The human vaginal microbiota plays a key role in urogenital health. Enhancing our understanding of the dynamics of the vaginal microbiota can provide valuable insights for maintaining health and design strategies to prevent urogenital diseases. Health status evolves over time. The work by Kamiya et al. (2024) addressed the dynamic interplay between vaginal microbiota and health using a robust, high-resolution longitudinal cohort of 125 reproductive-aged women, followed for a median duration of 8.6 months in Montpellier, France. The participants were recruited within the PAPCLEAR study, which aimed to better understand the course and natural history of human papillomaviruses infections in healthy, young women (Murall et al. 2019). Each participant contributed at least three vaginal samples, from which microbiota barcoding was performed.

The vaginal microbiota was clustered using the approach developed by Ravel et al. (2011) which categorizes microbial communities in 5 community state types with varying health implications. Transitions between community states were estimated using a hierarchical Bayesian Markov model. These transitions were associated with 16 covariates covering lifestyle, sexual practices and medication. This hierarchical approach allowed for the quantification of individual differences among women. The study characterized the stability of vaginal microbial communities and identified alcohol consumption as the strongest covariate driving community transitions. The results indicated that alcohol consumption promotes non-optimal communities. 

The modelling approach, however, indicated that individual variability among the women was not fully accounted for by the selected 16 covariates, suggesting the need to explore additional key factors, including dynamic covariates. The authors clearly identified several  potential limitations of the study, including the variability associated to home sampling,  the resolution of the microbial categories, and the impact of the clustering method on the analysis.    

My decision to recommend this manuscript is supported by the solid and rigorous analysis of the study, strengthened by the clear presentation of methods, data and analysis. While applying advanced computational techniques, the authors provide a solid biological interpretation of their results. This work makes a substantial contribution by expanding the understanding of vaginal microbiota dynamics and its interplay with health. It sets a framework for further evaluation of strategies aimed at promoting vaginal health. Moreover, it presents a generic methodology that could be applied to other microbial ecosystems.   

References

Kamiya T, Tessandier N, Elie B, Bernat C, Boué V, Grasset S, Groc S, Rahmoun M, Selinger C, Humphrys MS, Bonneau M, Graf C, Foulongne V, Reynes J, Tribout V, Segondy M, Boulle N, Ravel J, Murall CL, Alizon S (2024) Factors shaping vaginal microbiota long-term community dynamics in young adult women. medRxiv, 2024.04.08.24305448, ver.3 peer-reviewed and recommended by PCI Microbiol. https://doi.org/10.1101/2024.04.08.24305448

Murall CL, Rahmoun M, Selinger C, Baldellou M, Bernat C, Bonneau M, Boué V, Buisson M, Christophe G, D’Auria G, Taroni F De, Foulongne V, Froissart R, Graf C, Grasset S, Groc S, Hirtz C, Jaussent A, Lajoie J, Lorcy F, Picot E, Picot MC, Ravel J, Reynes J, Rousset T, Seddiki A, Teirlinck M, Tribout V, Tuaillon É, Waterboer T, Jacobs N, Bravo IG, Segondy M, Boulle N, Alizon S (2019) Natural history, dynamics, and ecology of human papillomaviruses in genital infections of young women: protocol of the PAPCLEAR cohort study. BMJ Open, 9, e025129. https://doi.org/10.1136/BMJOPEN-2018-025129

Ravel J, Gajer P, Abdo Z, Schneider GM, Koenig SSK, McCulle SL, Karlebach S, Gorle R, Russell J, Tacket CO, Brotman RM, Davis CC, Ault K, Peralta L, Forney LJ (2011) Vaginal microbiome of reproductive-age women. Proceedings of the National Academy of Sciences of the United States of America, 108. https://doi.org/10.1073/pnas.1002611107

Fermented vegetables, traditionally consumed in Asian and Eastern countries, are gaining increasing interest in Western countries due to the growing demand for more natural, healthy, and sustainable food. Their potential health effects have only recently begun to be scientifically studied (Thierry et al., 2023).

