@article {pmid39852521,
year = {2025},
author = {De Domenico, S and Toso, A and De Rinaldis, G and Mammone, M and Fumarola, LM and Piraino, S and Leone, A},
title = {Wild or Reared? Cassiopea andromeda Jellyfish as a Potential Biofactory.},
journal = {Marine drugs},
volume = {23},
number = {1},
pages = {},
doi = {10.3390/md23010019},
pmid = {39852521},
issn = {1660-3397},
support = {No. 774499 - GoJelly_ Research and Innovation Program project//European Union/ ; Practice code AFD9B120, project idea UNISAL119//Apulian Region program "REFIN-Research for Innovation"/ ; n.3138-"National Biodiversity Future Center-NBFC", Project code CN_00000033, Concession Decree No. 1034 of 17 June 2022,NextGenerationEU, Italian National Recovery and Resilience Plan (NRRP)//European Union/ ; },
mesh = {Animals ; *Scyphozoa/chemistry ; *Antioxidants/chemistry/pharmacology ; Mediterranean Sea ; Dinoflagellida/chemistry ; },
abstract = {The zooxanthellate jellyfish Cassiopea andromeda (Forsskål, 1775), a Lessepsian species increasingly common in the western and central Mediterranean Sea, was investigated here to assess its potential as a source of bioactive compounds from medusa specimens both collected in the wild (the harbor of Palermo, NW Sicily) and reared under laboratory-controlled conditions. A standardized extraction protocol was used to analyze the biochemical composition of the two sampled populations in terms of protein, lipid, and pigment contents, as well as for their relative concentrations of dinoflagellate symbionts. The total extracts and their fractions were also biochemically characterized and analyzed for their in vitro antioxidant activity to quantify differences in functional compounds between wild and reared jellyfish. The two populations were similar in terms of extract yield, but with substantial differences in biomass, the number of zooxanthellae, protein and lipid contents, and fatty acid composition. The hydroalcoholic extracts obtained from jellyfish grown under controlled conditions showed greater antioxidant activity due to the presence of a higher content of bioactive compounds compared to wild jellyfish. This study could be the basis for considering the sustainable breeding of this holobiont or other similar organisms as a source of valuable compounds that can be used in the food, nutraceutical, or pharmaceutical sectors.},
}

Animals
*Scyphozoa/chemistry
*Antioxidants/chemistry/pharmacology
Mediterranean Sea
Dinoflagellida/chemistry

@article {pmid39844957,
year = {2025},
author = {Martins, V and Abdallah, C and Teixeira, A and Moreira, C and Nóbrega, M and Lanoue, A and Gerós, H},
title = {Subregional pedoclimatic conditions with contrasted UV-radiation shape host-microbiome and metabolome phenotypes in the grape berry.},
journal = {Food chemistry: X},
volume = {25},
number = {},
pages = {102139},
pmid = {39844957},
issn = {2590-1575},
abstract = {This study used integrative omics to address the response of key elements of the grapevine holobiont to contrasted pedoclimatic conditions found in distinct subregions of Douro Valley (Portugal). A metabolic OPLS-DA model predicted with 100 % accuracy the geographic origin of berries; higher UV radiation, higher temperature and lower precipitation stimulated the accumulation of phenolic acids, flavonols and malvidin conjugates, in detriment of amino acids, organic acids, flavan-3-ols, proanthocyanidins and non-malvidin anthocyanins. Metabarcoding showed a trade-off between bacteria and fungal diversity among subregions, with Pseudomonas, Lactobacillus, Aspergillus and Penicillium acting as intraregional microbial markers. The high phenotypic plasticity of berries and the role of microbes in this process are relevant upon current projections for increased UV radiation and temperature in Southern European viticulture, in a climate change scenario, with predicted impacts on regional wine quality and on the development of adaptation strategies for resilient viticulture.},
}

@article {pmid39844274,
year = {2025},
author = {Camper, BT and Kanes, AS and Laughlin, ZT and Manuel, RT and Bewick, SA},
title = {Transgressive hybrids as hopeful holobionts.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {19},
pmid = {39844274},
issn = {2049-2618},
mesh = {*Hybridization, Genetic ; *Symbiosis ; *Microbiota ; Animals ; Biological Evolution ; Bacteria/genetics/classification ; },
abstract = {BACKGROUND: Hybridization between evolutionary lineages has profound impacts on the fitness and ecology of hybrid progeny. In extreme cases, the effects of hybridization can transcend ecological timescales by introducing trait novelty upon which evolution can act. Indeed, hybridization can even have macroevolutionary consequences, for example, as a driver of adaptive radiations and evolutionary innovations. Accordingly, hybridization is now recognized as a motor for macrobial evolution. By contrast, there has been substantially less progress made towards understanding the positive eco-evolutionary consequences of hybridization on holobionts. Rather, the emerging paradigm in holobiont literature is that hybridization disrupts symbiosis between a host lineage and its microbiome, leaving hybrids at a fitness deficit. These conclusions, however, have been drawn based on results from predominantly low-fitness hybrid organisms. Studying "dead-end" hybrids all but guarantees finding that hybridization is detrimental. This is the pitfall that Dobzhansky fell into over 80 years ago when he used hybrid sterility and inviability to conclude that hybridization hinders evolution. Goldschmidt, however, argued that rare saltational successes-so-called hopeful monsters-disproportionately drive positive evolutionary outcomes. Goldschmidt's view is now becoming a widely accepted explanation for the prevalence of historical hybridization in extant macrobial lineages. Aligning holobiont research with this broader evolutionary perspective requires recognizing the importance of similar patterns in host-microbiome systems. That is, rare and successful "hopeful holobionts" (i.e., hopeful monsters at the holobiont scale) might be disproportionately responsible for holobiont evolution. If true, then it is these successful systems that we should be studying to assess impacts of hybridization on the macroevolutionary trajectories of host-microbiome symbioses.

RESULTS: In this paper, we explore the effects of hybridization on the gut (cloacal) and skin microbiota in an ecologically successful hybrid lizard, Aspidoscelis neomexicanus. Specifically, we test the hypothesis that hybrid lizards have host-associated (HA) microbiota traits strongly differentiated from their progenitor species. Across numerous hybrid microbiota phenotypes, we find widespread evidence of transgressive segregation. Further, microbiota restructuring broadly correlates with niche restructuring during hybridization. This suggests a relationship between HA microbiota traits and ecological success.

CONCLUSION: Transgressive segregation of HA microbiota traits is not only limited to hybrids at a fitness deficit but also occurs in ecologically successful hybrids. This suggests that hybridization may be a mechanism for generating novel and potentially beneficial holobiont phenotypes. Supporting such a conclusion, the correlations that we find between hybrid microbiota and the hybrid niche indicate that hybridization might change host microbiota in ways that promote a shift or an expansion in host niche space. If true, hybrid microbiota restructuring may underly ecological release from progenitors. This, in turn, could drive evolutionary diversification. Using our system as an example, we elaborate on the evolutionary implications of host hybridization within the context of holobiont theory and then outline the next steps for understanding the role of hybridization in holobiont research. Video Abstract.},
}

*Hybridization, Genetic
*Symbiosis
*Microbiota
Animals
Biological Evolution
Bacteria/genetics/classification

@article {pmid39838803,
year = {2025},
author = {Chan, WY and Sakamoto, R and Doering, T and Narayana, VK and De Souza, DP and McConville, MJ and van Oppen, MJH},
title = {Heat-Evolved Microalgae (Symbiodiniaceae) Are Stable Symbionts and Influence Thermal Tolerance of the Sea Anemone Exaiptasia diaphana.},
journal = {Environmental microbiology},
volume = {27},
number = {1},
pages = {e70011},
doi = {10.1111/1462-2920.70011},
pmid = {39838803},
issn = {1462-2920},
support = {DE240100317//Australian Research Council/ ; FL180100036//Australian Research Council/ ; APP1154540//National Health and Medical Research Council/ ; //Westpac Research Fellowship/ ; },
mesh = {*Sea Anemones/physiology ; *Symbiosis ; Animals ; *Thermotolerance ; *Hot Temperature ; Microalgae/metabolism ; Dinoflagellida/physiology ; },
abstract = {Symbiotic cnidarians, such as sea anemones and corals, rely on their mutualistic microalgal partners (Symbiodiniaceae) for survival. Marine heatwaves can disrupt this partnership, and it has been proposed that introducing experimentally evolved, heat-tolerant algal symbionts could enhance host thermotolerance. To test this hypothesis, the sea anemone Exaiptasia diaphana (a coral model) was inoculated with either the heterologous wild type or heat-evolved algal symbiont, Cladocopium proliferum, and homologous wild-type Breviolum minutum. The novel symbioses persisted for 1.5 years and determined holobiont thermotolerance during a simulated summer heatwave. Anemones hosting SS8, one of the six heat-evolved strains tested, exhibited the highest thermotolerance. Notably, anemones hosting the wild-type C. proliferum (WT10) were the second most thermally tolerant group, whereas anemones hosting the heat-evolved SS5 or SS9 strains were among the most thermosensitive. Elevated temperatures led to an increase in the levels of many amino acids and a decrease in tricarboxylic acid (TCA) metabolites in all anemone hosts, potentially indicating an increase in autophagy and a reduction in energy and storage production. Some consistent differences were observed in changes in metabolite levels between anemone groups in response to elevated temperature, suggesting that the algal symbiont influenced host metabolome and nutritional budget.},
}

*Sea Anemones/physiology
*Symbiosis
Animals
*Thermotolerance
*Hot Temperature
Microalgae/metabolism
Dinoflagellida/physiology

@article {pmid39832281,
year = {2025},
author = {Middelboe, M and Traving, SJ and Castillo, D and Kalatzis, PG and Glud, RN},
title = {Prophage-encoded chitinase gene supports growth of its bacterial host isolated from deep-sea sediments.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf004},
pmid = {39832281},
issn = {1751-7370},
abstract = {Auxiliary metabolic genes encoded by bacteriophages can influence host metabolic function during infection. In temperate phages, auxiliary metabolic genes may increase host fitness when integrated as prophages into the host genome. However, little is known about the contribution of prophage-encoded auxiliary metabolic genes to host metabolic properties. In this study, we examined a temperate bacteriophage, and its piezotolerant Pseudomonas sp. host obtained from sediment samples collected from the Kermadec Trench at ~10 000 m water depth. Both the phage and host were present throughout the sediment profiles from the surface to 30 cm into the sediment, covering large gradients of environmental conditions. The host and phage each carried one chitinase gene, which differed from each other, suggesting that chitin degradation plays a role in their substrate supply. We demonstrated that prophage-encoded chitinase supported host chitin degradation and growth in the presence of chitin. Furthermore, prophage induction dynamics were strongly substrate-dependent, suggesting that the host controls the lysis-lysogeny switch in response to the presence of chitin, thus optimizing the trade-off between the loss of cells from prophage induction and prophage enhancement of host performance. Overall, the results demonstrate prophage-encoded auxiliary metabolic genes as collaborative goods for their hosts and emphasize the potential role of phage-host interactions in benthic biogeochemical cycling, as well as for the capability of deep-sea bacteria to efficiently adapt and thrive at a wide range of environmental conditions.},
}

@article {pmid39827902,
year = {2025},
author = {Brown, TM and Dunn, AM and Quinnell, RJ and Clarke, E and Cunningham, AA and Goodman, SJ},
title = {An interdisciplinary approach to improving conservation outcomes for parasites.},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
volume = {},
number = {},
pages = {e14431},
doi = {10.1111/cobi.14431},
pmid = {39827902},
issn = {1523-1739},
support = {//The Leverhulme Trust/ ; },
abstract = {Parasites represent a significant proportion of Earth's biodiversity and play important roles in the ecology and biology of ecosystems and hosts, making them an important target for conservation. Despite increasing calls to prioritize protection for parasites in the academic literature, they remain undervalued and underrepresented in global biodiversity conservation efforts, not least due to the perception that the interests of parasite and host conservation are opposing and the common misconception that parasites are a threat, rather than a benefit, to conservation. We considered whether taking an interdisciplinary approach to parasite conservation research will generate novel insights and solutions concerning why and how parasite conservation should be practiced for the benefit of parasites, their hosts, ecosystems, and people. We argue that 2 of the main barriers to more widespread parasite conservation are the knowledge gap concerning the role of sociocultural factors affecting the willingness to enact parasite conservation and the lack of a consistent and cohesive philosophical basis for parasite conservation. Possible sociocultural barriers to parasite conservation include misconceptions of the risks posed by parasites, taxonomic bias, differences in conservation values, economic constraints, and technical challenges. The use of social science can generate insights into levels of awareness and support for parasite conservation and improve understanding of how human values and attitudes mediate conservation practices concerning parasites. Such knowledge will have a critical role in addressing sociocultural barriers and improving support for parasite conservation. Issues with the current philosophical basis for parasite conservation include contradictory accounts of which parasites merit conservation, insufficient explanation of how different conservation values apply to parasite biodiversity, and the existence of a false antagonism between host and parasite conservation. Greater engagement with philosophical work on environmental ethics and biological unitization will strengthen existing arguments for parasite conservation and will support conservation decision-making processes.},
}

@article {pmid39827366,
year = {2025},
author = {Liu, HJ and Liu, J and Zhai, Z and Dai, M and Tian, F and Wu, Y and Tang, J and Lu, Y and Wang, H and Jackson, D and Yang, X and Qin, F and Xu, M and Fernie, AR and Zhang, Z and Yan, J},
title = {Maize2035: A decadal vision for intelligent maize breeding.},
journal = {Molecular plant},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.molp.2025.01.012},
pmid = {39827366},
issn = {1752-9867},
abstract = {Maize, a cornerstone of global food security, has undergone remarkable transformations through breeding, yet it faces mounting challenges in a changing world. In this review, we trace the historical successes of maize breeding which laid the foundation for present opportunities. We examine both the specific and shared breeding goals related to diverse geographies and end-use demands. Achieving these coordinated breeding objectives requires a holistic approach to trait improvement for sustainable agriculture. We discuss cutting-edge solutions, including multi-omics approaches from single-cell analysis to holobionts, smart breeding with advanced technologies and algorithms, and the transformative potential of rational design with synthetic biology. A transition towards a data-driven future is currently underway, with large-scale precision agriculture and autonomous systems poised to revolutionize farming practice. Realizing these futuristic opportunities hinges on collaborative efforts spanning scientific discoveries, technology translations, and socioeconomic considerations in maximizing human and environmental well-being.},
}

