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Latest recommendations
Id | Title * | Authors * | Abstract * ▼ | Picture * | Thematic fields * | Recommender | Reviewers | Submission date | |
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29 Aug 2023
Comparison of metabarcoding taxonomic markers to describe fungal communities in fermented foodsOlivier Rué, Monika Coton, Eric Dugat-Bony, Kate Howell, Françoise Irlinger, Jean-Luc Legras, Valentin Loux, Elisa Michel, Jérôme Mounier, Cécile Neuvéglise, Delphine Sicard https://doi.org/10.1101/2023.01.13.523754Towards a more accurate metabarcoding approach for studying fungal communities of fermented foodsRecommended by Caroline Strub based on reviews by Johannes Schweichhart and 2 anonymous reviewersImproved characterization of food microbial ecosystems, especially those fermented is key to the development of food sustainability. Short-read metabarcoding is one of the most popular ways to study microbial communities. However, this approach remains complex because of the locks and biases it may entail particularly when applied to fungal communities. Building and using four mock communities from fermented food (bread, wine, cheese, fermented meat), Rué et al., 2023 demonstrate that combined DADA2 denoising algorithm followed to the FROGS tools gives a more accurate description of fungal communities compared to several commonly used bioinformatic workflows, dealing with all amplicon lengths. Moreover, Rué et al., 2023 provide guidance on which barcode to use (ITS1, ITS2, D1/D2 and RPB2), depending on the fermented food studied. Practices in metabarcoding of fungi have been recently reviewed by Tedersoo et al., 2022 and their synthesis comes to the same conclusion as Rué et al., 2023. As the reference databases are far from being complete notably for food ecosystems, the development of specific sequences public databases will enable the scientific community to lift the veil on this whole area of microbial ecology. The study conducted by Rué et al. (2023) provides a particularly detailed approach from a technical point of view, which contributes to improving the general practices in the metabarcoding of fungi. The design and the use of mock communities to compare the performances of the different pipelines is a strong point of this study. Another key element is the creation and use of an in-house database of fungal barcode sequences which improved the species-level affiliations However, the study of fungal communities by metabarcoding is still a promising avenue of research in agri-food sciences. Thus, short-read sequencing, combined with suitable pipelines and databases, should remain of interest to the microbial ecology community (Pauvert et al., 2019; Furneaux et al., 2021). References Furneaux, B., Bahram, M., Rosling, A., Yorou, N. S., & Ryberg, M. (2021). Long‐and short‐read metabarcoding technologies reveal similar spatiotemporal structures in fungal communities. Molecular Ecology Resources, 21(6), 1833-1849. https://doi.org/10.1111/1755-0998.13387 Pauvert, C., Buée, M., Laval, V., Edel-Hermann, V., Fauchery, L., Gautier, A., ... & Vacher, C. (2019). Bioinformatics matters: The accuracy of plant and soil fungal community data is highly dependent on the metabarcoding pipeline. Fungal Ecology, 41, 23-33. https://doi.org/10.1016/j.funeco.2019.03.005 Rué, O., Coton, M., Dugat-Bony, E., Howell, K., Irlinger, F., Legras, J. L., ... & Sicard, D. (2023). Comparison of metabarcoding taxonomic markers to describe fungal communities in fermented foods. BioRxiv, 2023-0113.523754, ver.3 peer-reviewed and recommended by Peer Community in Microbiology. https://doi.org/10.1101/2023.01.13.523754 Tedersoo, L., Bahram, M., Zinger, L., Nilsson, R. H., Kennedy, P. G., Yang, T., ... & Mikryukov, V. (2022). Best practices in metabarcoding of fungi: From experimental design to results. Molecular ecology, 31(10), 2769-2795. https://doi.org/10.1111/mec.16460 | Comparison of metabarcoding taxonomic markers to describe fungal communities in fermented foods | Olivier Rué, Monika Coton, Eric Dugat-Bony, Kate Howell, Françoise Irlinger, Jean-Luc Legras, Valentin Loux, Elisa Michel, Jérôme Mounier, Cécile Neuvéglise, Delphine Sicard | <p>Next generation sequencing offers several ways to study microbial communities. For agri-food sciences, identifying species in diverse food ecosystems is key for both food sustainability and food security. The aim of this study was to compare me... | Bioinformatics dedicated to microbial studies | Caroline Strub | 2023-01-20 12:37:03 | View | ||
04 Jan 2024
