: A bit of a hyped title for something actually very cool. This study presents an interesting approach combining ML models to predict antimicrobial activity from predicted peptides, and identified a large number of those in extinct organisms! Notably, they found that mammuthusin-2 from the woolly mammoth, elephasin-2 from the straight-tusked elephant, hydrodamin-1 from the ancient sea cow, mylodonin-2 from the giant sloth and megalocerin-1 from the extinct giant elk had some anti-infective activity in a mouse model of infectious skin absess.

(c) Other general interest

• Co‐evolution of early Earth environments and microbial life
  Timothy W. Lyons et al. Nature Reviews Microbiology — 29 May 2024.
  Comment: This very nice review presents geobiological, geochemical, and genomic perspectives on how early microbial life co-evolved with Earth’s environments, particularly focusing on the transition from an anoxic to an oxygen-rich atmosphere (really like the figures!). It presents an interesting angle on the distinction between the emergence of early metabolic processes and their subsequent proliferation, highlighting how these metabolisms were not only a product of environmental conditions but also a driving force in shaping the chemical properties of the oceans, continents, and atmosphere. There are also some cool astrobiological implications, suggesting that similar biosignatures could be used to detect life on other planets, and that understanding Earth’s past could inform the search for extraterrestrial life. A bit wild, I know, but fun!

• A gene with a thousand alleles: The hyper-variable effectors of plant-parasitic nematodes
  Unnati Sonawala et al. Cell Genomics — 29 May 2024.
  Comment: If you had to guess, which gene might have the most described alleles? Pathogen effectors are probably up in this list, and in this paper, authors describe HYP effectors with potentially 1000s alleles from cyst nematodes that are necessary for their parasitism in potato plants. Alleles are due to particularly variable domains termed hyper-variable domains (HVD). Authors suggest a mechanism of programmed, locus-specific, somatic genome editing for these peculiar and very diverse genes.