Shorter list this week but still some cool microbiome, microbial genomics/ecology studies of interest.

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Noteworthy publications

(a) Microbiome

• STUDY: Clinical sequelae of gut microbiome development and disruption in hospitalized preterm infants.
  Robert Thänert et al. Cell Host & Microbe — 27 August 2024.
  Comment: Authors looked at >2.5k stool samples from 236 preterm infants in 3 NICUs to characterize gut microbiome development. Key findings included the identification of shared strains of Clostridioides difficile and Staphylococcus epidermidis (!) among infants, the fact that both AB and non-AB medications impact the infant gut microbiota composition and that there waas a persistant fraction of the low-diversity microbiome that could be associated with necrotizing enterocolitis after 40d of life.
  Topics: infant microbiota, early life, NEC, S. epidermidis

• STUDY: Gut Microbiome in Children with Congenital Heart Disease After Cardiopulmonary Bypass Surgery (GuMiBear Study).
  Fatma Koc et al. Pediatric Cardiology — 22 August 2024.
  Comment: This 16S rRNA work from Ireland shows that infants with congenital CHD (GuMiBear study, with INFANTMET cohort as healthy controls) have an altered gut microbiome when compared with healthy controls and there might be a possible link between an abundance of virulent species and necrotising enterocolitis.
  Topics: infant microbiome, congenital heart disease, 16S rRNA

• STUDY: Gut microbiota metabolically mediate intestinal helminth infection in zebrafish.
  Austin J. Hammer et al. mSystems — 27 August 2024.
  Comment: Parasitic infection, although low in developped countries with increased hygiene, has been an infectious burden for the entirety of humanity and still is in various parts of the world. It is quite fascinating to try and understand how the gut microbiome adapted to this pressure. Using a zebrafish model here and a joint gut 16S + untargeted metabolomics approach, authors identify a significant association between composition and infection burden by Pseudocapillaria tomentosa, as well as a role for salicylaldehyde, a metabolite inversely related to worm burden and potentially produced by Pelomonas, completely inhibited P. tomentosa egg larvation in vitro and, which showed anthelmintic activity in vivo.
  Topics: parasitic infection, gut microbiota

• STUDY: The impact of small intestinal bacterial overgrowth on the efficacy of fecal microbiota transplantation in patients with chronic constipation.
  Le Wang et al. mBio — 28 August 2024.
  Comment: In cases of chronic constipation, bacteria are observed to overgrow in parts of the GI tract abnormally, something sometimes called “SIBO” for “small intestine bacterial overgrowth” and which is quantifiable with breath tests. In this work, 218 patients with chronic constipation are categorized as SIBO/non-SIBO to investigate the impact of FMT on symptoms and the gut microbiota (16S-based). Post-FMT, patients with SIBO experienced better outcomes, including increased bowel movement frequency and enhanced quality of life. The small intestinal microbiota showed more significant shifts than the colonic microbiota after treatment, with baseline differences in microbial composition, such as varying abundances of Veillonella, Escherichia-Shigella, and Acinetobacter, potentially impacting the effectiveness of FMT.
  Topics: constipation, gut microbiota, FMT, 16S rRNA

• PREPRINT: The breath volatilome is shaped by the gut microbiota.
  Ariel J. Hernandez-Leyva et al. medRxiv — 8 August 2024.
  Comment: In this preprint, authors show a significant correlation between the composition of the gut microbiota and the volatile organic compounds (VOCs) in breath, both using a clever gnotobiotic mouse model with a tracheostomy step bypassing the potential effects of the oral microbiota, and a small sample of 27 healthy children. Gut microbes accounted for 40% of the variance in breath VOCs in humans.
  Topics: volatile organic compounds, gut-oral links

(b) Microbial and pathogen genetics, ecology, evolution and AMR

• STUDY: High sugar diets can increase susceptibility to bacterial infection in Drosophila melanogaster.
  Andrea M. Darby et al. Plos Pathogens — 12 August 2024.
  Comment: Here, authors look at the diet-immunity-infection dynamics using the Drosophila model. They show that adult flies fed a high-sugar diet exhibit increased susceptibility to Gram-negative bacterial infections, specifically Providencia rettgeri and Serratia marcescens. High sugar intake led to hyperglycemia and elevated pathogen burden, with S. marcescens capitalizing on the host’s increased glucose levels functionally. Also, high-sugar diet impaired the immune response by reducing the production of antimicrobial peptides at the translational level, despite normal gene expression.
  Topics: Drosophila, role of diet in infection susceptibility, functional microbiome

• STUDY: Host species shapes genotype, antimicrobial resistance, and virulence profiles of enterotoxigenic Escherichia coli (ETEC) from livestock in the United States.
  Yezhi Fu et al. Applied and Environmental Microbiology — 31 July 2024.
  Comment: Interesting US survey from a couple of months ago, describing ETEC isolated from livestock over a 53-year period (since the 1970s). More precisely, authors look at the evolution of AMR gene acquisition over time, and identify key genetic and virulence elements differentiating pig from cattle ETEC.
  Topics: E. coli, food microbiology, comparative genomics

• STUDY: Natural products from food sources can alter the spread of antimicrobial resistance plasmids in Enterobacterales.
  Ilyas Alav et al. Microbiology — 27 August 2024.
  Comment: It is sometimes a bit unclear how various food components act on microbial physiology, and a lot of studies are often underpowered or unclear. In this interesting small-scale attempt, authors use a fluorescence-based flow cytometry-based approach to suggest that extracts from black pepper, ginger, and kamala, as well as the compounds 6-gingerol, capsaicin, and rottlerin, can reduce plasmid conjugation frequency in Escherichia coli and Klebsiella pneumoniae. Rottlerin, in particular, seemed to be effective in both bacterial species. It is unclear how this fits into the broad aspect of things, but a good reminder that the complexity of foods does interact with the complexity of microbes!
  Topics: AMR, plasmid conjugation

(c) Other general interest

• STUDY: Highly parallelized laboratory evolution of wine yeasts for enhanced metabolic phenotypes.
  Payam Ghiaci et al. Molecular Systems Biology — 22 August 2024.
  Comment: Harnessing evolution to control wine production and taste? This work shows the outcome of experimental evolution of 10,000 wine yeast strains, selecting for variants that can tolerate higher alcohol levels, produce various aromatic compounds while maintaining their growth rate.
  Topics: wine yeast evolution, food bioengineering