Invasions of Host-Associated Microbiome Networks

Impact of epizootics on mussel farms: Insights into microbiota composition of Mytilus species

Outbreaks of marine mussel mortality on French farms could have different aetiologies. One of them implies Vibrio splendidus strains. Beyond the involvement of this pathogen, there is considerable evidence that diseases often result from interactions between several microbes and the host. In this study, we explored the bacterial communities associated with mussel species and the surrounding water collected from a mussel farm affected by mortalities. The microbiota of Mytilus edulis, Mytilus galloprovincialis and their hybrids displayed an abnormal abundance of Proteobacteria, in particular the genera Vibrio, Cobetia and Arcobacter. Despite the dysbiosis, the Mediterranean mussel showed a different microbiota profile with a higher richness and presence of the phylum Bacteroidetes. Bipartite network analyses at the level of bacteria families confirmed this finding and showed that the microbiomes of M. edulis and the hybrids tended to cluster together. In addition, injection of mussels with the virulent V. splendidus induced less mortality rate in M. galloprovincialis compared to the other Mytilus sp. suggesting a better resistance of the Mediterranean mussel to infection. Our findings point to a probable aetiology of pathobiome-mediated disease in mussels. To fully understand this phenomenon, more knowledge is needed on the roles of pathobiotic systems and their development during disease establishment.

Tuning Expectations to Reality: Don't Expect Increased Gut Microbiota Diversity with Dietary Fiber

Dietary approaches, particularly those including fiber supplementation, can be used to promote health benefits by shaping gut microbial communities. Whereas community diversity measures, such as richness and evenness, are often used in microbial ecology to make sense of these complex and vast microbial ecosystems, it is less clear how these concepts apply when dietary fiber supplementation is given. In this perspective, we summarize and demonstrate how factors including experimental approach, number of bacteria sharing a dietary fiber, and initial relative abundances of bacteria that use a fiber can significantly affect diversity outcomes in fiber fermentation studies. We also show that a reduction in alpha diversity is possible, and perhaps expected, for most approaches that use fermentable fibers to beneficially shape the gut microbial community while still achieving health-related improvements.

Network structural origin of instabilities in large complex systems

A central issue in the study of large complex network systems, such as power grids, financial networks, and ecological systems, is to understand their response to dynamical perturbations. Recent studies recognize that many real networks show nonnormality and that nonnormality can give rise to reactivity-the capacity of a linearly stable system to amplify its response to perturbations, oftentimes exciting nonlinear instabilities. Here, we identify network structural properties underlying the pervasiveness of nonnormality and reactivity in real directed networks, which we establish using the most extensive dataset of such networks studied in this context to date. The identified properties are imbalances between incoming and outgoing network links and paths at each node. On the basis of this characterization, we develop a theory that quantitatively predicts nonnormality and reactivity and explains the observed pervasiveness. We suggest that these results can be used to design, upgrade, control, and manage networks to avoid or promote network instabilities.

Probiotics in Fish Nutrition—Long-Standing Household Remedy or Native Nutraceuticals?

Over the last decades, aquaculture production increased rapidly. The future development of the industry highly relies on the sustainable utilization of natural resources. The need for improving disease resistance, growth performance, food conversion, and product safety for human consumption has stimulated the application of probiotics in aquaculture. Probiotics increase growth and feed conversion, improve health status, raise disease resistance, decrease stress susceptibility, and improve general vigor. Currently, most probiotics still originate from terrestrial sources rather than fish. However, host-associated (autochthonous) probiotics are likely more persistent in the gastrointestinal tract of fish and may, therefore, exhibit longer-lasting effects on the host. Probiotic candidates are commonly screened in in vitro assays, but the transfer to in vivo assessment is often problematic. In conclusion, modulation of the host-associated microbiome by the use of complex probiotics is promising, but a solid understanding of the interactions involved is only in its infancy and requires further research. Probiotics could be used to explore novel ingredients such as chitin-rich insect meal, which cannot be digested by the fish host alone. Most importantly, probiotics offer the opportunity to improve stress and disease resistance, which is among the most pressing problems in aquaculture.

Microbial networks inferred from environmental DNA data for biomonitoring ecosystem change: Strengths and pitfalls

Environmental DNA contains information on the species interaction networks that support ecosystem functions and services. Next-generation biomonitoring proposes the use of this data to reconstruct ecological networks in real time and then compute network-level properties to assess ecosystem change. We investigated the relevance of this proposal by assessing: (i) the replicability of DNA-based networks in the absence of ecosystem change, and (ii) the benefits and shortcomings of community- and network-level properties for monitoring change. We selected crop-associated microbial networks as a case study because they support disease regulation services in agroecosystems and analysed their response to change in agricultural practice between organic and conventional systems. Using two statistical methods of network inference, we showed that network-level properties, especially β-properties, could detect change. Moreover, consensus networks revealed robust signals of interactions between the most abundant species, which differed between agricultural systems. These findings complemented those obtained with community-level data that showed, in particular, a greater microbial diversity in the organic system. The limitations of network-level data included (i) the very high variability of network replicates within each system; (ii) the low number of network replicates per system, due to the large number of samples needed to build each network; and (iii) the difficulty in interpreting links of inferred networks. Tools and frameworks developed over the last decade to infer and compare microbial networks are therefore relevant to biomonitoring, provided that the DNA metabarcoding data sets are large enough to build many network replicates and progress is made to increase network replicability and interpretation.

Diet and Genotype of an Aquatic Invertebrate Affect the Composition of Free-Living Microbial Communities

In spite of the growing interest in the role of the gut microbiome (GM) in host physiology and health, the mechanisms governing its assembly and its effects on the environment are poorly understood. In this article, we show that the host genotype and the GM of Daphnia influence the community structure of the surrounding bacterioplankton (BPK). When Daphnia genotypes were placed in an identical environment, both the GM and BPK showed a genotype and diet-dependent taxonomic composition. Overall, the GM strongly differed from the BPK in taxonomic composition and was characterized by a lower α-diversity, suggesting a selective rejecting of bacteria from the regional species pool. In a microbiome transplant experiment, the assembly of both the GM and BPK was strongly affected by the host genotype and the inoculum to which germ-free Daphnia were exposed. The combination of these results suggests a strong interaction between the host genotype, its GM and free-living microbial communities. Currently, it is generally assumed that an animal’s diet has a strong effect on the animal’s GM, but only a negligible (if any) effect on the surrounding environment. However, our results indicate that the diet/microbiome inocula have a small effect on the gut community and a large effect on the community in the surrounding environment. This structuring genotype × microbiome × environment effect is an essential prerequisite that could indicate that microbiomes play an important role in eco-evolutionary processes.

Protective Microbiota: From Localized to Long-Reaching Co-Immunity

Resident microbiota do not just shape host immunity, they can also contribute to host protection against pathogens and infectious diseases. Previous reviews of the protective roles of the microbiota have focused exclusively on colonization resistance localized within a microenvironment. This review shows that the protection against pathogens also involves the mitigation of pathogenic impact without eliminating the pathogens (i.e., “disease tolerance”) and the containment of microorganisms to prevent pathogenic spread. Protective microorganisms can have an impact beyond their niche, interfering with the entry, establishment, growth, and spread of pathogenic microorganisms. More fundamentally, we propose a series of conceptual clarifications in support of the idea of a “co-immunity,” where an organism is protected by both its own immune system and components of its microbiota.