@article {pmid39823339,
year = {2025},
author = {van der Loos, LM and Steinhagen, S and Stock, W and Weinberger, F and D'hondt, S and Willems, A and De Clerck, O},
title = {Low functional change despite high taxonomic turnover characterizes the Ulva microbiome across a 2000-km salinity gradient.},
journal = {Science advances},
volume = {11},
number = {3},
pages = {eadr6070},
doi = {10.1126/sciadv.adr6070},
pmid = {39823339},
issn = {2375-2548},
mesh = {*Ulva/genetics ; *Salinity ; *Microbiota ; Bacteria/genetics/classification/metabolism ; Metagenome ; Metagenomics/methods ; },
abstract = {The green seaweed Ulva relies on associated bacteria for morphogenesis and is an important model to study algal-bacterial interactions. Ulva-associated bacteria exhibit high turnover across environmental gradients, leading to the hypothesis that bacteria contribute to the acclimation potential of the host. However, the functional variation of these bacteria in relation to environmental changes remains unclear. We analyzed 91 Ulva samples across a 2000-kilometer Atlantic-Baltic Sea salinity gradient using metagenomic sequencing. Metabolic reconstruction of 639 metagenome-assembled genomes revealed widespread potential for carbon, nitrogen, sulfur, and vitamin metabolism. Although the R[2] value for salinity explained 70% of taxonomic variation, it accounted only for 17% of functional variation. The limited variation was attributed to typical high-salinity bacteria exhibiting enrichment in genes for thiamine, pyridoxal, and betaine biosynthesis, which likely contribute to stress mitigation and osmotic homeostasis in response to salinity variations. Our results emphasize the importance of functional profiling to understand the seaweed holobiont and its collective response to environmental change.},
}

*Ulva/genetics
*Salinity
*Microbiota
Bacteria/genetics/classification/metabolism
Metagenome
Metagenomics/methods

@article {pmid39823335,
year = {2025},
author = {Santoro, EP and Cárdenas, A and Villela, HDM and Vilela, CLS and Ghizelini, AM and Duarte, GAS and Perna, G and Saraiva, JP and Thomas, T and Voolstra, CR and Peixoto, RS},
title = {Inherent differential microbial assemblages and functions associated with corals exhibiting different thermal phenotypes.},
journal = {Science advances},
volume = {11},
number = {3},
pages = {eadq2583},
doi = {10.1126/sciadv.adq2583},
pmid = {39823335},
issn = {2375-2548},
mesh = {*Anthozoa/microbiology/metabolism/physiology ; Animals ; *Microbiota ; *Phenotype ; Symbiosis ; Metagenomics/methods ; Bacteria/metabolism/genetics ; },
abstract = {Certain coral individuals exhibit enhanced resistance to thermal bleaching, yet the specific microbial assemblages and their roles in these phenotypes remain unclear. We compared the microbial communities of thermal bleaching-resistant (TBR) and thermal bleaching-sensitive (TBS) corals using metabarcoding and metagenomics. Our multidomain approach revealed stable distinct microbial compositions between thermal phenotypes. Notably, TBR corals were inherently enriched with microbial eukaryotes, particularly Symbiodiniaceae, linked to photosynthesis, and the biosynthesis of antibiotic and antitumor compounds and glycosylphosphatidylinositol-anchor proteins, crucial for cell wall regulation and metabolite exchange. In contrast, TBS corals were dominated by bacterial metabolic genes related to nitrogen, amino acid, and lipid metabolism. The inherent microbiome differences between TBR and TBS corals, already observed before thermal stress, point to distinct holobiont phenotypes associated to thermal bleaching resistance, offering insights into mechanisms underlying coral response to climate-induced stress.},
}

*Anthozoa/microbiology/metabolism/physiology
Animals
*Microbiota
*Phenotype
Symbiosis
Metagenomics/methods
Bacteria/metabolism/genetics

@article {pmid39822124,
year = {2025},
author = {Doonan, JM and Budde, KB and Kosawang, C and Lobo, A and Verbylaite, R and Brealey, JC and Martin, MD and Pliura, A and Thomas, K and Konrad, H and Seegmüller, S and Liziniewicz, M and Cleary, M and Nemesio-Gorriz, M and Fussi, B and Kirisits, T and Gilbert, MTP and Heuertz, M and Kjær, ED and Nielsen, LR},
title = {Multiple, Single Trait GWAS and Supervised Machine Learning Reveal the Genetic Architecture of Fraxinus excelsior Tolerance to Ash Dieback in Europe.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.15361},
pmid = {39822124},
issn = {1365-3040},
support = {//This research was supported by the Independent Research Fund Denmark (DFF|Technology and Production Sciences) under the grant no. 8022-00355B. Field work in Austria was supported by BML DaFNE grant no. 101476 ("Esche in Not-Phase II") funded by the Austrian Federal Ministry of Agriculture, Forestry, Regions and Water Management, the Austrian Chamber of Agriculture, the governments of all Austrian provinces, the Forest Office and Urban Agriculture (MA 49) of the Vienna City Administration and "Österreichischer Forstverein"; as well as by BML DaFNE grant no. 101684 ("Waldfonds" project "AshBack") funded by the Austrian Federal Ministry of Agriculture, Forestry, Regions and Water Management. The establishment of the German trial site "Chiemsee" was supported by the Bavarian Ministry under the projects KLIP1 and ST272. J.C.B. was funded by the European Union's Horizon 2020 Action grant 8177291009 "HoloFood"./ ; },
abstract = {Common ash (Fraxinus excelsior) is under intensive attack from the invasive alien pathogenic fungus Hymenoscyphus fraxineus, causing ash dieback at epidemic levels throughout Europe. Previous studies have found significant genetic variation among genotypes in ash dieback susceptibility and that host phenology, such as autumn yellowing, is correlated with susceptibility of ash trees to H. fraxineus; however, the genomic basis of ash dieback tolerance in F. excelsior requires further investigation. Here, we integrate quantitative genetics based on multiple replicates and genome-wide association analyses with machine learning to reveal the genetic architecture of ash dieback tolerance and of phenological traits in F. excelsior populations in six European countries (Austria, Denmark, Germany, Ireland, Lithuania, Sweden). Based on phenotypic data of 486 F. excelsior replicated genotypes we observed negative genotypic correlations between crown damage caused by ash dieback and intensity of autumn leaf yellowing within multiple sampling sites. Our results suggest that the examined traits are polygenic and using genomic prediction models, with ranked single nucleotide polymorphisms (SNPs) based on GWAS associations as input, a large proportion of the variation was predicted by unlinked SNPs. Based on 100 unlinked SNPs, we can predict 55% of the variation in disease tolerance among genotypes (as phenotyped in genetic trials), increasing to a maximum of 63% when predicted from 9155 SNPs. In autumn leaf yellowing, 52% of variation is predicted by 100 unlinked SNPs, reaching a peak of 72% using 3740 SNPs. Based on feature permutations within genomic prediction models, a total of eight nonsynonymous SNPs linked to ash dieback crown damage and autumn leaf yellowing (three and five SNPs, respectively) were identified, these were located within genes related to plant defence (pattern triggered immunity, pathogen detection) and phenology (regulation of flowering and seed maturation, auxin transport). We did not find an overlap between genes associated with crown damage level and autumn leaf yellowing. Hence, our results shed light on the difference in the genomic basis of ADB tolerance and autumn leaf yellowing despite these two traits being correlated in quantitative genetic analysis. Overall, our methods show the applicability of genomic prediction models when combined with GWAS to reveal the genomic architecture of polygenic disease tolerance enabling the identification of ash dieback tolerant trees for breeding or conservation purposes.},
}

@article {pmid39116436,
year = {2025},
author = {Voolstra, CR and Alderdice, R and Colin, L and Staab, S and Apprill, A and Raina, JB},
title = {Standardized Methods to Assess the Impacts of Thermal Stress on Coral Reef Marine Life.},
journal = {Annual review of marine science},
volume = {17},
number = {1},
pages = {193-226},
doi = {10.1146/annurev-marine-032223-024511},
pmid = {39116436},
issn = {1941-0611},
mesh = {*Coral Reefs ; Animals ; *Climate Change ; *Anthozoa/physiology ; Hot Temperature ; Stress, Physiological ; Oceans and Seas ; Environmental Monitoring/methods ; },
abstract = {The Earth's oceans have absorbed more than 90% of the excess, climate change-induced atmospheric heat. The resulting rise in oceanic temperatures affects all species and can lead to the collapse of marine ecosystems, including coral reefs. Here, we review the range of methods used to measure thermal stress impacts on reef-building corals, highlighting current standardization practices and necessary refinements to fast-track discoveries and improve interstudy comparisons. We also present technological developments that will undoubtedly enhance our ability to record and analyze standardized data. Although we use corals as an example, the methods described are widely employed in marine sciences, and our recommendations therefore apply to all species and ecosystems. Enhancing collaborative data collection efforts, implementing field-wide standardized protocols, and ensuring data availability through dedicated, openly accessible databases will enable large-scale analysis and monitoring of ecosystem changes, improving our predictive capacities and informing active intervention to mitigate climate change effects on marine life.},
}

*Coral Reefs
Animals
*Climate Change
*Anthozoa/physiology
Hot Temperature
Stress, Physiological
Oceans and Seas
Environmental Monitoring/methods

@article {pmid39816161,
year = {2025},
author = {Parreira, BR and Gopalakrishnan, S and Chikhi, L},
title = {Effects of Social Structure on Effective Population Size Change Estimates.},
journal = {Evolutionary applications},
volume = {18},
number = {1},
pages = {e70063},
pmid = {39816161},
issn = {1752-4571},
abstract = {Most methods currently used to infer the "demographic history of species" interpret this expression as a history of population size changes. The detection, quantification, and dating of demographic changes often rely on the assumption that population structure can be neglected. However, most vertebrates are typically organized in populations subdivided into social groups that are usually ignored in the interpretation of genetic data. This could be problematic since an increasing number of studies have shown that population structure can generate spurious signatures of population size change. Here, we simulate microsatellite data from a species subdivided into social groups where reproduction occurs according to different mating systems (monogamy, polygynandry, and polygyny). We estimate the effective population size (N e) and quantify the effect of social structure on estimates of changes in N e. We analyze the simulated data with two widely used methods for demographic inference. The first approach, BOTTLENECK, tests whether the samples are at mutation-drift equilibrium and thus whether a single N e can be estimated. The second approach, msvar, aims at quantifying and dating changes in N e. We find that social structure may lead to signals of departure from mutation-drift equilibrium including signals of expansion and bottlenecks. We also find that expansion signals may be observed under simple stationary Wright-Fisher models with low diversity. Since small populations tend to characterize many endangered species, we stress that methods trying to infer N e should be interpreted with care and validated with simulated data incorporating information about structure. Spurious expansion signals due to social structure can mask critical population size changes. These can obscure true bottleneck events and be particularly problematic in endangered species.},
}

@article {pmid39813343,
year = {2025},
author = {Aichelman, HE and Benson, BE and Gomez-Campo, K and Martinez-Rugerio, MI and Fifer, JE and Tsang, L and Hughes, AM and Bove, CB and Nieves, OC and Pereslete, AM and Stanizzi, D and Kriefall, NG and Baumann, JH and Rippe, JP and Gondola, P and Castillo, KD and Davies, SW},
title = {Cryptic coral diversity is associated with symbioses, physiology, and response to thermal challenge.},
journal = {Science advances},
volume = {11},
number = {3},
pages = {eadr5237},
doi = {10.1126/sciadv.adr5237},
pmid = {39813343},
issn = {2375-2548},
mesh = {*Symbiosis ; *Anthozoa/physiology ; Animals ; *Coral Reefs ; Climate Change ; Biodiversity ; Temperature ; Phylogeny ; },
abstract = {Coral persistence in the Anthropocene depends on interactions among holobiont partners (coral animals and microbial symbionts) and their environment. Cryptic coral lineages-genetically distinct yet morphologically similar groups-are critically important as they often exhibit functional diversity relevant to thermal tolerance. In addition, environmental parameters such as thermal variability may promote tolerance, but how variability interacts with holobiont partners to shape responses to thermal challenge remains unclear. Here, we identified three cryptic lineages of Siderastrea siderea in Bocas del Toro, Panamá that differ in distributions across inshore and offshore reefs, microbial associations, phenotypic traits of holobiont partners (i.e., phenomes), and skeleton morphologies. A thermal variability experiment failed to increase thermal tolerance, but subsequent thermal challenge and recovery revealed that one lineage maintained elevated energetic reserves, photochemical efficiency, and growth. Last, coral cores highlighted that this lineage also exhibited greater growth historically. Functional variation among cryptic lineages highlights their importance in predicting coral reef responses to climate change.},
}

*Symbiosis
*Anthozoa/physiology
Animals
*Coral Reefs
Climate Change
Biodiversity
Temperature
Phylogeny

