Thanks to all who gave feedback last week on my first attempt to assemble reading lists of noteworthy things in the field of microbiome, microbial ecology and other generalities! I’ll attempt to add more comments this week, perhaps this could be good Of course, this is all subjective and personal but hopefully interesting to some? 🙂

Studies of interest

(a) Microbiome

• Gut microbiome and metabolome profiling in Framingham heart study reveals cholesterol-metabolizing bacteria.
  Chenhao Li et al. Cell — 2 April 2024.
  Comment: Multi-omic profiling in the US-based Framingham Heart Study identifies microbes/metabolites associated with CVD. Oscillibacter sp. are associated with decreased blood and stool cholesterol, and are found to encode for conserved cholesterol-metabolizing enzymes.

• Infant microbes and metabolites point to childhood neurodevelopmental disorders.
  Angelica P. Ahrens et al. Cell — 3 April 2024.
  Comment: Very exhaustive and impressive study! Using the All Babies in Southeast Sweden (ABIS) cohort, a birth cohort with 20 years follow-up (n=16,440; with n=1,197 developing an ND), these authors show that microbes and associated metabolites in infants contribute to future neurodevelopmental disorders (NDs) (other contributors to higher ND risk are preterm birth, infection, stress, parental smoking and a specific HLA variant). Other results include early-life otitus lowering Coprococcus sp. and increasing Citrobacter sp. in future NDs, potentially once again highlighting the role of early infection in incident disease risk/development.

• Placental TLR recognition of salivary and subgingival microbiota is associated with pregnancy complications.
  Kazune Pax et al. Microbiome — 26 March 2024.
  Comment: “Pre-term birth, the leading cause of neonatal mortality, has been associated with maternal periodontal disease and the presence of oral pathogens in the placenta.” This study finds evidence to suggest that oral bacteria might translocate to the placenta via serum and trigger immune signaling pathways capable of inducing placental vascular pathology

• Microbial composition associated with biliary stents in patients undergoing pancreatic resection for cancer.
  Aitor Blanco-Míguez et al. npj Biofilms and Microbiomes — 30 March 2024.
  Comment: Intriguing observation! Authors examined biliary stents from pancreatic cancer patients and found that 17 of 36 prevalent stent species are also common oral microbiome members, associate with disease conditions when present in the gut, and include dozens of biofilm- and AMR-related genes. Not a lot is hypothesised yet on the origin of these microbes or the infection route…

• An in-depth evaluation of metagenomic classifiers for soil microbiomes.
  Niranjana Rose Edwin et al. Environmental Microbiome (19) — 28 March 2024.
  Comment: Interesting benchmarking study looking at various different conditions and classifiers with mock soil metagenomic datasets, with the conclusion: “Our findings suggest that employing Kraken2 with Bracken, coupled with a custom database of GTDB-TK genomes and fungal genomes at a relative abundance threshold of 0.001% provides optimal accuracy in soil shotgun metagenome analysis.“. It somehow mirrors what we have been using (among other things) in our group for metagenomics classification, with the tweaking of confidence parameters for Kraken2.

• A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota.
  Joshua M. Kirsch et al. Cell Host & Microbes — 01 April 2024.
  Comment: New catalogue and tool to detect IS insertions. Intestinal bacteria have diverse IS insertions maintained over long timescales, which are enriched in accessory genes, such as susCD/tonB transporters. IS insertion activity seems to be affected by perturbations like nutrients and phage.

• The wound microbiota: microbial mechanisms of impaired wound healing and infection.
  Aayushi Uberoi et al. Nature Review in Microbiology — 4 April 2024.
  Comment: Microbiologists often think of sepsis and entry of pathogens through wounds or epidermis disruption of some kind. This recent review is a good summary of what we know on what happens in wounds re: microbial diversity and immune responses.

• Microbiota-derived indoles alleviate intestinal inflammation and modulate microbiome by microbial cross-feeding.
  Wang et al. Microbiome— 19 March 2024.

• Lose-lose consequences of bacterial community-driven invasions in soil.
  Xipeng Liu et al. Microbiome — 18 March 2024.

• Incomplete immunity in a natural animal-microbiota interaction selects for higher pathogen virulence.
  Kim Hoang et al. Current Biology — 25 March 2024.

(b) Microbial ecology, evolution and AMR

• “Metabolic burden” explained: stress symptoms and its related responses induced by (over)expression of (heterologous) proteins in Escherichia coli.
  Sofie Snoeck et al. Microbial Cell Factories — 30 March 2024.
  Comment: Interesting review summarizing what is likely to happen in a bacterial cell when a protein is overexpressed. Authors focus on bioengineering and synthetic biology applications, but I think this could be generally speaking something quite fundamental to understand when thinking of bacterial evolution, horizontal gene transfer and adaptation.

• Uncovering the boundaries of Campylobacter species through large-scale phylogenetic and nucleotide identity analyses.
  Ruochen Wu et al. mSystems — 26 March 2024.
  Comment: Interesting new improved genus-wide dataset from the zoonotic pathogen Campylobacter. This paper provides with a good new addition from our previous genus-wide study in eLife (link) led by Evangelos Mourkas (now Uppsala University).

