BMAC Weekly — 2026-W32
8 papers selected for 2026-W32.
2026-07-28–2026-08-03 · 8 papers
misosoup: a metabolic modeling tool for identifying minimal microbial communities, facilitates the exploration of microbial ecology and biotechnological applications
Nicolas Ochsner, Magdalena San Román, Adrián Jiménez-Fernández, Sebastian Bonhoeffer, Alberto Pascual‐García
2026-07-28 · mSystems
TL;DR. misosoup is a Python package that uses genome-scale constraint-based metabolic modeling to identify minimal microbial communities that can grow in environments where individual strains cannot, validated against known cooperative interactions and applied to 60 marine microbes to reveal cross-feeding-driven niche expansion.
Key signal. The tool predicts pervasive cross-feeding-driven niche expansion in marine microbes and provides detailed outputs that can identify functional groups.
Why it matters here. This directly supports your interest in microbial community ecology and synthetic community design by providing a computational method to predict metabolic cooperation and minimal community composition.
Division of Synthetic Cells Using a Genomically Encoded One-Protein Divisome
C Sharma, N Nafar, J Kerssemakers, JF Gutierrez…
2026-01-01 · bioRxiv
TL;DR. The paper reports the division of synthetic cells using a genomically encoded one-protein divisome, as described in a preprint from bioRxiv.
Why it matters here. This connects to your work on synthetic biology circuits and microbial growth and division, offering a minimal genetic module for controlling cell division in engineered cells.
Phenotypic heterogeneity in the human gut microbiome revealed by subspecies-resolution single-cell transcriptomics
Dmitry Sutormin, Karl D. Gaisser, Jacqueline Haring, Anjana Punniamoorthy, Theinmozhi Arulraj, Crystal Perez, Christian Diener, Katherine Ramos Sarmiento, Alex V. Carr, Noa Rappaport, Sean M. Gibbons, Anna Kuchina
2026-07-31 · bioRxiv (Cold Spring Harbor Laboratory)
TL;DR. The study presents metaSPLiT, a scalable single-cell RNA sequencing method for microbiomes, and applies it to healthy human fecal samples to reconstruct 21,598 single-cell transcriptomes across 70 bacterial species, revealing subspecies-level functional specialization.
Key signal. The method uncovered coexisting genomovars of Segatella copri with distinct expression profiles and showed that microbiome context drives phenotypic heterogeneity not captured by bulk measurements.
Why it matters here. This provides a high-resolution view of phenotypic heterogeneity in microbial communities, directly relevant to your interests in population dynamics and cell-state diversity.
Hierarchical control of bacterial growth efficiency by substrate and taxonomy
Vaibhhav Sinha, Seppe Kuehn
2026-07-27 · bioRxiv (Cold Spring Harbor Laboratory)
TL;DR. The authors develop a high-throughput method to measure CO2 production during bacterial growth and quantify growth efficiency for 23 strains across three phyla on two substrates, finding substrate identity hierarchically controls efficiency.
Key signal. Growth efficiency varies as much across resources as across phyla, and a physiological model predicts no global correlation between growth rate and growth efficiency, which is supported by data.
Why it matters here. This links carbon allocation and energy metabolism to growth physiology, relevant to your work on growth laws and dynamic metabolism.
Phage VP882 possesses quorum-sensing-driven lytic induction and stress-mediated host growth suppression mechanisms
Grace A. Beggs, Bonnie L. Bassler
2026-07-27 · bioRxiv (Cold Spring Harbor Laboratory)
TL;DR. The paper shows that Vibriophage VP882 can either launch a lytic cascade or induce host growth arrest via quorum-sensing-triggered pathways, with a novel protein QtiQ inactivating the growth-arrest complex.
Key signal. QtiQ is the first identified protein inactivator of a TraR or DksA-like homolog, and the phage can suppress host growth through a cI-derepressed DksA homolog and QisA complex.
Why it matters here. This illustrates phage-host regulatory interactions and quorum-sensing-driven decisions, relevant to your interests in microbial decision-making and population dynamics.
Seed-applied multi-kingdom synthetic communities selectively reshape bacterial communities and highlight key criteria for strain selection
Logan Suteau, Claire Campion, Coralie MARAIS, Martial Briand, Anais Hardouin, Kaat Hellyn, Kenji Maurice, Muriel Marchi, Marie Simonin, Natalia Guschinskaya
2026-07-16 · bioRxiv
TL;DR. The study constructs 20 multi-kingdom synthetic communities (bacteria, yeasts, fungi) and applies them to Brassica napus seeds in soil, showing that strain selection is more critical than assembly strategy for seedling colonization.
Key signal. SynCom inoculation altered seedling bacterial community assembly in 14 SynComs, and high seed abundance and low in vitro lag-time were key traits for efficient colonization.
Why it matters here. This provides empirical criteria for synthetic community design and highlights ecological processes that shape microbial community assembly.
Quorum sensing in Klebsiella pneumoniae: An interconnected regulatory network driving virulence and antimicrobial resistance
Sergio Silva-Bea, Sonia Rey, Manuel Romero, Ana Otero
2026-07-27 · Microbiological Research
TL;DR. This review integrates current knowledge on Klebsiella pneumoniae quorum sensing, covering four main QS systems (AHL-SdiA, AI-2-Lsr, QseBC-AI-3, indole-CpxAR) and their potential interactions in controlling virulence and antimicrobial resistance.
Key signal. Quorum sensing in K. pneumoniae likely functions as an interconnected regulatory network rather than independent pathways, and targeting QS is proposed as an anti-virulence strategy.
Why it matters here. This connects to your interests in antibiotic resistance and microbial decision-making by examining how QS networks coordinate virulence and resistance.
Structural characterization of stochastic detailed balance in chemical reaction networks
Shangbin Ma, Youming Li
2026-07-28 · bioRxiv (Cold Spring Harbor Laboratory)
TL;DR. The paper provides a structural characterization of stochastic detailed balance in chemical reaction networks, showing that detailed balance can depend on system volume and introducing four types of detailed balance.
Key signal. The authors identify conditions under which detailed balance at one volume extends to all volumes and construct networks satisfying detailed balance for every volume and positive rate constants, with double-well global potentials.
Why it matters here. This is an enabling-method wildcard: volume-dependent detailed balance could inform modeling of biochemical reaction networks in cellular compartments where volume changes, relevant to your interest in biomolecular reaction networks.