@article {pmid39812892,
year = {2025},
author = {Kerlin, JR and Barnas, DM and Silbiger, NJ},
title = {Conspecific interactions between corals mediate the effect of submarine groundwater discharge on coral physiology.},
journal = {Oecologia},
volume = {207},
number = {1},
pages = {21},
pmid = {39812892},
issn = {1432-1939},
support = {1924281//Division of Ocean Sciences/ ; 1637396//Division of Ocean Sciences/ ; },
mesh = {Animals ; *Anthozoa/physiology ; *Symbiosis ; *Groundwater ; Photosynthesis ; Coral Reefs ; Chlorophyll A ; Ecosystem ; },
abstract = {Land-based inputs, such as runoff, rivers, and submarine groundwater, can alter biologic processes on coral reefs. While the abiotic factors associated with land-based inputs have strong effects on corals, corals are also affected by biotic interactions, including other neighboring corals. The biologic responses of corals to changing environmental conditions and their neighbors are likely interactive; however, few studies address both biotic and abiotic interactions in concert. In a manipulative field experiment, we tested how the natural environmental gradient created by submarine groundwater discharge (SGD) affected holobiont and symbiont metabolic rates and endosymbiont physiology of Porites rus. We further tested how the effect of SGD on the coral was mediated by intra and interspecific interactions. SGD is a natural land-sea connection that delivers nutrients, inorganic carbon, and other solutes to coastal ecosystems worldwide. Our results show that a natural gradient of nutrient enrichment and pH variability as a result of acute SGD exposure generally benefited P. rus, increasing gross photosynthesis, respiration, endosymbiont densities, and chlorophyll a content. Conspecifics in direct contact with the a neighboring coral, however, altered the relationship between coral physiology and SGD, lowering the photosynthetic and respiration rates from expected values when the coral had no neighbor. We show that the response of corals to environmental change is dependent on the types of nearby neighbor corals and how neighbors alter the chemical or physical environment around the coral. Our study underscores the importance of considering biotic interactions when predicting the physiologic responses of corals to the environment.},
}

Animals
*Anthozoa/physiology
*Symbiosis
*Groundwater
Photosynthesis
Coral Reefs
Chlorophyll A
Ecosystem

@article {pmid39810029,
year = {2025},
author = {de Freitas Neto, LL and Santos, RFB and da Silva, MA and de Souza Bezerra, R and Saldanha-Corrêa, F and Espósito, BP},
title = {Zinc speciation promotes distinct effects on dinoflagellate growth and coral trypsin-like enzyme activity.},
journal = {Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine},
volume = {},
number = {},
pages = {},
pmid = {39810029},
issn = {1572-8773},
support = {2021/07153-3//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2021/10894-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 372742/2022-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
abstract = {Zinc is an essential metal to living organisms, including corals and their symbiotic microalgae (Symbiodiniaceae). Both Zn(II) deprivation and overload are capable of leading to dysfunctional metabolism, coral bleaching, and even organism death. The present work investigated the effects of chemically defined Zn species (free Zn, ZnO nanoparticles, and the complexes Zn-histidinate and Zn-EDTA) over the growth of the dinoflagellates Symbiodinium microadriaticum, Breviolum minutum, and Effrenium voratum, and on the trypsin-like proteolytic activity of the hydrocoral Millepora alcicornis. B. minutum was the most sensitive strain to any form of added Zn. For the other strains, the complex [Zn(His)2] better translated metal load into growth. This complex was the only tested compound that did not interfere with the trypsin-like activity of Millepora alcicornis extracts. Also, histidine was able to recover the activity of the enzyme inhibited by zinc. [Zn(His)2] is a potential biocarrier of zinc for microalgae or coral cultivation. These findings suggest that the control of chemical speciation of an essential metal could lead to useful compounds that assist autotrophy, while not affecting heterotrophy, in the coral holobiont.},
}

@article {pmid39799372,
year = {2025},
author = {Perez, V and Boulo, V and De Lorgeril, J and Pham, D and Ansquer, D and Plougoulen, G and Ballan, V and Lam, JS and Romatif, O and Le Luyer, J and Falchetto, C and Basset, C and Flohr, S and Maamaatuaiahutapu, M and Lafille, MA and Lau, C and Saulnier, D and Wabete, N and Callac, N},
title = {Hemolymph microbiota and immune effectors' expressions driven by geographical rearing acclimation of the aquacultured Penaeus stylirostris.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {5},
pmid = {39799372},
issn = {2524-4671},
abstract = {BACKGROUND: In holobiont, microbiota is known to play a central role on the health and immunity of its host. Then, understanding the microbiota, its dynamic according to the environmental conditions and its link to the immunity would help to react to potential dysbiosis of aquacultured species. While the gut microbiota is highly studied, in marine invertebrates the hemolymph microbiota is often set aside even if it remains an important actor of the hemolymph homeostasis. Indeed, the hemolymph harbors the factors involved in the animal homeostasis that interacts with the microbiota, the immunity. In the Southwest Pacific, the high economical valued shrimp Penaeus stylirostris is reared in two contrasted sites, in New Caledonia (NC) and in French Polynesia (FP).

RESULTS: We characterized the active microbiota inhabiting the hemolymph of shrimps while considering its stability during two seasons and at a one-month interval and evidenced an important microbial variability between the shrimps according to the rearing conditions and the sites. We highlighted specific biomarkers along with a common core microbiota composed of 6 ASVs. Putative microbial functions were mostly associated with bacterial competition, infections and metabolism in NC, while they were highly associated with the cell metabolism in FP suggesting a rearing site discrimination. Differential relative expression of immune effectors measured in the hemolymph of two shrimp populations from NC and FP, exhibited higher level of expression in NC compared to FP. In addition, differential relative expression of immune effectors was correlated to bacterial biomarkers based on their geographical location.

CONCLUSIONS: Our data suggest that, in Pacific shrimps, both the microbiota and the expression of the immune effectors could have undergone differential immunostimulation according to the rearing site as well as a geographical adaptative divergence of the shrimps as an holobiont, to their rearing sites. Further, the identification of proxies such as the core microbiota and site biomarkers, could be used to guide future actions to monitor the bacterial microbiota and thus preserve the productions.},
}

@article {pmid39797569,
year = {2025},
author = {Rogers, AB and Kale, V and Baldi, G and Alberdi, A and Gilbert, MTP and Gupta, D and Limborg, MT and Li, S and Payne, T and Petersen, B and Rasmussen, JA and Richardson, L and Finn, RD},
title = {HoloFood Data Portal: holo-omic datasets for analysing host-microbiota interactions in animal production.},
journal = {Database : the journal of biological databases and curation},
volume = {2025},
number = {},
pages = {},
doi = {10.1093/database/baae112},
pmid = {39797569},
issn = {1758-0463},
mesh = {Animals ; *Chickens/microbiology ; Host Microbial Interactions/genetics ; Salmon/microbiology ; Microbiota ; Databases, Genetic ; Gastrointestinal Microbiome ; },
abstract = {The HoloFood project used a hologenomic approach to understand the impact of host-microbiota interactions on salmon and chicken production by analysing multiomic data, phenotypic characteristics, and associated metadata in response to novel feeds. The project's raw data, derived analyses, and metadata are deposited in public, open archives (BioSamples, European Nucleotide Archive, MetaboLights, and MGnify), so making use of these diverse data types may require access to multiple resources. This is especially complex where analysis pipelines produce derived outputs such as functional profiles or genome catalogues. The HoloFood Data Portal is a web resource that simplifies access to the project datasets. For example, users can conveniently access multiomic datasets derived from the same individual or retrieve host phenotypic data with a linked gut microbiome sample. Project-specific metagenome-assembled genome and viral catalogues are also provided, linking to broader datasets in MGnify. The portal stores only data necessary to provide these relationships, with possible linking to the underlying repositories. The portal showcases a model approach for how future multiomics datasets can be made available. Database URL: https://www.holofooddata.org.},
}

Animals
*Chickens/microbiology
Host Microbial Interactions/genetics
Salmon/microbiology
Microbiota
Databases, Genetic
Gastrointestinal Microbiome

@article {pmid39769364,
year = {2024},
author = {Grzyb, T and Szulc, J},
title = {Deciphering Molecular Mechanisms and Diversity of Plant Holobiont Bacteria: Microhabitats, Community Ecology, and Nutrient Acquisition.},
journal = {International journal of molecular sciences},
volume = {25},
number = {24},
pages = {},
doi = {10.3390/ijms252413601},
pmid = {39769364},
issn = {1422-0067},
mesh = {*Microbiota ; *Bacteria/genetics/classification/metabolism ; *Plants/microbiology ; Biodiversity ; Ecosystem ; Phosphorus/metabolism ; Nitrogen/metabolism ; Symbiosis ; Nutrients/metabolism ; },
abstract = {While gaining increasing attention, plant-microbiome-environment interactions remain insufficiently understood, with many aspects still underexplored. This article explores bacterial biodiversity across plant compartments, including underexplored niches such as seeds and flowers. Furthermore, this study provides a systematic dataset on the taxonomic structure of the anthosphere microbiome, one of the most underexplored plant niches. This review examines ecological processes driving microbial community assembly and interactions, along with the discussion on mechanisms and diversity aspects of processes concerning the acquisition of nitrogen, phosphorus, potassium, and iron-elements essential in both molecular and ecological contexts. These insights are crucial for advancing molecular biology, microbial ecology, environmental studies, biogeochemistry, and applied studies. Moreover, the authors present the compilation of molecular markers for discussed processes, which will find application in (phylo)genetics, various (meta)omic approaches, strain screening, and monitoring. Such a review can be a valuable source of information for specialists in the fields concerned and for applied researchers, contributing to developments in sustainable agriculture, environmental protection, and conservation biology.},
}

*Microbiota
*Bacteria/genetics/classification/metabolism
*Plants/microbiology
Biodiversity
Ecosystem
Phosphorus/metabolism
Nitrogen/metabolism
Symbiosis
Nutrients/metabolism

@article {pmid39762949,
year = {2025},
author = {Ferreira, C and Burgsdorf, I and Perez, T and Ramírez, G and Lalzar, M and Huchon, D and Steindler, L},
title = {Comparative genomics analyses of Actinobacteriota identify Golgi phosphoprotein 3 (GPP34) as a widespread ancient protein family associated with sponge symbiosis.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {4},
pmid = {39762949},
issn = {2049-2618},
support = {GBMF9352//Gordon and Betty Moore Foundation/ ; 933/23//Israel Science Foundation/ ; },
abstract = {BACKGROUND: Sponges harbor microbial communities that play crucial roles in host health and ecology. However, the genetic adaptations that enable these symbiotic microorganisms to thrive within the sponge environment are still being elucidated. To understand these genetic adaptations, we conducted a comparative genomics analysis on 350 genomes of Actinobacteriota, a phylum commonly associated with sponges.

RESULTS: Our analysis uncovered several differences between symbiotic and free-living bacteria, including an increased abundance of genes encoding prokaryotic defense systems (PDSs) and eukaryotic-like proteins (ELPs) in symbionts. Furthermore, we identified GPP34 as a novel symbiosis-related gene family, found in two symbiotic Actinobacteriota clades, but not in their closely related free-living relatives. Analyses of a broader set of microbes showed that members of the GPP34 family are also found in sponge symbionts across 16 additional bacterial phyla. While GPP34 proteins were thought to be restricted to eukaryotes, our phylogenetic analysis shows that the GPP34 domain is found in all three domains of life, suggesting its ancient origin. We also show that the GPP34 family includes genes with two main structures: a short form that includes only the GPP34 domain and a long form that encompasses a GPP34 domain coupled with a cytochrome P450 domain, which is exclusive to sponge symbiotic bacteria.

CONCLUSIONS: Given previous studies showing that GPP34 is a phosphatidylinositol-4-phosphate (PI4P)-binding protein in eukaryotes and that other PI4P-binding proteins from bacterial pathogens can interfere with phagolysosome maturation, we propose that symbionts employ GPP34 to modulate phagocytosis to colonize and persist within sponge hosts. Video Abstract.},
}

@article {pmid39750118,
year = {2025},
author = {Butdee, W and Saimee, Y and Suriyachadkun, C and Duangmal, K},
title = {Pseudonocardia spirodelae sp. nov., isolated from duckweed and formal proposal to reclassify Pseudonocardia antarctica as a later heterotypic synonym of Pseudonocardia alni and reclassify Pseudonocardia carboxydivorans as Pseudonocardia alni subsp. carboxydivorans.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {75},
number = {1},
pages = {},
doi = {10.1099/ijsem.0.006608},
pmid = {39750118},
issn = {1466-5034},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Phylogeny ; *Nucleic Acid Hybridization ; *Vitamin K 2/analogs & derivatives/analysis ; *Fatty Acids/chemistry ; *Sequence Analysis, DNA ; *DNA, Bacterial/genetics ; *Bacterial Typing Techniques ; *Araceae/microbiology ; Base Composition ; Phospholipids ; },
abstract = {A novel Pseudonocardia strain DW16-2[T], isolated from duckweed (Spirodela polyrhiza), was taxonomically studied in detail. The analysis based on its 16S rRNA gene sequence revealed that the strain was most closely related to Pseudonocardia carboxydivorans Y8[T] (98.8%), followed by Pseudonocardia tropica YIM 61452[T] (98.7%), Pseudonocardia antarctica DVS 5a1[T] (98.7%) and Pseudonocardia alni DSM 44104[T] (98.7%). The average nucleotide identity (ANI) based on blast and digital DNA-DNA hybridization (dDDH) relatedness values between strain DW16-2[T] and their closest type strains were below the threshold values for identifying a novel species. Morphological, physiological and chemotaxonomic features of strain DW16-2[T] were typical for the genus Pseudonocardia by forming extensively branched substrate mycelium and aerial mycelium that fragmented into rod-shaped spore, with a smooth surface. The whole-cell hydrolysates of strain DW16-2[T] contained meso-diaminopimelic acid as the diagnostic diamino acid, and the whole-cell sugars were arabinose, galactose, glucose and a trace amount of ribose. The polar lipids contained phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol and unidentified phospholipids. The menaquinone (MK) was MK-8(H4). The cellular fatty acids (>5 %) were iso-C16 : 0, iso-C16 : 1 H, summed feature 3: C16 : 1 ω7c/C16 : 1 ω6c; C16 : 1 ω6c/C16 : 1 ω7c, C17 : 1 ω8c and anteiso-C17 : 0. Characterization based on chemotaxonomic, phenotypic, genotypic and phylogenetic evidence demonstrated that strain DW16-2[T] represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia spirodelae sp. nov. (type strain DW16-2[T] = TBRC 16418[T] = NBRC 115857[T]) is proprosed. In addition, the comparison of the whole genome sequences suggested that P. alni and P. antarctica belong to the same species and P. carboxydivorans is a subspecies of P. alni. Therefore, it is proposed that P. antarctica Prabahar et al. 2004 is reclassified as a later heterotypic synonym of P. alni (Evtushenko et al. 1989) Warwick et al. 1994, and P. carboxydivorans Park et al. 2008 is proposed as a subspecies of P. alni (Evtushenko et al. 1989) Warwick et al. 1994.},
}

