In fed aquaculture, fishes are commonly fed with a fish-oil based diet mostly coming from captured fishes. This is one main global issue leading to overfishing of wild species (Cashion et al., 2017; Tacon & Metian, 2008). Several alternatives in lipid sources for fish diet have been tested and promising alternatives such as plants (e.g. rapeseed oil) or microalgae (e.g. Schizochytrium sp.) have been identified (Pérez-Pascual et al., 2020). Like other animals, fishes’ digestive tract is composed of a microbiota whose composition is linked to the host physiological state as well as its diet (Yukgehnaish et al., 2020). In reared fishes such as the European sea bass (Dicentrarchus labrax), replacing fish oil by other sources such as microalgae in their diet has been shown to modify the digestive microbiota composition (Pérez-Pascual et al., 2020).

Here, the aim of Katsoulis-Dimitriou et al. (2024), was to test the effect of three dietary microalgae blends on the midgut microbiota composition of the reared fishes. The authors compared the effect of a control diet (i.e. with only fish oil as lipid source, namely, FO) with that of three experimental diets with two thirds of the fish oil replaced by either a mixture of the microalgae Microchloropsis gaditana and Isochrysis sp. (now known as Tisochrysis lutea, MI), Phaeodactylum tricornutum and Isochrysis sp. (PI) or Schizochytrium sp. and P. tricornutum (SP). For each diet, 25 fishes were reared in each of the triplicated tanks and, after 80 days of experiment, a total of 10 fishes per diet were sampled. DNA was extracted from the midgut part of the intestine and a 16S rDNA-based metabarcoding approach was conducted to survey the associated bacterial community. Each diet type, FO, MI, PI and SP, was mostly characterized by a composition of specific abundant OTUs, indicating the clear influence of the oil composition on the digestive microbiota. When feeding with the MI diet, the authors also highlighted the presence of some candidate genera (e.g. Pseudoalteromonas, Pseudomonas, Bacillus and Rhodopseudomonas) as potential probiotics for fish aquaculture. Finally, in comparison to the fish oil diet, a predictive metabolic analysis of the bacterial community could suggest a differential expression of some polysaccharide metabolisms with the microalgae-based diets, highlighting a probable diet-based effect on the microbiota functioning.

The work from Katsoulis-Dimitriou et al. (2024) completes the current knowledge on using sustainable alternatives to traditional fish feed and its effect on the digestive microbiota composition of fishes. This work also opens new ways to be explored considering the enrichment of potential probiotics using microalgae-base diets. Further analyses testing specific functional approaches (e.g. transcriptomics, metabolomics) may allow completing the understanding of the gut microbiota functioning linked to diet composition. Finally, measurements on fish biometrics in a similar experiment should help understanding the contribution of a microalgal-diet to fish fitness.

References

Cashion, T., Le Manach, F., Zeller, D., & Pauly, D. (2017). Most fish destined for fishmeal production are food‐grade fish. Fish and Fisheries, 18(5), 837–844. https://doi.org/10.1111/faf.12209

Katsoulis-Dimitriou, S., Nikouli, E., Gkalogianni, E., Karapanagiotidis, I., Kormas, K. (2024) The effect of dietary fish oil replacement by microalgae on the gilthead sea bream midgut bacterial microbiota. BioRxiv, ver.3 peer-reviewed and recommended by PCI Microbiol https://doi.org/10.1101/2024.01.24.576938

Pérez-Pascual, D., Estellé, J., Dutto, G., Rodde, C., Bernardet, J.-F., Marchand, Y., Duchaud, E., Przybyla, C., & Ghigo, J.-M. (2020). Growth Performance and Adaptability of European Sea Bass (Dicentrarchus labrax) Gut Microbiota to Alternative Diets Free of Fish Products. Microorganisms, 8(9), 1346. https://doi.org/10.3390/microorganisms8091346

Tacon, A. G. J., & Metian, M. (2008). Global overview on the use of fish meal and fish oil in industrially compounded aquafeeds: Trends and future prospects. Aquaculture, 285(1–4), 146–158. https://doi.org/10.1016/j.aquaculture.2008.08.015

Yukgehnaish, K., Kumar, P., Sivachandran, P., Marimuthu, K., Arshad, A., Paray, B. A., & Arockiaraj, J. (2020). Gut microbiota metagenomics in aquaculture: Factors influencing gut microbiome and its physiological role in fish. Reviews in Aquaculture, 12(3), 1903–1927. https://doi.org/10.1111/raq.12416

Improved 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

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

The 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. 

Reference

Navarro-Escalante​ L., Benavides​ P. and Acevedo​, F.E. (2023) Diversity of bacterial symbionts associated with the tropical plant bug Monalonion velezangeli (Hemiptera: Miridae) revealed by high-throughput 16S-rRNA sequencing. Research Square​, ver. 7 peer-reviewed and recommended by PCI Microbiology. https://doi.org/10.21203/rs.3.rs-2022560/v7​

The issue of whether there is a clear and detectable relationship -either deterministic or stochastic- of fish gut microbiota with evolutionary processes is far from being resolved. Studies on fish microbiota are more perplexed as this animal group includes species both from wild and farmed populations (for food production, ornamental fish and animal models), with variable life cycles and ecophysiologies, and all these features expand the type of interactions to be studied. Based on this biological features variability, multiple methodological limitations, especially for the species with wild populations, are perhaps among of the central reasons for this knowledge gap. Therefore, experimental approaches, which can eliminate some of this variability, seem to be the best approach.

The preprint by Evangelista et al. (2023) entitled "Within-species variation in the gut microbiome of medaka (Oryzias latipes) is driven by the interaction of light intensity and genetic background" is an example of such a targeted study with a freshwater fish species. Due to the paper's finely detailed experimental design, the interdisciplinary skills of the participating co-authors and exhaustive data analysis, this paper manages to draw solid and reproducible results and conclusions. This renders it not only an insightful contribution towards the more general host-microbe interactions in an evolutionary framework, but also a perfect example on how current and future relevant research should be conducted. I feel confident that this paper will assist other scientits of the field to move forward with their current working hypotheses but also to generate novel ones.

Reference :

Evangelista C, Kamenova S, Diaz Pauli B, Sandkjenn J, Vollestad A, Edeline E, Trosvik P, de Muinck E (2023) Within-species variation in the gut microbiome of medaka (Oryzias latipes) is driven by the interaction of light intensity and genetic background. bioRxiv, 2023.02.17.528956, ver. 2 peer-reviewed and recommended by Peer Community in Microbiology. https://doi.org/10.1101/2023.02.17.528956