The manufacturing process of fermented vegetables consists of cutting and packing raw vegetables with salt or brine, that will draw water and nutrients out from the vegetable tissue, thus providing microorganisms with the necessary substrates to initiate spontaneous fermentation (Buckenhueskes, 2015). Various parameters, including the cutting method, which may influence the rate of solute diffusion from vegetable tissue, can affect fermentation speed and, consequently, the quality of fermented vegetables. However, the role of cutting type has rarely been addressed.

The study by Valence et al. (2025) used a comprehensive range of methods to investigate how cutting types and a slight reduction in salt concentration influence the spontaneous fermentation of two vegetables, carrot and cabbage. Two cutting types, finely or roughly cut, and two salt levels, 1% (the minimum concentration usually used) and a lower salt level in line with health recommendations (0.8%), were tested. Carrot and cabbage fermentations were performed under controlled conditions in duplicate, and microbiological and biochemical characteristics were monitored over one month by combining several approaches and extensive experiments in culturomics, 16S rRNA gene and gyrB metataxonomics for bacterial community analysis, and targeted metabolomics.

The study shows the sequential establishment of microbial communities during the fermentation of both vegetables. In the early stages, Enterobacteriaceae replaced the initial microbiota, but they were rapidly outcompeted by Lactic Acid Bacteria (LAB). LAB growth acidified the medium, inhibiting enterobacteria and ensuring microbial safety. Their dominance was attributed to their ability to ferment carbohydrates into lactic acid and possibly the production of antimicrobial compounds. The results of targeted metabolomic analysis show that the main fermentation byproducts are mannitol, lactic acid, and acetic acid, which is consistent with previous studies on fermented vegetables.​

Most notably, this study demonstrated for the first time that the type of vegetable cutting has a major impact on fermentation dynamics by influencing the release of solutes into the brine. Finer cuts, which provide a greater surface area, facilitate nutrient diffusion, thereby promoting LAB proliferation and acidification.

​​​​​​The study also shows that salt addition improved solute release, though the microbial effects were less clear due to variability between replicates. Indeed, significant variability between jars was noted, affecting microbial composition, metabolite profiles, and acidification rates.

The work of Valence et al. (2025) highlights for the first time the crucial role of cutting type in vegetable fermentation, demonstrating that finer cuts accelerate acidification, improve microbial safety, and enhance fermentation efficiency. Their findings contribute to the optimization of fermentation processes, providing valuable insights for enhancing the quality of fermented vegetables.​​​​​

​​​References:
Buckenhueskes HJ. Quality improvement and fermentation control in vegetables. Advances in Fermented Foods and Beverages. Elsevier, 2015, 515–39. https://doi.org/10.1016/B978-1-78242-015-6.00022-0

Thierry A, Baty C, Marché L, Chuat V, Picard O, Lortal S, Valence F. Lactofermentation of vegetables: An ancient method of preservation matching new trends. Trends Food Sci Technol. 2023. https://doi.org/10.1016/j.tifs.2023.07.009

Valence F, Junker R, Baty C, Rué O, Mariadassou M, Madec M, Maillard M, Bage A, Chuat V, Marché L, Thierry A. The cutting type of vegetables influences the spontaneous fermentation rate. HAL, ver.2 2025. https://hal.science/hal-04701063v2​

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Mycoplasma mycoides subsp. mycoides (Mmm), a pathogenic wall-less bacterium, is the etiological agent of contagious bovine pleuropneumonia (CBPP). This highly contagious respiratory disease may develop in severe pneumonia, with associated high mortality rates in cattle. Mmm can display different immune evasion mechanisms; in addition, a host uncontrolled inflammatory response stands for lung lesions and chronic carrier animals.

Macrophages are among the most important lines of defense against Mmm of the lower respiratory tract. Although their importance in defense and immune response modulation is known, results about their role and mechanisms of action are scarce and sometimes conflicting.

In the present study, Totté et al. (1) aimed to investigate the interaction of bovine macrophages (isolated from cattle peripheral blood mononuclear cells) with Mmm, under in vitro conditions. The authors highlight that the study was performed under physiological conditions (in the presence of complement prepared from the same cell donor).