*RNA, Ribosomal, 16S/genetics
*Phylogeny
*Nucleic Acid Hybridization
*Vitamin K 2/analogs & derivatives/analysis
*Fatty Acids/chemistry
*Sequence Analysis, DNA
*DNA, Bacterial/genetics
*Bacterial Typing Techniques
*Araceae/microbiology
Base Composition
Phospholipids

@article {pmid39748821,
year = {2024},
author = {Senizza, B and Araniti, F and Lewin, S and Wende, S and Kolb, S and Lucini, L},
title = {A multi-omics approach to unravel the interaction between heat and drought stress in the Arabidopsis thaliana holobiont.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1484251},
pmid = {39748821},
issn = {1664-462X},
abstract = {The impact of combined heat and drought stress was investigated in Arabidopsis thaliana and compared to individual stresses to reveal additive effects and interactions. A combination of plant metabolomics and root and rhizosphere bacterial metabarcoding were used to unravel effects at the plant holobiont level. Hierarchical cluster analysis of metabolomics signatures pointed out two main clusters, one including heat and combined heat and drought, and the second cluster that included the control and drought treatments. Overall, phenylpropanoids and nitrogen-containing compounds, hormones and amino acids showed the highest discriminant potential. A decrease in alpha-diversity of Bacteria was observed upon stress, with stress-dependent differences in bacterial microbiota composition. The shift in beta-diversity highlighted the pivotal enrichment of Proteobacteria, including Rhizobiales, Enterobacteriales and Azospirillales. The results corroborate the concept of stress interaction, where the combined heat and drought stress is not the mere combination of the single stresses. Intriguingly, multi-omics interpretations evidenced a good correlation between root metabolomics and root bacterial microbiota, indicating an orchestrated modulation of the whole holobiont.},
}

@article {pmid39738126,
year = {2024},
author = {Zhang, S and Song, W and Marinos, G and Waschina, S and Zimmermann, J and Kaleta, C and Thomas, T},
title = {Genome-scale metabolic modelling reveals interactions and key roles of symbiont clades in a sponge holobiont.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {10858},
pmid = {39738126},
issn = {2041-1723},
mesh = {*Symbiosis ; *Porifera/microbiology/metabolism ; Animals ; *Microbiota/genetics ; *Metabolic Networks and Pathways/genetics ; Bacteria/metabolism/genetics/classification ; Phylogeny ; Genome ; Genome, Bacterial ; Models, Biological ; Metagenomics/methods ; },
abstract = {Sponges harbour complex microbiomes and as ancient metazoans and important ecosystem players are emerging as powerful models to understand the evolution and ecology of symbiotic interactions. Metagenomic studies have previously described the functional features of sponge symbionts, however, little is known about the metabolic interactions and processes that occur under different environmental conditions. To address this issue, we construct here constraint-based, genome-scale metabolic networks for the microbiome of the sponge Stylissa sp. Our models define the importance of sponge-derived nutrients for microbiome stability and discover how different organic inputs can result in net heterotrophy or autotrophy of the symbiont community. The analysis further reveals the key role that a newly discovered bacterial taxon has in cross-feeding activities and how it dynamically adjusts with nutrient inputs. Our study reveals insights into the functioning of a sponge microbiome and provides a framework to further explore and define metabolic interactions in holobionts.},
}

*Symbiosis
*Porifera/microbiology/metabolism
Animals
*Microbiota/genetics
*Metabolic Networks and Pathways/genetics
Bacteria/metabolism/genetics/classification
Phylogeny
Genome
Genome, Bacterial
Models, Biological
Metagenomics/methods

@article {pmid39735181,
year = {2024},
author = {Trefault, N},
title = {Editorial: Impact of anthropogenic stressors on marine sponge holobiomes.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1533416},
pmid = {39735181},
issn = {1664-302X},
}

@article {pmid39731136,
year = {2024},
author = {Balamurugan, BS and Marimuthu, MMC and Sundaram, VA and Saravanan, B and Chandrababu, P and Chopra, H and Malik, T},
title = {Micro nutrients as immunomodulators in the ageing population: a focus on inflammation and autoimmunity.},
journal = {Immunity & ageing : I & A},
volume = {21},
number = {1},
pages = {88},
pmid = {39731136},
issn = {1742-4933},
abstract = {Immunosenescence, the slow degradation of immune function over time that is a hallmark and driver of aging, makes older people much more likely to be killed by common infections (such as flu) than young adults, but it also contributes greatly to rates of chronic inflammation in later life. Such micro nutrients are crucial for modulating effective immune responses and their deficiencies have been associated with dysfunctional immunity in the elderly. In this review, we specifically focused on the contribution of major micro nutrients (Vitamins A, D and E, Vitamin C; Zinc and Selenium) as immunomodulators in ageing population especially related to inflame-ageing process including autoimmunity. This review will cover these hologenomic interactions, including how micro nutrients can modulate immune cell function and/or cytokine production to benefit their hosts with healthy mucous-associated immunity along with a sustainable immunologic homeostasis. For example, it points out the modulatory effects of vitamin D on both innate and adaptive immunity, with a specific focus on its ability to suppress pro-inflammatory cytokines synthesis while enhancing regulatory T-cell function. In the same context, also zinc is described as important nutrient for thymic function and T-cell differentiation but exhibits immunomodulatory functions by decreasing inflammation. In addition, the review will go over how micro nutrient deficiencies increase systemic chronic low-grade inflammation and, inflammaging as well as actually enhance autoimmune pathologies in old age. It assesses the potential role of additional targeted nutritional supplementation with micro nutrients to counteract these effects, promoting wider immune resilience in older adults. This review collates the current evidence and highlights the role of adequate micro nutrient intake on inflammation and autoimmunity during ageing, providing plausible origins for nutritional interventions to promote healthy immune aging.},
}

@article {pmid39730835,
year = {2024},
author = {Orkin, JD and Kuderna, LFK and Hermosilla-Albala, N and Fontsere, C and Aylward, ML and Janiak, MC and Andriaholinirina, N and Balaresque, P and Blair, ME and Fausser, JL and Gut, IG and Gut, M and Hahn, MW and Harris, RA and Horvath, JE and Keyser, C and Kitchener, AC and Le, MD and Lizano, E and Merker, S and Nadler, T and Perry, GH and Rabarivola, CJ and Rasmussen, L and Raveendran, M and Roos, C and Wu, DD and Zaramody, A and Zhang, G and Zinner, D and Pozzi, L and Rogers, J and Farh, KK and Marques Bonet, T},
title = {Ecological and anthropogenic effects on the genomic diversity of lemurs in Madagascar.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
pmid = {39730835},
issn = {2397-334X},
support = {LCF/BQ/PI20/11760004//"la Caixa" Foundation (Caixa Foundation)/ ; DGECR-2023-00272//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada)/ ; STF 8286//European Molecular Biology Organization (EMBO)/ ; NE/T000341/1//RCUK | Natural Environment Research Council (NERC)/ ; BCS 1926215//National Science Foundation (NSF)/ ; BCS 1926105//National Science Foundation (NSF)/ ; 864203//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Excellent Science (H2020 Priority Excellent Science)/ ; },
abstract = {Ecological variation and anthropogenic landscape modification have had key roles in the diversification and extinction of mammals in Madagascar. Lemurs represent a radiation with more than 100 species, constituting roughly one-fifth of the primate order. Almost all species of lemurs are threatened with extinction, but little is known about their genetic diversity and demographic history. Here, we analyse high-coverage genome-wide resequencing data from 162 unique individuals comprising 50 species of Lemuriformes, including multiple individuals from most species. Genomic diversity varies widely across the infraorder and yet is broadly consistent among individuals within species. We show widespread introgression in multiple genera and generally high levels of genomic diversity likely resulting from allele sharing that occurred during periods of connectivity and fragmentation during climatic shifts. We find distinct patterns of demographic history in lemurs across the ecogeographic regions of Madagascar within the last million years. Within the past 2,000 years, lemurs underwent major declines in effective population size that corresponded to the timing of human population expansion in Madagascar. In multiple regions of the island, we identified chronological trajectories of inbreeding that are consistent across genera and species, suggesting localized effects of human activity. Our results show how the extraordinary diversity of these long-neglected, endangered primates has been influenced by ecological and anthropogenic factors.},
}

@article {pmid39729906,
year = {2024},
author = {Abdelghany, S and Simancas-Giraldo, SM and Zayed, A and Farag, MA},
title = {How does the coral microbiome mediate its natural host fitness under climate stress conditions? Physiological, molecular, and biochemical mechanisms.},
journal = {Marine environmental research},
volume = {204},
number = {},
pages = {106920},
doi = {10.1016/j.marenvres.2024.106920},
pmid = {39729906},
issn = {1879-0291},
abstract = {Although the symbiotic partnership between corals and algal endosymbionts has been extensively explored, interactions between corals, their algal endosymbionts and microbial associates are still less understood. Screening the response of natural microbial consortiums inside corals can aid in exploiting them as markers for dysbiosis interactions inside the coral holobiont. The coral microbiome includes archaea, bacteria, fungi, and viruses hypothesized to play a pivotal vital role in coral health and tolerance to heat stress condition via different physiological, biochemical, and molecular mechanisms. The dynamic behaviour of microbial associates could denote their potential role in coral adaptation to future climate change, with microbiome shifts occurring independently as a response to thermal stress or as a response to host stress response. Associated adaptations include regulation of coral-algal-microbial interactions, expression of heat shock proteins, microbial composition changes, and accumulation of secondary metabolites to aid in sustaining the coral's overall homeostasis under ocean warming scenarios.},
}

@article {pmid39715180,
year = {2024},
author = {Bjørnsen, MB and Valerón, NR and Vásquez, DP and Velasco, EM and Hansen, AJ and Hauptmann, AL},
title = {Microbiota in the ptarmigan intestine-An Inuit delicacy and its potential in popular cuisine.},
journal = {PloS one},
volume = {19},
number = {12},
pages = {e0305317},
doi = {10.1371/journal.pone.0305317},
pmid = {39715180},
issn = {1932-6203},
mesh = {Animals ; *Inuit ; *Intestines/microbiology ; *Gastrointestinal Microbiome ; *RNA, Ribosomal, 16S/genetics ; Humans ; Galliformes/microbiology ; Greenland ; },
abstract = {The consumption of prey intestines and their content, known as gastrophagy, is well-documented among Arctic Indigenous peoples, particularly Inuit. In Greenland, Inuit consume intestines from various animals, including the ptarmigan, a small herbivorous grouse bird. While gastrophagy provides the potential to transfer a large number of intestinal microorganisms from prey to predator, including to the human gut, its microbial implications remain to be investigated. This study addresses this gap by investigating the microbial composition of the Greenlandic rock ptarmigan's gastrointestinal tract by analyzing the crop, stomach, and intestines while also comparing it with the microbiota found in garum, a fermented sauce made from ptarmigan meat and intestines. Through 16S rRNA gene sequencing, we assessed whether garum made from ptarmigan intestines provides access to microbial diversity otherwise only accessible through gastrophagy. Our findings reveal that garum made from ptarmigan intestines displayed distinct flavors and microbial composition similar to that found in the ptarmigan gut and intestines, highlighting the potential role of fermented products in mediating food microbial diversity associated with Indigenous food practices. Furthermore, our study underscores the broader importance of understanding microbial diversity in different food systems, particularly in the context of shifting dietary patterns and concerns about diminishing food microbial diversity. By elucidating the microbial richness gained through gastrophagy this research contributes to a deeper understanding of traditional and Indigenous foodways and their implications for human gut health.},
}

Animals
*Inuit
*Intestines/microbiology
*Gastrointestinal Microbiome
*RNA, Ribosomal, 16S/genetics
Humans
Galliformes/microbiology
Greenland

@article {pmid39710259,
year = {2024},
author = {Callaway, T and Perez, HG and Corcionivoschi, N and Bu, D and Fluharty, FL},
title = {The Holobiont concept in ruminant physiology - more of the same, or something new and meaningful to food quality, food security, and animal health?.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2024-25847},
pmid = {39710259},
issn = {1525-3198},
abstract = {The holobiont concept has emerged as an attempt to recognize and describe the myriad interactions and physiological signatures inherent to a host organism, as impacted by the microbial communities that colonize and/or co-inhabit the environment within which the host resides. The field acknowledges and draws upon principles from evolution, ecology, genetics, and biology, and in many respects has been "pushed" by the advent of high throughput DNA sequencing and, to a lesser extent, other "omics"-based technologies. Despite the explosion in data generation and analyses, much of our current understanding of the human and ruminant "holobiont" is based on compositional forms of data and thereby, restricted to describing host phenotypes via associative or correlative studies. So, where to from here? We will discuss some past findings arising from ruminant and human gut microbiota research and seek to evaluate the rationale, progress, and opportunities that might arise from the "holobiont" approach to the ruminant and human host. In particular, we will consider what is a "good" or "bad" host gastrointestinalmicrobiome in different scenarios, as well as potential avenues to sustain or alter the holobiont. While the holobiont approach might improve food quality, food security and animal health, these benefits will be most likely achieved via a judicious and pragmatic compromise in data generation, both in terms of its scale, as well as its generation in context with the "forgotten" knowledge of ruminant and human physiology.},
}