Diversity of bacterial symbionts associated with the tropical plant bug Monalonion velezangeli (Hemiptera: Miridae) revealed by high-throughput 16S-rRNA sequencingLucio Navarro-Escalante, Pablo Benavides, Flor Edith Acevedo https://doi.org/10.21203/rs.3.rs-2022560/v7Shedding light on bacteria associated with an agricultural pest, the tropical plant bug Monalonion velezangeli: a foundational descriptive studyRecommended by Jean-Marie Volland based on reviews by 2 anonymous reviewersThe paper "Diversity of bacterial symbionts associated with the tropical plant bug Monalonion velezangeli (Hemiptera: Miridae) revealed by high-throughput 16S rRNA sequencing" by Navarro-Escalante et al. (2023) is a valuable contribution to entomological research, particularly in the context of pest management. This descriptive study, while not delving into the functional characterization of the associated bacterial strains, lays an essential groundwork for understanding the bacterial components of the microbiota of this agricultural pest. This study is interesting because it provides new information on insect microbiota, especially in a family for which the knowledge of the diversity of bacterial symbionts is very limited. One of the study's core strengths lies in its exploration and definition of the core microbiota of M. velezangeli, which could serve as a foundation for future research aimed at pest control strategies. The use of 16S rRNA sequencing, despite its known limitations, has enabled the profiling of these bacterial communities. The paper highlights the absence of differences in the bacterial communities associated with the nymph and adult stages of the pest, indicating a stable association of these microbes throughout the insect's life cycle. A standout point in the study is the overwhelming presence of the symbiont Wolbachia, accounting for approximately 92% of the bacterial composition. However, intriguingly, the authors also note the absence of Wolbachia in some individuals, suggesting a more complex dynamic that warrants further investigation. This finding is particularly noteworthy, as it opens up questions about the role of Wolbachia and its impact on the biology and ecology of M. velezangeli. The researchers have carefully addressed all the reviewers’ comments and suggestions. They also addressed a potential bias in their study - the overwhelming presence of Wolbachia - by analyzing the bacterial community after the removal of Wolbachia sequences. This careful approach enriches the study's credibility and ensures a more accurate representation of the pest's microbiota. The identification of potentially culturable strains within the core microbiome represents an interesting perspective of this research. This information could be used in future efforts to develop pest control strategies, particularly those employing paratransgenic approaches. The possibility of manipulating these culturable strains to combat M. velezangeli presents an exciting avenue for sustainable pest management. While the study does not investigate the localization of these associated bacteria, whether in the gut or elsewhere, including potentially in dedicated symbiotic organs, it nevertheless offers a valuable descriptive account. This baseline knowledge will be useful for any subsequent functional or localization studies, which could further unravel the complex interactions between M. velezangeli and its microbial partners. In conclusion, the work of Navarro-Escalante et al. is a notable effort to set the stage for future research into the biology of M. velezangeli and its associated microbiota. The findings from this study provide a good reference point for further investigations aimed at pest's biology and exploring innovative pest control strategies. It also represents a valuable contribution to understanding the basic biology of insect-bacteria interactions.
| Diversity of bacterial symbionts associated with the tropical plant bug *Monalonion velezangeli* (Hemiptera: Miridae) revealed by high-throughput 16S-rRNA sequencing | Lucio Navarro-Escalante, Pablo Benavides, Flor Edith Acevedo | <p>Insects and microbes have developed complex symbiotic relationships that evolutionarily and ecologically play beneficial roles for both, the symbiont and the host. In most Hemiptera insects, bacterial symbionts offer mainly nutritional, defensi... | Microbial ecology and environmental microbiology, Microbial symbiosis | Jean-Marie Volland | 2022-10-31 20:31:54 | View | ||
29 May 2024
The bacterial microbiome of symbiotic and menthol-bleached polyps of long-term aquarium-reared Galaxea fascicularisGiulia Puntin, Jane C.Y. Wong, Till Roethig, David M. Baker, Michael Sweet, Maren Ziegler https://doi.org/10.1101/2023.08.23.554380An important step forward in deciphering coral symbiosis through manipulative approachesRecommended by Yui Sato based on reviews by Tony Robinet and 1 anonymous reviewerAs complex multipartite interactions among the coral host and coral-associated microbial entities including the dinoflagellate symbionts, bacteria, archaea and viruses, have been appreciated, a manipulatable, less-complex study system is desired to deepen our functional understanding of this fascinating symbiotic system. Among experimental manipulation approaches, removal of the algal symbionts using menthol is widely implemented; however, its effect on the rest of the coral-associated symbiotic members has not been explored, which is critical knowledge to assess experimental works using this popular method. This preprint by