In their study, using different approaches, the authors provide interesting and original results, proposing a pivotal role of complement in controlling the inflammatory response, which is crucial in the CBPP pathogenesis. 

The authors reported that macrophages did not kill Mmm in the presence of a non-bactericidal concentration of bovine serum. However, Mmm inactivation was observed when antiserum from CBPP convalescent animals was used. They also observed that Mmm induced the production of TNF by macrophages (when a high MOI was assessed). However, complement could even abolish Mmm-induced TNF response when used at bactericidal activity concentrations. This role of complement could be combined with the development of potentially protective antibodies against particular Mmm antigens involved in the interaction with identified macrophage receptors to propose control strategies against CBPP. 

Overall, the study by Totté et al. provides new fundamental insight for the research on preventive or therapeutic strategies for a poorly understood disease that still represents a serious concern for livestock production. 

REFERENCES

1. Totté, P., Bonnefois, T., Manso-Silván, L. Interactions between Mycoplasma mycoides subsp. mycoides and bovine macrophages under physiological conditions. bioRxiv 2022.12.06.519279, ver. 2 peer-reviewed and recommended by Peer Community In Microbiology. https://doi.org/10.1101/2022.12.06.519279

Host-microbe symbioses are an essential component of many ecological systems, playing critical roles in the physiology and evolution of all involved partners. In this context, the bacterial family that includes Coxiella burnetii, the causative agent of Q fever, is of particular interest. The Coxiellaceae family is a complex group with members that have adopted a variety of specializations. Closely related lineages to C. burnetii are tick mutualists (Coxiella-like endosymbionts) and aquatic bacteria that may include both free living and symbiotic species. Additionally, four related genera within this family include symbionts of insects and amoebae. Exactly how and when pathogenicity and mutualism evolved in this lineage is not clear, thus remaining a valuable line of enquiry that can help establish general principles on these lifestyle transitions.

A new study by Santos-Garcia and colleagues (2023) places the spotlight on this bacterial group, obtaining new insights through comparative genomics. The authors add two genomes, one of them a circular contig representing a highly reduced (0.9 Mb) chromosome, that increase the resolution of key branches in the Coxiella evolutionary tree. These include a sister group to C. burnetii and the group immediately subtending them, both entirely containing Coxiella-like endosymbionts. By analyzing genetic potential for metabolism, cell dimorphism, virulence and acidophily, the authors find evidence for the ancestrality of genes associated with a pathogenic lifestyle, and support a scenario by which mutualism arose multiple times in a parasitic lineage. In this context shines a pathogenicity island acquired in the common ancestor of this group and subsequently eroded in mutualistic lineages. This scenario highlights the importance of pre-adaptations that facilitate evolutionary specializations, such as the capabilities for B vitamin biosynthesis (key feature in the adaptation to a mutualistic relationship with organisms with B-vitamin-poor diets) and pH homeostasis (harnessed by C. burnetii for infection). 

Microbial groups at the crossroads of parasitism and mutualism help us understand the mechanisms underpinning these evolutionary strategies (see e.g. Drew et al, 2021). Transitions in endosymbiosis, including shifts in the parasitism-mutualism continuum, adaptation to new partners, or switches between free-living and host-associated lifestyles, affect the structure of ecological networks, and understanding them can yield crucial insights into how to manipulate microbial symbioses for health outcomes, sustainable agriculture or ecosystem conservation. The Coxiellaceae, by including a diverse set of mutualistic, parasitic and possibly free-living lineages, are a fantastic model group to tackle these questions. Together with other host-associated bacteria, such as Sodalis (Clayton et al, 2012) or Pantoea (Walterson and Stavrinides, 2015) species, these ecologically diverse microbes are valuable assets in the quest to decipher the molecular basis of lifestyle transitions in endosymbiosis.