@article {pmid39709663,
year = {2024},
author = {Augusto, AM and Pereira, S and Rodrigues, S and Marques, F and Aizpurua, O and Alberdi, A and Jones, G and Razgour, O and Marques, TA and Russo, D and Rebelo, H},
title = {Landscape influences bat suppression of pine processionary moth: Implications for pest management.},
journal = {Journal of environmental management},
volume = {373},
number = {},
pages = {123803},
doi = {10.1016/j.jenvman.2024.123803},
pmid = {39709663},
issn = {1095-8630},
abstract = {Bats provide important ecosystem services, particularly in agriculture, yet integrating bat management into conservation plans remains challenging. Some landscape features considerably influence bat presence, diversity, and ecosystem service provision. Understanding the relationship between landscape structure, composition, pest suppression, and ecosystem services is crucial. We modelled areas where bats most effectively suppress pine processionary moths (Thaumetopoea pityocampa), considering landscape characteristics to predict ecosystem services and optimise pest suppression in Serra da Estrela, Portugal. Faecal samples collected during fieldwork were analysed for pine processionary moth presence in bat diets. Lasso regression assessed spatial landscape variables to create an "optimal landscape" for predation. Landscape structure and composition influenced pest suppression differently, with the greatest impact within a 5000-m buffer. "Riparian edge" and "tree cover density" were key habitat structure variables supporting bat navigation and access to hunting areas, while "other forest" and "vineyard/orchard" areas were important composition variables. Optimising landscape composition involves incorporating diverse forest within agroforestry systems to enhance pest suppression by creating habitats reflecting bats' foraging preferences. We recommend strategies focusing on riparian edge conservation, selective canopy reduction, and promoting diverse forest compositions. These strategies aim to create mosaic landscapes balancing land uses, fostering optimal conditions for bat foraging. Our study shows edges provide the highest rates of bats-pine processionary moth interactions. However, caution is needed to avoid excessive fragmentation, which may reduce habitat suitability and increase pest presence before effective bat predation. A balanced approach, focusing on edge creation without over-fragmenting the landscape, is key to promoting sustainable pest management.},
}

@article {pmid39702455,
year = {2024},
author = {García, FC and Osman, EO and Garcias-Bonet, N and Delgadillo-Ordoñez, N and Santoro, EP and Raimundo, I and Villela, HDM and Voolstra, CR and Peixoto, RS},
title = {Seasonal changes in coral thermal threshold suggest species-specific strategies for coping with temperature variations.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1680},
pmid = {39702455},
issn = {2399-3642},
support = {BAS/1/1095-01-01//King Abdullah University of Science and Technology (KAUST)/ ; FCC/1/1973-51-01//King Abdullah University of Science and Technology (KAUST)/ ; URF/1/4723-01-01//King Abdullah University of Science and Technology (KAUST)/ ; },
mesh = {*Anthozoa/physiology ; Animals ; *Seasons ; *Temperature ; *Species Specificity ; Acclimatization ; Thermotolerance ; Photosynthesis ; Indian Ocean ; },
abstract = {Coral thermotolerance research has focused on the ability of coral holobionts to maximize withstanding thermal stress exposure. Yet, it's unclear whether thermal thresholds adjust across seasons or remain constant for a given species and location. Here, we assessed the thermal tolerance thresholds over time spanning the annual temperature variation in the Red Sea for Pocillopora verrucosa and Acropora spp. colonies. Utilizing the Coral Bleaching Automated Stress System (CBASS), we conducted standardized acute thermal assays by exposing corals to a range of temperatures (30 to 39 °C) and measuring their photosynthetic efficiency (Fv/Fm). Our results reveal species-specific thermal tolerance patterns. P. verrucosa exhibited significant seasonal changes in their thermal thresholds of around 3 °C, while Acropora spp. remained rather stable, showing changes of around 1 °C between seasons. Our work shows that thermal thresholds can vary with seasonal temperature fluctuations, suggesting that coral species may acclimate to these natural temperature hanges over short periods in a species-specific manner.},
}

*Anthozoa/physiology
Animals
*Seasons
*Temperature
*Species Specificity
Acclimatization
Thermotolerance
Photosynthesis
Indian Ocean

@article {pmid39701859,
year = {2024},
author = {Barnes, CJ and Bahram, M and Nicolaisen, M and Gilbert, MTP and Vestergård, M},
title = {Microbiome selection and evolution within wild and domesticated plants.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2024.11.011},
pmid = {39701859},
issn = {1878-4380},
abstract = {Microbes are ubiquitously found across plant surfaces and even within their cells, forming the plant microbiome. Many of these microbes contribute to the functioning of the host and consequently affect its fitness. Therefore, in many contexts, including microbiome effects enables a better understanding of the phenotype of the plant rather than considering the genome alone. Changes in the microbiome composition are also associated with changes in the functioning of the host, and there has been considerable focus on how environmental variables regulate plant microbiomes. More recently, studies suggest that the host genome also preconditions the microbiome to the environment of the plant, and the microbiome is therefore subject to evolutionary forces. Here, we outline how plant microbiomes are governed by both environmental variables and evolutionary processes and how they can regulate plant health together.},
}

@article {pmid39691438,
year = {2024},
author = {Armstrong, KC and Lippert, M and Hanson, E and Nestor, V and Cornwell, B and Walker, NS and Golbuu, Y and Palumbi, SR},
title = {Fine-Scale Geographic Variation of Cladocopium in Acropora hyacinthus Across the Palauan Archipelago.},
journal = {Ecology and evolution},
volume = {14},
number = {12},
pages = {e70650},
doi = {10.1002/ece3.70650},
pmid = {39691438},
issn = {2045-7758},
abstract = {Symbiont genotype plays a vital role in the ability of a coral host to tolerate rising ocean temperatures, with some members of the family Symbiodiniaceae possessing more thermal tolerance than others. While existing studies on genetic structure in symbiont populations have focused on broader scales of 10-100 s of km, there is a noticeable gap in understanding the seascape genetics of coral symbionts at finer-yet ecologically and evolutionarily relevant-scales. Here, we mapped short reads from 271 holobiont genome libraries of individual Acropora hyacinthus colonies to protein coding genes from the chloroplast genome to identify patterns of symbiont population genetic structure. Utilizing this low-pass method, we assayed over 13,000 bases from every individual, enabling us to discern genetic variation at a finer geographic scale than previously reported at the population level. We identified five common Cladocopium chloroplast SNP profiles present across Palau, with symbiont structure varying between Northern, mid-lagoon, and Southern regions, and inshore-offshore gradients. Although symbiont populations within reefs typically contained significant genetic diversity, we also observed genetic structure between some nearby reefs. To explore whether coral hosts retain their symbionts post-transplantation, we experimentally moved 79 corals from their native reefs to transplant sites with both different and similar chloroplast SNP profiles. Over 12 months, we observed 12 instances where transplanted corals changed profiles, often transitioning to a profile present in adjacent corals. Symbiont genetic structure between reefs suggests either low dispersal of symbionts or environmental selection against dispersers, both resulting in the potential for significant adaptive differentiation across reef environments. The extent to which local corals and their symbionts are co-adapted to environments on a reef-by-reef scale is currently poorly known. Chloroplast sequences offer an additional tool for monitoring symbiont genetics and coral-symbiont interactions when assisted migration is used in restoration.},
}

@article {pmid39681619,
year = {2024},
author = {Niedzwiedz, S and Schmidt, C and Yang, Y and Burgunter-Delamare, B and Andersen, S and Hildebrandt, L and Pröfrock, D and Thomas, H and Zhang, R and Damsgård, B and Bischof, K},
title = {Run-off impacts on Arctic kelp holobionts have strong implications on ecosystem functioning and bioeconomy.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {30506},
pmid = {39681619},
issn = {2045-2322},
support = {869154//European Union's Horizon 2020 research and innovation programme/ ; 869383//European Union's Horizon 2020 research and innovation programme/ ; 869154//European Union's Horizon 2020 research and innovation programme/ ; 869383//European Union's Horizon 2020 research and innovation programme/ ; 869154//European Union's Horizon 2020 research and innovation programme/ ; 869154//European Union's Horizon 2020 research and innovation programme/ ; 101136480//European Union's Horizon research and innovation programme/ ; 101136480//European Union's Horizon research and innovation programme/ ; 101136480//European Union's Horizon research and innovation programme/ ; 101136480//European Union's Horizon research and innovation programme/ ; 2021YFE0193000//National Key Research and Development Program of China/ ; 2021YFE0193000//National Key Research and Development Program of China/ ; SML2023SP218//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2023SP218//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; },
mesh = {*Kelp ; Arctic Regions ; *Ecosystem ; *Climate Change ; Food Chain ; },
abstract = {Kelps (Laminariales, Phaeophyceae) are foundation species along Arctic rocky shores, providing the basis for complex ecosystems and supporting a high secondary production. Due to ongoing climate change glacial and terrestrial run-off are currently accelerating, drastically changing physical and chemical water column parameters, e.g., water transparency for photosynthetically active radiation or dissolved concentrations of (harmful) elements. We investigated the performance and functioning of Arctic kelp holobionts in response to run-off gradients, with a focus on the effect of altered element concentrations in the water column. We found that the kelp Saccharina latissima accumulates harmful elements (e.g., cadmium, mercury) originating from coastal run-off. As kelps are at the basis of the food web, this might lead to biomagnification, with potential consequences for high-latitude kelp maricultures. In contrast, the high biosorption potential of kelps might be advantageous in monitoring environmental pollution or potentially extracting dissolved rare earth elements. Further, we found that the relative abundances of several kelp-associated microbial taxa significantly responded to increasing run-off influence, changing the kelps functioning in the ecosystem, e.g., the holobionts nutritional value and elemental cycling. The responses of kelp holobionts to environmental changes imply cascading ecological and economic consequences for Arctic kelp ecosystems in future climate change scenarios.},
}

*Kelp
Arctic Regions
*Ecosystem
*Climate Change
Food Chain

@article {pmid39680902,
year = {2024},
author = {Lipowska, MM and Sadowska, ET and Kohl, KD and Koteja, P},
title = {Experimental Evolution of a Mammalian Holobiont? Genetic and Maternal Effects on the Cecal Microbiome in Bank Voles Selectively Bred for Herbivorous Capability.},
journal = {Ecological and evolutionary physiology},
volume = {97},
number = {5},
pages = {274-291},
doi = {10.1086/732781},
pmid = {39680902},
issn = {2993-7973},
mesh = {Animals ; *Arvicolinae/microbiology/genetics ; *Herbivory ; *Gastrointestinal Microbiome/genetics ; Female ; Cecum/microbiology ; Biological Evolution ; Maternal Inheritance/genetics ; Selective Breeding/genetics ; Male ; Diet/veterinary ; },
abstract = {AbstractMammalian herbivory represents a complex adaptation requiring evolutionary changes across all levels of biological organization, from molecules to morphology to behavior. Explaining the evolution of such complex traits represents a major challenge in biology, as it is simultaneously muddled and enlightened by a growing awareness of the crucial role of symbiotic associations in shaping organismal adaptations. The concept of hologenomic evolution includes the partnered unit of the holobiont, the host with its microbiome, as a selection unit that may undergo adaptation. Here, we test some of the assumptions underlying the concept of hologenomic evolution using a unique experimental evolution model: lines of the bank vole (Myodes [=Clethrionomys] glareolus) selected for increased ability to cope with a low-quality herbivorous diet and unselected control lines. Results from a complex nature-nurture design, in which we combined cross-fostering between the selected and control lines with dietary treatment, showed that the herbivorous voles harbored a cecal microbiome with altered membership and structure and changed abundances of several phyla and genera regardless of the origin of their foster mothers. Although the differences were small, they were statistically significant and partially robust to changes in diet and housing conditions. Microbial characteristics also correlated with selection-related traits at the level of individual variation. Thus, the results support the hypothesis that selection on a host performance trait leads to genetic changes in the host that promote the maintenance of a beneficial microbiome. Such a result is consistent with some of the assumptions underlying the concept of hologenomic evolution.},
}

Animals
*Arvicolinae/microbiology/genetics
*Herbivory
*Gastrointestinal Microbiome/genetics
Female
Cecum/microbiology
Biological Evolution
Maternal Inheritance/genetics
Selective Breeding/genetics
Male
Diet/veterinary

@article {pmid39670091,
year = {2024},
author = {Garzon-Machado, M and Luna-Fontalvo, J and García-Urueña, R},
title = {Disease prevalence and bacterial isolates associated with Acropora palmata in the Colombian Caribbean.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e16886},
pmid = {39670091},
issn = {2167-8359},
mesh = {*Anthozoa/microbiology ; Animals ; Colombia/epidemiology ; Caribbean Region/epidemiology ; Prevalence ; RNA, Ribosomal, 16S/genetics ; Coral Reefs ; Vibrio/isolation & purification/genetics/pathogenicity ; },
abstract = {The decline in Acropora palmata populations in Colombian reefs has been mainly attributed to diseases outbreaks. The population size structure and prevalence of white pox and white band disease were evaluated in six localities of the Colombian Caribbean. Here, we aimed to isolate enteric bacteria and Vibrios from healthy and diseased coral mucus to relate its presence to the health status of Acropora palmata. The isolated bacteria were identified using molecular analyses with the 16S rRNA gene. Larger colonies had the highest percentage of the prevalence of both diseases. The strains that were identified as Vibrio sp. and Bacillus sp. were common in the healthy and diseased mucus of the holobiont. The Exiguobacterium sp. and Cobetia sp. strains isolated from diseased mucus may indicate maintenance and resilience mechanisms in the coral. Enterococcus sp. and other bacteria of the Enterobacteriaceae family were isolated from some localities, suggesting that probably contamination due to poor treatment of domestic wastewater and contributions from river discharges can affect coral health. The spatial heterogeneity of Colombian coral reefs exhibited variability in the bacteria, wherein environmental alterations can trigger signs of disease.},
}