Puntin et al. (https://doi.org/10.1101/2023.08.23.554380) presents an important observation in this aspect. Their initial observations suggest that menthol-induced coral bleaching introduces stochastic changes in associated bacterial communities, which resemble dysbiosis, making bacterial communities more dissimilar from each other. They also observed low taxonomic diversity in bacterial communities on the corals maintained in aquaria over several months, worth noting as a positive value as an experimental system. Their data are preliminary by nature, while they present intriguing ideas that warrant further studies. Reference Puntin G, Wong JCY, Röthig T, Baker DM, Sweet M, Ziegler M (2024). The bacterial microbiome of symbiotic and menthol-bleached polyps of long-term aquarium-reared Galaxea fascicularis (2024). bioRxiv, ver.4., peer-reviewed and recommended by Peer Community In Microbiology. https://doi.org/10.1101/2023.08.23.554380
| The bacterial microbiome of symbiotic and menthol-bleached polyps of long-term aquarium-reared *Galaxea fascicularis* | Giulia Puntin, Jane C.Y. Wong, Till Roethig, David M. Baker, Michael Sweet, Maren Ziegler | <p>Coral reefs support the livelihood of half a billion people but are at high risk of collapse due to the vulnerability of corals to climate change and local anthropogenic stressors. While understanding coral functioning is essential to guide con... | Microbial symbiosis, Microbiomes | Yui Sato | 2023-08-26 04:50:01 | View | ||
02 Mar 2023
Comparative genomics and transcriptomic response to root exudates of six rice root-associated Burkholderia sensu lato speciesAdrian Wallner, Agnieszka Klonowska, Ludivine Guigard, Isabelle Rimbault, Eddy LM Ngonkeu, Phuong V Nguyen, Gilles Bena, Lionel Moulin https://doi.org/10.1101/2022.10.04.510755Burkholderia strains go it aloneRecommended by Romain Barnard based on reviews by Vittorio Venturi and 1 anonymous reviewerThe Burkholderia sensu lato group is predominant in the rhizosphere of rice. It includes both plant growth promoting rhizobacteria (typically members of the Paraburkholderia genus) and phytopathogens (typically members of the Burkholderia genus). Better understanding the interaction between Burkholderia sensu lato and their host plant is therefore crucial to advance our knowledge of the ecology of rice, a plant that feeds more than half of the humans on the planet. The perception of root exudates from their host is key for rhizobacteria. Is the response to root exudates more related to the phylogeny of the bacteria, i.e. genus-dependent, or is it strain-specific? This question is not trivial for the Burkholderia sensu lato group, which has experienced shifting outlines over the last twenty years. During the early stages of rice root colonization, Wallner et al. [1] investigated the transcriptomic regulation of three strains of each Burkholderia and Paraburkholderia genera, in addition to a genomic comparison, in order to better understand their early colonization strategies. While these six strains possess a large proportion of gene homologues, their experiment shows their response to root exudates to be strain-specific. In the study, rice root exudates affected several metabolic pathways of interest in most strains, noticeably including i) the Entner-Doudoroff pathway, which had never been reported to be activated in relation to root colonization and ii) the putrescine pathway, which may reflect signaling controlling root colonization. The work by Wallner et al. provides new insights on the strain-level response of the transcriptomic regulation of Burkholderia sensu lato in response to root exudates in the early stages of root colonization. Beyond this, the next steps will hopefully shed light on what happens in more complex environments, within a complex bacterial community and during later colonization stages.
Reference Wallner A, Klonowska A, Guigard L, King E, Rimbault I, Ngonkeu E, Nguyen P, Béna G, Moulin L (2022) Comparative genomics and transcriptomic response to root exudates of six rice root-associated Burkholderia sensu lato species. BioRxiv, 2022.10.04.510755, version 2 peer-reviewed and recommended by PCI Microbiol. https://doi.org/10.1101/2022.10.04.510755 | Comparative genomics and transcriptomic response to root exudates of six rice root-associated Burkholderia sensu lato species | Adrian Wallner, Agnieszka Klonowska, Ludivine Guigard, Isabelle Rimbault, Eddy LM Ngonkeu, Phuong V Nguyen, Gilles Bena, Lionel Moulin | <p>Beyond being a reliable nutrient provider, some bacteria will perceive the plant as a potential host and undertake root colonization leading to mutualistic or parasitic interactions. Bacteria of the <em>Burkholderia</em> and <em>Paraburkholderi... | Microbe-microbe and microbe-host interactions, Microbial symbiosis | Romain Barnard | Kateryna Zhalnina , Trent Northern , Oscar Kuipers , Cara Haney , Joëlle Schläpfer , Vittorio Venturi, Anonymous, Steffen Kolb, Paulina Estrada-de los Santos | 2022-10-06 09:48:59 | View |
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