• The emergence of artemisinin partial resistance in Africa: how do we respond?
  Philip J Rosenthal et al. The Lancet Infectious Diseases — 26 March 2024.
  Comment: A very concerning prospect: “Major priorities at present are the expansion of genomic surveillance for ART-R mutations across the continent, more frequent testing of the efficacies of artemisinin-based regimens against uncomplicated and severe malaria in trials, more regular assessment of ex-vivo antimalarial drug susceptibilities, consideration of changes in treatment policy to deter the spread of ART-R, and accelerated development of new antimalarial regimens to overcome the impacts of ART-R.“

• Archaeal actins and the origin of a multi-functional cytoskeleton.
  Arthur Charles-Orszag et al. Journal of Bacteriology — 23 February 2024.
  Comment: Interesting minireview (with absolutely stunning figures) if you are also puzzled about the variability and prevalence of actin-like proteins in microbes (over 40 classes found in bacterial genomes and plasmids, remarkably divergent compared to eukaryotes). The current hypothesis supported by this review is for an engulfment model for eukaryogenesis, where archaeal membrane protrusions encircling a bacterial partner eventually fused to produce an archaeal host cell with a stably engulfed bacterial endosymbiont. Cool stuff!

• Antibiotic resistance begets more resistance: chromosomal resistance mutations mitigate fitness costs conferred by multi-resistant clinical plasmids.
  Ramith Nair et al. Microbiology Spectrum — 27 March 2024.

• Plasmid-mediated phenotypic noise leads to transient antibiotic resistance in bacteria.
  J. Carlos R. Hernandez-Beltran et al. Nature Communications 15:2610 — 23 March 2024

• Staphylococcus aureus colonisation and strategies for decolonisation.
  Pipat Piewngam & Michael Otto, The Lancet Microbe — 19 March 2024.

(c) Other general interest

• Complexity of avian evolution revealed by family-level genomes.
  Josefin Stiller et al. Nature — 1 April 2024.
  Comment: Very important paper for those with an interest in birds (like I do)! The approach is something quite nice that we had somehow also done for bacteria in some early studies (but not on that scale at all!): in this study, authors reconstructed local phylogenies at 150,000 loci from 363 avian species, building thousands of species trees and test the impact of data quantity and taxon sampling. They found many incongruences of these local trees with the species trees (great examples here from a second paper from some of the authors published in PNAS on the same day), suggesting gene dynamics at the family-level. Not entirely surprising when you know bird, ring species and how promiscuous bird ecology can be sometimes. Very cool stuff!

• Fungal and bacterial species richness in biodeteriorated seventeenth century Venetian manuscripts.
  Maria Stratigaki et al. Scientific Reports 14:7003 — 25 March 2024.
  Comment: Just because how cool is that!! Findings are as expected, finding usual suspects and possible new taxa to consider for the field of historical artefact conservation.

• New estimates indicate that males are not larger than females in most mammal species.
  Kaia J. Tombak et al. Nature Communications — 12 March 2024.
  Comment: Authors suggests that biases in scientific literature might have led to the common belief that males are generally larger than females, while the opposite is true for most mammal species.

• Association of Coffee Consumption and Prediagnostic Caffeine Metabolites With Incident Parkinson Disease in a Population-Based Cohort.
  Yujia Zhao, Yunjia Lai et al. Neurology — 21 March 2024.
  Comment: Caffeine consumption (mainly through 2 metabolites, paraxanthine and theophylline) has been indicated to play a significant role in reducing risk of PD, as well as mitigating PD symptoms in animal models. In this study, authors looked at a population-based 20y-long longitudinal cohort across 6 European countries (EPIC4PD study) to show that coffee consumption inversely correlated with risk of developing PD. Those who consumed the highest amounts of coffee exhibited ~40% lower risk of PD compared to coffee non-consumers.

• Long-Distance Avian Migrants Fail to Bring 2.3.4.4b HPAI H5N1 Into Australia for a Second Year in a Row.
  Michelle Wille et al. Influenza Other Respi. Viruses — 31 March 2024

Promising preprints:

• Elementary methods provide more replicable results in microbial differential abundance analysis.
  Juho Pelto, Kari Auranen, Janne Kujala, Leo Lahti aRxiv — 3 April 2024.
  Comment: Very comprehensive and nice assessment of differential abundance methods (DAA) in microbiome science.

• Seamless, rapid and accurate analyses of outbreak genomic data using Split K-mer Analysis (SKA).
  Romain Derelle et al. (John Lees lab) bioRxiv –29 March 2024.

• Massively parallel combination screen reveals small molecule sensitization of antibiotic-resistant Gram-negative ESKAPE pathogens.
  Megan W. Tse et al. bioRxiv — 26 March 2024.

• Unraveling interindividual differences and functional consequences of gut microbial metabolism of immunosuppressants.
  Maral Baghai Arassi et al. bioRxiv — 29 March 2024.

• Challenges in quantifying functional redundancy and selection in microbial communities.
  Po-Yi Ho & Kerwyn Huang, bioRxiv — 29 March 2024. And the debate on functional redundancy continues!

Other interesting things:

• Interesting advice for group leaders/academics from GV Pavan Kumar on Twitter.
• Great piece in Nature News about “How does a cancer vaccine work?”. It would seem that “[a]fter decades of slow progress, therapeutic vaccines that direct the immune system to attack tumours could soon become a fixture of cancer treatment“.
• There is a Klebsiella Virtual Seminar Series if you are interested in hearing talks on the topic. Times aren’t great for Australian researchers but still interesting! More information here.