*Anthozoa/microbiology
Animals
Colombia/epidemiology
Caribbean Region/epidemiology
Prevalence
RNA, Ribosomal, 16S/genetics
Coral Reefs
Vibrio/isolation & purification/genetics/pathogenicity

@article {pmid39658219,
year = {2024},
author = {Juéry, C and Auladell, A and Füssy, Z and Chevalier, F and Yee, DP and Pelletier, E and Corre, E and Allen, AE and Richter, DJ and Decelle, J},
title = {Transportome remodeling of a symbiotic microalga inside a planktonic host.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae239},
pmid = {39658219},
issn = {1751-7370},
abstract = {Metabolic exchange is one of the foundations of symbiotic associations between organisms and is a driving force in evolution. In the ocean, photosymbiosis between heterotrophic hosts and microalgae is powered by photosynthesis and relies on the transfer of organic carbon to the host (e.g. sugars). Yet, the identity of transferred carbohydrates as well as the molecular mechanisms that drive this exchange remain largely unknown, especially in unicellular photosymbioses that are widespread in the open ocean. Combining genomics, single-holobiont transcriptomics, and environmental metatranscriptomics, we revealed the transportome of the marine microalga Phaeocystis in symbiosis within acantharia, with a focus on sugar transporters. At the genomic level, the sugar transportome of Phaeocystis is comparable to non-symbiotic haptophytes. By contrast, we found significant remodeling of the expression of the transportome in symbiotic microalgae compared to the free-living stage. More particularly, 36% of sugar transporter genes were differentially expressed. Several of them, such as GLUTs, TPTs, and aquaporins, with glucose, triose-phosphate sugars, and glycerol as potential substrates, were upregulated at the holobiont and community level. We also showed that algal sugar transporter genes exhibit distinct temporal expression patterns during the day. This reprogrammed transportome indicates that symbiosis has a major impact on sugar fluxes within and outside the algal cell, and highlights the complexity and the dynamics of metabolic exchanges between partners. This study improves our understanding of the molecular players of the metabolic connectivity underlying the ecological success of planktonic photosymbiosis and paves the way for more studies on transporters across photosymbiotic models.},
}

@article {pmid39653763,
year = {2024},
author = {Forrester, JV and McMenamin, PG},
title = {Evolution of the ocular immune system.},
journal = {Eye (London, England)},
volume = {},
number = {},
pages = {},
pmid = {39653763},
issn = {1476-5454},
abstract = {The evolution of the ocular immune system should be viewed within the context of the evolution of the immune system, and indeed organisms, as a whole. Since the earliest time, the most primitive responses of single cell organisms involved molecules such as anti-microbial peptides and behaviours such as phagocytosis. Innate immunity took shape ~2.5 billion years ago while adaptive immunity and antigen specificity appeared with vertebrate evolution ~ 500 million years ago. The invention of the microscope and the germ theory of disease precipitated debate on cellular versus humoral immunity, resolved by the discovery of B and T cells. Most recently, our understanding of the microbiome and consideration of the host existing symbiotically with trillions of microbial genes (the holobiont), suggests that the immune system is a sensor of homoeostasis rather than simply a responder to pathogens. Each tissue type in multicellular organisms, such as vertebrates, has a customised response to immune challenge, with powerful reactions most evident in barrier tissues such as the skin and gut mucosa, while the eye and brain occupy the opposite extreme where responses are attenuated. The experimental background which historically led to the concept of immune privilege is discussed in this review; however, we propose that the ocular immune response should not be viewed as unique but simply an example of how the tissues variably respond in nature, more or less to the same challenge (or danger).},
}

@article {pmid39651872,
year = {2024},
author = {Marques, M and da Silva, DM and Santos, E and Baylina, N and Peixoto, R and Kyrpides, NC and Woyke, T and Whitman, WB and Keller-Costa, T and Costa, R},
title = {Genome sequences of four novel Endozoicomonas strains associated with a tropical octocoral in a long-term aquarium facility.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0083324},
doi = {10.1128/mra.00833-24},
pmid = {39651872},
issn = {2576-098X},
abstract = {We report the genome sequences of four Endozoicomonas sp. strains isolated from the octocoral Litophyton maintained long term at an aquarium facility. Our analysis reveals the coding potential for versatile polysaccharide metabolism; Type II, III, IV, and VI secretion systems; and the biosynthesis of novel ribosomally synthesized and post-translationally modified peptides.},
}

@article {pmid39637852,
year = {2024},
author = {Ramos-Madrigal, J and Fritz, GJ and Schroeder, B and Smith, B and Sánchez-Barreiro, F and Carøe, C and Runge, AKW and Boer, S and McGrath, K and Vieira, FG and Liu, S and da Fonseca, RR and Guo, C and Zhang, G and Petersen, B and Sicheritz-Pontén, T and Gopalakrishnan, S and Gilbert, MTP and Wales, N},
title = {The genomic origin of early maize in eastern North America.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2024.11.003},
pmid = {39637852},
issn = {1097-4172},
abstract = {Indigenous maize varieties from eastern North America have played an outsized role in breeding programs, yet their early origins are not fully understood. We generated paleogenomic data to reconstruct how maize first reached this region and how it was selected during the process. Genomic ancestry analyses reveal recurrent movements northward from different parts of Mexico, likely culminating in at least two dispersals from the US Southwest across the Great Plains to the Ozarks and beyond. We find that 1,000-year-old Ozark specimens carry a highly differentiated wx1 gene, which is involved in the synthesis of amylose, highlighting repeated selective pressures on the starch metabolic pathway throughout maize's domestication. This population shows a close affinity with the lineage that ultimately became the Northern Flints, a major contributor to modern commercial maize.},
}

@article {pmid39633476,
year = {2024},
author = {Manrique-de-la-Cuba, MF and Parada-Pozo, G and Rodríguez-Marconi, S and López-Rodríguez, MR and Abades, S and Trefault, N},
title = {Evidence of habitat specificity in sponge microbiomes from Antarctica.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {100},
pmid = {39633476},
issn = {2524-6372},
support = {Fondecyt N° 1230758//Agencia Nacional de Investigación y Desarrollo/ ; Fondecyt N° 1230758//Agencia Nacional de Investigación y Desarrollo/ ; Fondecyt N° 1230758//Agencia Nacional de Investigación y Desarrollo/ ; Fondecyt N° 1230758//Agencia Nacional de Investigación y Desarrollo/ ; Fondecyt N° 1230758//Agencia Nacional de Investigación y Desarrollo/ ; DG_02-22//Instituo Antartico Chileno- INACH/ ; Doctoral fellowship N° 21211164//Agencia Nacional de Investigación e Innovación/ ; },
abstract = {BACKGROUND: Marine sponges and their microbiomes are ecosystem engineers distributed across the globe. However, most research has focused on tropical and temperate sponges, while polar regions like Antarctica have been largely neglected. Despite its harsh conditions and geographical isolation, Antarctica is densely populated by sponges. In this study, we explored the extent of habitat specificity in the diversity, community composition, and microbial co-occurrence within Antarctic sponge microbiomes, in comparison to those from other marine environments. We used massive sequencing of 16S rRNA genes and integrated multiple databases to incorporate Antarctic sponges as a habitat in global microbiome analyses.

RESULTS: Our study revealed significant differences in microbial diversity and community composition between Antarctic and non-Antarctic sponges. We found that most microorganisms present in Antarctic sponges are unique to the South Shetland Islands. Nitrosomonas oligotropha, Candidatus Nitrosopumilus, Polaribacter, SAR116 clade, and Low Salinity Nitrite-Oxidizing Bacteria (LS-NOB) are microbial members characterizing the Antarctic sponge microbiomes. Based on their exclusivity and presence across different sponges worldwide, we identified habitat-specific and habitat-generalist bacteria associated with each habitat. They are particularly abundant and connected within all the Antarctic sponges, suggesting that they may play a crucial role as keystone species within these sponge ecosystems.

CONCLUSIONS: This study provides significant insights into the microbial diversity and community composition of sponges in Antarctica and non-Antarctic ecoregions. Our findings provide evidence for habitat-specific patterns that differentiate the microbiomes of Antarctic sponges from elsewhere, indicating the strong influence of environmental selection and dispersal limitation wrapped into the Antarctic ecoregions to shape more similar microbial communities in distantly related sponges. This study contributes to understanding signatures of microbial community assembly in the Antarctic sponges and has important implications for the ecology and evolution of these unique marine environments.},
}

@article {pmid39631125,
year = {2024},
author = {Zhang, JY and Li, XY and Li, DX and Zhang, ZH and Hu, LQ and Sun, CX and Zhang, XN and Wu, M and Liu, LT},
title = {Endoplasmic reticulum stress in intestinal microecology: A controller of antineoplastic drug-related cardiovascular toxicity.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {181},
number = {},
pages = {117720},
doi = {10.1016/j.biopha.2024.117720},
pmid = {39631125},
issn = {1950-6007},
abstract = {Endoplasmic reticulum (ER) stress is extensively studied as a pivotal role in the pathological processes associated with intestinal microecology. In antineoplastic drug treatments, ER stress is implicated in altering the permeability of the mechanical barrier, depleting the chemical barrier, causing dysbiosis, exacerbating immune responses and inflammation in the immune barrier. Enteric dysbiosis and intestinal dysfunction significantly affect the circulatory system in various heart disorders. In antineoplastic drug-related cardiovascular (CV) toxicity, ER stress constitutes a web of relationships in the host-microbiome symbiotic regulatory loop. Therefore, understanding the holobiont perspective will help de-escalate spatial and temporal restrictions. This review investigates the role of ER stress-mediated gut microecological alterations in antineoplastic treatment-induced CV toxicity.},
}

@article {pmid39620136,
year = {2024},
author = {Ellegaard, MR and Ebenesersdóttir, SS and Moore, KHS and Petersén, A and Vågene, ÅJ and Bieker, VC and Denham, SD and Cavalleri, GL and Gilbert, E and Werge, T and Hansen, TF and Kockum, I and Alfredsson, L and Olsson, T and Hovig, E and Gilbert, MTP and Stefánsson, K and Stenøien, HK and Helgason, A and Martin, MD},
title = {Corroborating written history with ancient DNA: The case of the Well-man described in an Old Norse saga.},
journal = {iScience},
volume = {27},
number = {11},
pages = {111076},
pmid = {39620136},
issn = {2589-0042},
abstract = {The potential of ancient DNA analyses to provide independent sources of information about events in the historical record remains to be demonstrated. Here we apply palaeogenomic analysis to human remains excavated from a medieval well at the ruins of Sverresborg Castle in central Norway. In Sverris Saga, the Old Norse saga of King Sverre Sigurdsson, one passage details a 1197-CE raid on the castle and mentions a dead man thrown into the well. Radiocarbon dating supports that these are that individual's remains. We sequenced the Well-man's nuclear genome to 3.4× and compared it to Scandinavian populations, revealing he was closely related to inhabitants of southern Norway. This was surprising because King Sverre's defeated army was assumed to be recruited from parts of central Norway, whereas the raiders were from the south. The findings also indicate that the unique genetic drift seen in present-day southern Norwegians already existed 800 years ago.},
}

@article {pmid39620087,
year = {2024},
author = {Zhang, X and Xi, T and Wang, Y and Fan, X and Xu, D and Zhang, P and Sun, K and Zhang, Y and Ma, J and Ye, N},
title = {Chemical interactions between kelp Macrocystis pyrifera and symbiotic bacteria under elevated CO2 condition.},
journal = {Marine life science & technology},
volume = {6},
number = {4},
pages = {700-712},
pmid = {39620087},
issn = {2662-1746},
abstract = {UNLABELLED: Kelps are pivotal to temperate coastal ecosystems, providing essential habitat and nutrients for diverse marine life, and significantly enhancing local biodiversity. The impacts of elevated CO2 levels on kelps may induce far-reaching effects throughout the marine food web, with potential consequences for biodiversity and ecosystem functions. This study considers the kelp Macrocystis pyrifera and its symbiotic microorganisms as a holistic functional unit (holobiont) to examine their collective response to heightened CO2 levels. Over a 4 month cultivation from the fertilization of M. pyrifera gametes to the development of juvenile sporophytes, our findings reveal that elevated CO2 levels influence the structure of the M. pyrifera symbiotic microbiome, alter metabolic profiles, and reshape microbe-metabolite interactions using 16S rRNA amplicon sequencing and liquid chromatography coupled to mass spectrometry analysis. Notably, Dinoroseobacter, Sulfitobacter, Methylotenera, Hyphomonas, Milano-WF1B-44 and Methylophaga were selected as microbiome biomarkers, which showed significant increases in comparative abundance with elevated CO2 levels. Stress-response molecules including fatty-acid metabolites, oxylipins, and hormone-like compounds such as methyl jasmonate and prostaglandin F2a emerged as critical metabolomic indicators. We propose that elevated CO2 puts certain stress on the M. pyrifera holobiont, prompting the release of these stress-response molecules. Moreover, these molecules may aid the kelp's adaptation by modulating the microbial community structure, particularly influencing potential pathogenic bacteria, to cope with environmental change. These results will enrich the baseline data related to the chemical interactions between the microbiota and M. pyrifera and provide clues for predicting the resilience of kelps to future climate change.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-024-00259-5.},
}