REFERENCES

Clayton, A.L., et al (2012). A novel human-infection-derived bacterium provides insights into the evolutionary origins of mutualistic insect–bacterial symbioses. PLoS Genetics, 8: e1002990. https://doi.org/10.1371/journal.pgen.1002990

Drew, G.C., Stevens, E.J., King, K.C. (2021). Microbial evolution and transitions along the parasite-mutualist continuum. Nature Reviews Microbiology, 19: 623-638. https://doi.org/10.1038/s41579-021-00550-7

Santos-Garcia, D., et al. (2023) Genomic changes during the evolution of the Coxiella genus along the parasitism-mutualism continuum. bioRxiv, 2022.10.26.513839, ver. 4 peer-reviewed and recommended by Peer Community In Microbiology. https://doi.org/10.1101/2022.10.26.513839

Walterson, A.M., Stavrinides, J. (2015). Pantoea: insights into a highly versatile and diverse genus within the Enterobacteriaceae. FEMS Microbiology Reviews, 39: 968-984. https://doi.org/10.1093/femsre/fuv027

Plant pathogens can cause devastating damage to crop (Strange and Scott 2005) greatly affecting a food resource in growing need on our planet. A significant proportion of global crops require irrigation, and with this, bare the risk of being affected by irrigation-borne pathogens (Lamichhane and Bartoli, 2015). Detection of plant pathogens in irrigation water can effectively be used to minimize this risk. River water makes up a major irrigation water source. Morris et al., (2023), propose monitoring whole river catchments to understand plant pathogen population dynamics and generate models to prevent outbreaks, similar to practices regarding water-borne human pathogens.

Monitoring 270 km of the river Durance, Morris et al., (2023) reveal that two groups of bacteria known to host pathogenic strains, Pseudomonas syringae and the Soft Rot Pectobacteriaceae are present in relatively high numbers across the entire catchment or significant parts of it, respectively, with their abundance mostly correlated to water temperature. Nevertheless, despite their presence no major outbreaks have been reported in recent years. The authors suggest that the current environmental conditions in the lower, agriculture-dominated part of the catchment may not generate the necessary environment for an outbreak. Alternatively, as also suggested, though some potentially pathogenic variants were detected in the study, they may not match the crops currently grown in the area (Morris et al., 2023).

The authors thus bring up the need for large scale monitoring and call for observations on potential land-use changes in the area that may alter the sensitive and seemingly stable conditions in such a way that outbreaks will be triggered. Change of land use, specifically from rural to agricultural use, has been repeatedly recognized to influence biodiversity (e.g., Ionescu et al., 2022). Furthermore, agricultural environments, with a dense network of irrigation channels, natural and man-made ponds, and larger reservoirs, will accelerate the spread of organisms through multiple biotic and abiotic vectors (Karnatak and Wollrab, 2020), and with this likely plant- (and other) pathogens. Overall, the work by Morris et al., (2023) highlights that studying the presence and distribution of plant pathogens in water used for irrigation across large areas, is bound to identify which potential pathogens are omnipresent, awaiting for the right condition for an outbreak; and which are rather spread from, isolated, local sources and thus can be effectively mitigated.

References

Strange, R. N., and Scott, P. R. (2005). Plant disease: a threat to global food security. Annu. Rev. Phytopathol. 43, 83–116. https://doi.org/10.1146/annurev.phyto.43.113004.133839

Lamichhane, J.R. and Bartoli, C. (2015), Plant pathogenic bacteria in open irrigation systems: what risk for crop health? Plant Pathol, 64: 757-766. https://doi.org/10.1111/ppa.12371

C.E. Morris, C. Lacroix, C. Chandeysson, C. Guilbaud, C. Monteil, S. Piry, Rochelle Newall E., S. Fiorini, F. Van Gijsegem, M.A. Barny, O. Berge (2023) Comparative abundance and diversity of populations of the Pseudomonas syringae and Soft Rot Pectobacteriaceae species complexes throughout the Durance River catchment from its French Alps sources to its delta. bioRxiv, 2022.09.06.506731, ver. 3 peer-reviewed and recommended by Peer Community in Microbiology. https://doi.org/10.1101/2022.09.06.506731 

Ionescu, D., Bizic, M., Karnatak, R., Musseau, C. L., Onandia, G., Kasada, M., Berger, S. A., et al. (2022). From Microbes to Mammals: Pond Biodiversity Homogenization across Different Land-Use Types in an Agricultural Landscape. Ecological Monographs 92(3): e1523. https://doi.org/10.1002/ecm.1523