@article {pmid39615101,
year = {2024},
author = {Huang, W and Huang, Z and Yang, E and Meng, L and Chen, J and Tan, R and Xiao, Z and Zhou, Y and Xu, M and Yu, K},
title = {High- and low-temperature stress responses of Porites lutea from the relatively high-latitude region of the South China Sea.},
journal = {Marine environmental research},
volume = {204},
number = {},
pages = {106858},
doi = {10.1016/j.marenvres.2024.106858},
pmid = {39615101},
issn = {1879-0291},
abstract = {Global climate change has led to more frequent extreme temperature (extreme heat and cold) events, posing a serious threat to coral reef ecosystems. Higher latitudes are considered potential refuges for reef-building corals, but their response to extreme temperature stress in these regions remain unclear. This study, indoor simulated stress experiments ranging on Porites lutea from Weizhou Island in the northern part of the South China Sea, simulating suitable (26 °C) to extreme high (34 °C) and extreme low (12 °C) temperatures. Physiological, biochemical, and transcriptional responses, were analysed. Results showed P. lutea's tentacles contracted, and symbiotic relationships broke down at both high and low temperatures; leading to oxidative stress, and a higher risk of disease. The coral host's response to temperature stress was positively regulated, mainly through apoptosis and metabolic inhibition pathways, whereas Symbiodiniaceae C15 showed no significant response to either high- or low-temperature stress. The coral host played a dominant role in the holobiont's stress response, using similar mechanisms for both high- and low-temperatures with some differences in the details. This study enhances understanding the temperature response mechanisms of the dominant coral species, P. lutea in the relatively high-latitude regions of the South China Sea.},
}

@article {pmid39603001,
year = {2024},
author = {Gao, X and Chen, J and Ma, Y and Zheng, Y and Bu, Y and Yu, X and Yu, K},
title = {Differential physiological and microbial responses of the octocoral Junceella squamata to high-temperature and cadmium stress.},
journal = {Marine environmental research},
volume = {204},
number = {},
pages = {106865},
doi = {10.1016/j.marenvres.2024.106865},
pmid = {39603001},
issn = {1879-0291},
abstract = {Global warming and heavy metals have become the major threat to the growth and reproduction of corals. However, unlike scleractinian corals, in the context of widespread coral degradation worldwide, there are few reports on the response of octocorallia corals to high-temperature stress and heavy metals. In the present study, we conducted indoor simulation experiments using Junceella squamata. We evaluated the physiological response of these corals under high-temperature stress at 33 °C and cadmium (Cd) stress by comparing the composition and diversity of their symbiotic bacteria and analyzing differences in their transcriptome. The results show that high-temperature stress has more severe adverse effects than cadmium stress. High-temperature stress disrupts coral symbiotic relationships, leading to an increase in alpha diversity associated with disease-causing bacteria, which may increase the risk of infection and potentially contribute to coral mortality. Meanwhile, cadmium stress increases the instability of the coral holobiont, potentially disrupting DNA stability and RNA transcriptional regulation. However, an increase in Cd-tolerant bacteria may help corals respond to cadmium stress. This study reveals the effects of harmful substances on coral and highlights the urgent need for action to protect octocorals in the face of environmental stress.},
}

@article {pmid39602985,
year = {2024},
author = {Gao, X and Chen, J and Yu, K and Bu, Y and Wang, L and Yu, X},
title = {Exposure to polypropylene microplastics induces the upregulation of protein digestion-associated genes and microbiome reorganization in the octocoral Junceella squamata.},
journal = {Marine pollution bulletin},
volume = {210},
number = {},
pages = {117331},
doi = {10.1016/j.marpolbul.2024.117331},
pmid = {39602985},
issn = {1879-3363},
abstract = {Microplastics, a new type of pollutants found in coral reefs, have attracted increasing attention. However, most of the current research focuses on the scleractinian corals and few reports on Octocorallia. To reveal the impact of microplastic exposure on Octocorallia, we analyzed the transcriptional response of the coral hosts Junceella squamata along with changes to the diversity and community structure of its symbiotic bacteria following exposure to polystyrene microplastics. These results suggest that the microplastics have adverse impacts on nutrient metabolism and absorption in J. squamata. The symbiotic bacteria of J. squamata exhibited a clear response after exposure to microplastics, which may also reflect an adaptation mechanism of corals, and help to maintain the physiological function of coral symbiotic function under the exposure of microplastics. This study has revealed the impact of microplastic exposure on J. squamata, providing new insights for coral protection against the background of increased microplastics pollution.},
}

@article {pmid39600252,
year = {2024},
author = {Grupstra, CGB and Meyer-Kaiser, KS and Bennett, MJ and Andres, MO and Juszkiewicz, DJ and Fifer, JE and Da-Anoy, JP and Gomez-Campo, K and Martinez-Rugerio, I and Aichelman, HE and Huzar, AK and Hughes, AM and Rivera, HE and Davies, SW},
title = {Holobiont Traits Shape Climate Change Responses in Cryptic Coral Lineages.},
journal = {Global change biology},
volume = {30},
number = {11},
pages = {e17578},
doi = {10.1111/gcb.17578},
pmid = {39600252},
issn = {1365-2486},
support = {2048589//The National Science Foundation's Division of Ocean Sciences/ ; 2048678//The National Science Foundation's Division of Ocean Sciences/ ; },
mesh = {*Anthozoa/microbiology/physiology ; Animals ; *Climate Change ; *Coral Reefs ; *Symbiosis ; Microbiota ; Dinoflagellida/physiology ; },
abstract = {As ocean warming threatens reefs worldwide, identifying corals with adaptations to higher temperatures is critical for conservation. Genetically distinct but morphologically similar (i.e. cryptic) coral populations can be specialized to extreme habitats and thrive under stressful conditions. These corals often associate with locally beneficial microbiota (Symbiodiniaceae photobionts and bacteria), obscuring the main drivers of thermal tolerance. Here, we leverage a holobiont (massive Porites) with high fidelity for C15 photobionts to investigate adaptive variation across classic ("typical" conditions) and extreme reefs characterized by higher temperatures and light attenuation. We uncovered three cryptic lineages that exhibit limited micro-morphological variation; one lineage dominated classic reefs (L1), one had more even distributions (L2), and a third was restricted to extreme reefs (L3). L1 and L2 were more closely related to populations ~4300 km away, suggesting that some lineages are widespread. All corals harbored Cladocopium C15 photobionts; L1 and L2 shared a photobiont pool that differed in composition between reef types, yet L3 mostly harbored unique photobiont strains not found in the other lineages. Assemblages of bacterial partners differed among reef types in lineage-specific ways, suggesting that lineages employ distinct microbiome regulation strategies. Analysis of light-harvesting capacity and thermal tolerance revealed adaptive variation underpinning survival in distinct habitats: L1 had the highest light absorption efficiency and lowest thermal tolerance, suggesting that it is a classic reef specialist. L3 had the lowest light absorption efficiency and the highest thermal tolerance, showing that it is an extreme reef specialist. L2 had intermediate light absorption efficiency and thermal tolerance, suggesting that is a generalist lineage. These findings reveal diverging holobiont strategies to cope with extreme conditions. Resolving coral lineages is key to understanding variation in thermal tolerance among coral populations, can strengthen our understanding of coral evolution and symbiosis, and support global conservation and restoration efforts.},
}

*Anthozoa/microbiology/physiology
Animals
*Climate Change
*Coral Reefs
*Symbiosis
Microbiota
Dinoflagellida/physiology

@article {pmid39593141,
year = {2024},
author = {Steiner, LX and Schmittmann, L and Rahn, T and Lachnit, T and Jahn, MT and Hentschel, U},
title = {Phage-induced disturbance of a marine sponge microbiome.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {97},
pmid = {39593141},
issn = {2524-6372},
support = {CRC1182-TP C04//Deutsche Forschungsgemeinschaft/ ; CRC1182-TP C04//Deutsche Forschungsgemeinschaft/ ; },
abstract = {BACKGROUND: Bacteriophages are known modulators of community composition and activity in environmental and host-associated microbiomes. However, the impact single phages have on bacterial community dynamics under viral predation, the extent and duration of their effect, are not completely understood. In this study, we combine morphological and genomic characterization of a novel marine phage, isolated from the Baltic sponge Halichondria panicea, and report on first attempts of controlled phage-manipulation of natural sponge-associated microbiomes.

RESULTS: We used culture-based and culture-independent (16S rRNA gene amplicon sequencing) methods to investigate bacterial community composition and dynamics in sponge microbiomes with and without the addition of phages. Upon application of a novel Maribacter specialist phage Panino under controlled conditions, we were able to detect community-wide shifts in the microbiome composition and load after 72 h. While bacterial community composition became more dissimilar over time in the presence of phages, species evenness and richness were maintained. Upon phage exposure, we observed the loss of several low-abundance constituent taxa of the resident microbiota, while other originally underrepresented taxa increased. Virulent phages likely induce community-wide disturbances, evident in changes in the total sponge microbial profile by specific elimination of constituent taxa, which leads to an increase in bacterial abundance of opportunistic taxa, such as the genera Vibrio, Pseudoalteromonas, and Photobacterium.

CONCLUSIONS: Our findings suggest that sponge microbiome diversity and, by extension, its resilience depend on the maintenance of resident bacterial community members, irrespective of their abundance. Phage-induced disturbances can significantly alter community structure by promoting the growth of opportunistic bacteria like Vibrio and shifting the microbiome to a dysbiotic state. These insights highlight the role of bacteriophages in shaping microbiome dynamics and underscore the potential for phage application in managing bacterial community composition in marine host-associated environments.},
}

@article {pmid39590502,
year = {2024},
author = {Schapheer, C and González, LM and Villagra, C},
title = {Microorganism Diversity Found in Blatta orientalis L. (Blattodea: Blattidae) Cuticle and Gut Collected in Urban Environments.},
journal = {Insects},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/insects15110903},
pmid = {39590502},
issn = {2075-4450},
abstract = {Pest cockroaches share urban habitats with us; their prevalence in urban areas prompts concerns regarding their effect on human health, as synanthropic cockroaches often host pathogenic microorganisms. Nonetheless, microbial associates in these insects can also be related to their biology, contributing to their physiological homeostasis and reproductive success. In this article, we present in detail, for the first time, the bacterial community associated with the oriental cockroach Blatta orientalis, one of the world's five most prominent pest cockroaches. We report the composition of the communities of bacteria found over the exoskeleton and inside the gut of this global pest. We collected B. orientalis in Santiago, Chile's capital city, and the urban nucleus in this country. We conducted DNA extractions and metabarcoding analysis. We found diverse bacterial lineages, including mutualist symbiotic strains, and microorganisms considered pathogenic to humans. We also analyzed the metabolic functions of the bacterial communities identified and discussed the role of B. orientalis as a reservoir and vector of pathogens in urban areas. We discuss to what extent the diversity of functions of the microbial community associated with cockroaches may contribute to emergent properties enabling these insects to inhabit human-modified habitats.},
}

@article {pmid39589622,
year = {2024},
author = {Wong, JM and Liu, AC and Lin, HT and Shinzato, C and Yang, SY and Yang, SH},
title = {An Improved RNA Extraction Method for Octocorals and Its Application in Transcriptome Analysis of Dark-Induced Bleaching Octocoral.},
journal = {Marine biotechnology (New York, N.Y.)},
volume = {27},
number = {1},
pages = {8},
pmid = {39589622},
issn = {1436-2236},
support = {NSTC 112-2311-B-002 -017//National Science and Technology Council/ ; NTU 112L2033-05//National Taiwan University/ ; },
mesh = {*Anthozoa/genetics/metabolism ; Animals ; *Gene Expression Profiling ; *RNA/isolation & purification/genetics ; *Dinoflagellida/genetics ; *Transcriptome ; Symbiosis ; Coral Reefs ; },
abstract = {Octocorals, vital components of reef ecosystems, inhabit various marine environments across diverse climate zones, spanning from tropical shallows to frigid deep-sea regions. Certain octocoral species, notably Lobophytum and Sinularia, are particularly intriguing due to their production of diverse metabolites, warranting continuous investigation. Although octocorals played the roles in coral ecosystems, the studies are rare in comparison to scleractinian corals, especially in transcriptomic and genomic data. However, RNA extraction was massively interfered by the polysaccharides and secondary metabolites produced from octocoral holobiont. For this purpose, five lysis buffer systems and two extraction processes were examined for the RNA extraction efficiency in octocorals. We found CTAB/10%SDS as a new method for RNA extraction from six different octocoral genera. Furthermore, our new method is enable to extract RNA with good quality for downstream application such as quantitative PCR and RNA sequencing. Finally, comparative transcriptomic analysis between healthy octocorals and those dark-induced bleaching corals in Lobophytum hsiehi revealed extracellular matrix and immunity-related genes may play the important roles in coral-symbiodinium symbiosis. We believe that this study's findings and the developed RNA extraction method will serve as valuable references for future research, particularly in octocorals.},
}

*Anthozoa/genetics/metabolism
Animals
*Gene Expression Profiling
*RNA/isolation & purification/genetics
*Dinoflagellida/genetics
*Transcriptome
Symbiosis
Coral Reefs

@article {pmid39589125,
year = {2024},
author = {Zhang, Z and Tong, M and Ding, W and Liu, S and Jong, M-C and Radwan, AA and Cai, Z and Zhou, J},
title = {Changes in the diversity and functionality of viruses that can bleach healthy coral.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0081624},
doi = {10.1128/msphere.00816-24},
pmid = {39589125},
issn = {2379-5042},
abstract = {UNLABELLED: Coral microbiomes play a crucial role in maintaining the health and functionality of holobionts. Disruption in the equilibrium of holobionts, including bacteria, fungi, and archaea, can result in the bleaching of coral. However, little is known about the viruses that can infect holobionts in coral, especially bacteriophages. Here, we employed a combination of amplicon and metagenomic analyses on Acropora muricata and Galaxea astreata to investigate the diversity and functionality of viruses in healthy and bleached corals. Analysis showed that the alpha diversity of holobionts (bacteria, eukaryotes, zooxanthellae, and lysogenic and lytic viruses) was higher in bleached corals than that in healthy corals. Meanwhile, bleached corals exhibited a relatively higher abundance of specific viral classes, including Revtraviricetes, Arfiviricetes, Faserviricetes, Caudoviricetes, Herviviricetes, and Tectiliviricetes; moreover, we found that the expression levels of functional genes involved in carbon and sulfur metabolism were enriched. An increase in Vibrio abundance has been reported as a notable factor in coral bleaching; our analysis also revealed an increased abundance of Vibrio in bleached coral. Finally, bleached corals contained a higher abundance of Vibrio phages and encoded more virulence factor genes to increase the competitiveness of Vibrio after coral bleaching. In conclusion, we attempted to understand the causes of coral bleaching from the perspective of phage-bacteria-coral tripartite interaction.

IMPORTANCE: Viruses, especially bacteriophages, outnumber other microorganisms by approximately 10-fold and represent the most abundant members of coral holobionts. Corals represent a model system for the study of symbiosis, the influence of viruses on organisms inhabiting healthy coral reef, the role of rapid horizontal gene transfer, and the expression of auxiliary metabolic genes. However, the least studied component of coral holobiont are viruses. Therefore, there is a critical need to investigate the viral community of viruses, and their functionality, in healthy and bleached coral. Here, we compared the composition and functionality of viruses in healthy and bleached corals and found that viruses may participate in the induction of coral bleaching by enhancing the expression of virulence genes and other auxiliary metabolic functions.},
}

@article {pmid39580487,
year = {2024},
author = {Rosenberg, E},
title = {Diversity of bacteria within the human gut and its contribution to the functional unity of holobionts.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {134},
pmid = {39580487},
issn = {2055-5008},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Bacteria/genetics/classification/isolation & purification ; Feces/microbiology ; Biodiversity ; Colon/microbiology ; },
abstract = {The composition of bacteria in the human colon has been a subject of interest since the beginning of microbiology. With the development of methods for culturing strict anaerobic bacteria under multiple culture conditions, it was shown the gut contained more than 400 bacterial species and different people harbor different abundant species. The term "gut microbiome" in this review refers to bacteria studied in stool samples. Molecular methods for determining the bacterial composition of human gut has revealed more than 3000 species and less than 130 genera, indicating that the diversity of human colonic bacteria is concentrated at the species and strain levels. This review concludes with a discussion of how diversity can lead to unity of individual holobionts, between holobionts, and between populations. One of the reasons for the unity is that different bacterial species can have similar functional genes.},
}

Humans
*Gastrointestinal Microbiome
*Bacteria/genetics/classification/isolation & purification
Feces/microbiology
Biodiversity
Colon/microbiology

@article {pmid39575186,
year = {2024},
author = {Verma, T and Hendiani, S and Carbajo, C and Andersen, SB and Hammarlund, EU and Burmølle, M and Sand, KK},
title = {Recurrence and propagation of past functions through mineral facilitated horizontal gene transfer.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1449094},
pmid = {39575186},
issn = {1664-302X},
abstract = {Horizontal gene transfer is one of the most important drivers of bacterial evolution. Transformation by uptake of extracellular DNA is traditionally not considered to be an effective mode of gene acquisition, simply because extracellular DNA is degraded in a matter of days when it is suspended in e.g. seawater. Recently the age span of stored DNA was increased to at least 2 Ma. Here, we show that Acinetobacter baylyi can incorporate 60 bp DNA fragments adsorbed to common sedimentary minerals and that the transformation frequencies scale with mineral surface properties. Our work highlights that ancient environmental DNA can fuel the evolution of contemporary bacteria. In contrast to heritable stochastic mutations, the processes by which bacteria acquire new genomic material during times of increased stress and needs, indicate a non-random mechanism that may propel evolution in a non-stochastic manner.},
}

@article {pmid39574203,
year = {2024},
author = {Rhimi, S and Jablaoui, A and Hernandez, J and Mariaule, V and Akermi, N and Méric, T and Mkaouar, H and Wysocka, M and Lesner, A and Borgi, MA and Maguin, E and Rhimi, M},
title = {Industrial diet intervention modulates the interplay between gut microbiota and host in semi-stray dogs.},
journal = {Animal microbiome},
volume = {6},
number = {1},
pages = {69},
pmid = {39574203},
issn = {2524-4671},
support = {twinning European project: 952583-MICAfrica//European Commission/ ; twinning European project: 952583-MICAfrica//European Commission/ ; twinning European project: 952583-MICAfrica//European Commission/ ; twinning European project: 952583-MICAfrica//European Commission/ ; twinning European project: 952583-MICAfrica//European Commission/ ; RestorPro no ANR-23-CE14-0073-01//Agence Nationale de la Recherche/ ; RestorPro no ANR-23-CE14-0073-01//Agence Nationale de la Recherche/ ; RestorPro no ANR-23-CE14-0073-01//Agence Nationale de la Recherche/ ; },
abstract = {BACKGROUND: The gut microbiota and derived metabolites play a key role in regulating host physiology. Diet is identified as a key regulatory factor of the microbiota composition and, potentially, of subsequent functionalities. Demonstrating the role of diet may be complex as most human studies are cross-sectional and dietary intervention is often accompanied by hygienic changes. The objective of the present study was to investigate the impact of an industrial diet on the modulation of the microbiota and targeted functionalities using a canine "natural" model.

RESULTS: We carried out a controlled dietary trial in a cohort of Tunisian semi-stray dogs. We made a transition from a natural diet to an industrial kibble diet and monitored the composition of the fecal microbiota, the concentration of short-chain fatty acids (SCFA) and bile acids (BAs), and protease activities. We demonstrated that dietary change significantly decreased fecal primary bile acids levels and protease activities. Interestingly, correlation analyses demonstrated that variation of specific microbial genera were associated with modulated physiological parameters.

CONCLUSIONS: Our study reveals that an industrial diet induces beneficial changes in microbial composition and functions characterised by increased diversity, synthesis of SCFA and secondary bile acids production, stressing the key role of the diet-microbiota-dog crosstalk.},
}

@article {pmid39574002,
year = {2024},
author = {Pereira, H and Chakarov, N and Caspers, BA and Gilles, M and Jones, W and Mijoro, T and Zefania, S and Székely, T and Krüger, O and Hoffman, JI},
title = {The gut microbiota of three avian species living in sympatry.},
journal = {BMC ecology and evolution},
volume = {24},
number = {1},
pages = {144},
pmid = {39574002},
issn = {2730-7182},
support = {316099922//Deutsche Forschungsgemeinschaft/ ; 316099922//Deutsche Forschungsgemeinschaft/ ; 316099922//Deutsche Forschungsgemeinschaft/ ; 316099922//Deutsche Forschungsgemeinschaft/ ; 316099922//Deutsche Forschungsgemeinschaft/ ; 316099922//Deutsche Forschungsgemeinschaft/ ; 316099922//Deutsche Forschungsgemeinschaft/ ; 316099922//Deutsche Forschungsgemeinschaft/ ; 316099922//Deutsche Forschungsgemeinschaft/ ; 316099922//Deutsche Forschungsgemeinschaft/ ; 396780709//Deutsche Forschungsgemeinschaft,/ ; 396780709//Deutsche Forschungsgemeinschaft,/ ; 396780709//Deutsche Forschungsgemeinschaft,/ ; 396780709//Deutsche Forschungsgemeinschaft,/ ; 396780709//Deutsche Forschungsgemeinschaft,/ ; 396780709//Deutsche Forschungsgemeinschaft,/ ; 396780709//Deutsche Forschungsgemeinschaft,/ ; 396780709//Deutsche Forschungsgemeinschaft,/ ; 396780709//Deutsche Forschungsgemeinschaft,/ ; 396780709//Deutsche Forschungsgemeinschaft,/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics/physiology ; *Sympatry ; Species Specificity ; Madagascar ; },
abstract = {BACKGROUND: Evolutionary divergence and genetic variation are often linked to differences in microbial community structure and diversity. While environmental factors and diet heavily influence gut microbial communities, host species contributions are harder to quantify. Closely related species living in sympatry provide a unique opportunity to investigate species differences without the confounding effects of habitat and dietary variation. We therefore compared and contrasted the gut microbiota of three sympatric plover species: the widespread Kittlitz's and white-fronted plovers (Anarhynchus pecuarius and A. marginatus) and the endemic and vulnerable Madagascar plover (A. thoracicus).

RESULTS: We found no significant differences in the beta diversity (composition) of the gut microbiota of the three species. However, A. thoracicus exhibited higher intraspecific compositional similarity (i.e. lower pairwise distances) than the other two species; this pattern was especially pronounced among juveniles. By contrast, microbial alpha diversity varied significantly among the species, being highest in A. pecuarius, intermediate in A. marginatus and lowest in A. thoracicus. This pattern was again stronger among juveniles. Geographical distance did not significantly affect the composition of the gut microbiota, but genetic relatedness did.

CONCLUSION: While patterns of microbial diversity varied across species, the lack of compositional differences suggests that habitat and diet likely exert a strong influence on the gut microbiota of plovers. This may be enhanced by their precocial, ground-dwelling nature, which could facilitate the horizontal transmission of microbes from the environment. We hypothesise that gut microbiota diversity in plovers primarily reflects the ecological pool of microbiota, which is subsequently modified by host-specific factors including genetics. The reduced microbial and genetic diversity of the endemic A. thoracicus may hinder its ability to adapt to environmental changes, highlighting the need for increased conservation efforts for this vulnerable species.},
}

Animals
*Gastrointestinal Microbiome/genetics/physiology
*Sympatry
Species Specificity
Madagascar

@article {pmid39570654,
year = {2024},
author = {Yan, C and Zhang, K and Shi, S and Jian, L and Chen, B and Quadri, SR and Tian, X},
title = {Alterisphingorhabdus coralli gen. nov. sp. nov., a novel aerobic anoxygenic phototrophic bacteria isolated from reef-building coral.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {74},
number = {11},
pages = {},
doi = {10.1099/ijsem.0.006577},
pmid = {39570654},
issn = {1466-5034},
mesh = {*Phylogeny ; *Anthozoa/microbiology ; Animals ; *Fatty Acids ; *DNA, Bacterial/genetics ; *Bacterial Typing Techniques ; *RNA, Ribosomal, 16S/genetics ; *Sequence Analysis, DNA ; *Ubiquinone ; *Coral Reefs ; Base Composition ; Sphingomonadaceae/genetics/isolation & purification/classification ; Nucleic Acid Hybridization ; Phototrophic Processes ; },
abstract = {The photosynthetic microorganisms within the coral holobiont produce energy and organic compounds through photosynthesis, which are vital for the biocalcification and heat tolerance of coral hosts. However, aerobic anoxygenic phototrophic bacteria (AAPB), which are one of the most important photosynthetic microorganisms, have not been thoroughly investigated in this environment. In this study, a novel AAPB, SCSIO 66989[T], was isolated from the reef-building coral Favia sp. and considered a beneficial microorganism for corals (BMC). The polyphasic taxonomic analysis showed that it had the highest similarities with Parasphingorhabdus litoris DSM 22379[T] (95.9%) and Altererythrobacter ishigakiensis ATCC BAA-2084[T] (95.7%). Phylogenetic analysis showed that it formed an independent clade, distinguishing it from other genera within the family Sphingomonadaceae. The predominant fatty acids were C18 : 1 ω7c and/or C18 : 1 ω6c and C16 : 0. The major respiratory quinone was ubiquinone-10 (Q-10). Sphingolipid, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine were the diagnostic polar lipids. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between SCSIO 66989[T] and the type strains of P. litoris DSM 22379[T] and A. ishigakiensis ATCC BAA-2084[T] were 69.2-70.0%, 58.6-61.2% and 19.2-19.7%, respectively. These results indicate that strain SCSIO 66989[T] represents a new species of a novel genus in the family Sphingomonadaceae, for which the name Alterisphingorhabdus coralli gen. nov. sp. nov. is proposed.},
}

*Phylogeny
*Anthozoa/microbiology
Animals
*Fatty Acids
*DNA, Bacterial/genetics
*Bacterial Typing Techniques
*RNA, Ribosomal, 16S/genetics
*Sequence Analysis, DNA
*Ubiquinone
*Coral Reefs
Base Composition
Sphingomonadaceae/genetics/isolation & purification/classification
Nucleic Acid Hybridization
Phototrophic Processes

@article {pmid39570026,
year = {2024},
author = {Waterworth, SC and Solomons, GM and Kalinski, J-CJ and Madonsela, LS and Parker-Nance, S and Dorrington, RA},
title = {The unique and enigmatic spirochete symbiont of latrunculid sponges.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0084524},
doi = {10.1128/msphere.00845-24},
pmid = {39570026},
issn = {2379-5042},
abstract = {Bacterial symbionts are critical members of many marine sponge holobionts. Some sponge-associated bacterial lineages, such as Poribacteria, sponge-associated unclassified lineage (SAUL), and Tethybacterales, appear to have broad-host ranges and associate with a diversity of sponge species, while others are more species-specific, having adapted to the niche environment of their host. Host-associated spirochete symbionts that are numerically dominant have been documented in several invertebrates including termites, starfish, and corals. However, dominant spirochete populations are rare in marine sponges, having thus far been observed only in Clathrina clathrus and various species within the Latrunculiidae family, where they are co-dominant alongside Tethybacterales symbionts. This study aimed to characterize these spirochetes and their potential role in the host sponge. Analysis of metagenome-assembled genomes from eight latrunculid sponges revealed that these unusual spirochetes are relatively recent symbionts and are phylogenetically distinct from other sponge-associated spirochetes. Functional comparative analysis suggests that the host sponge may have selected for these spirochetes due to their ability to produce terpenoids and/or possible structural contributions.IMPORTANCESouth African latrunculid sponges are host to co-dominant Tethybacterales and Spirochete symbionts. While the Tethybacterales are broad-host range symbionts, the spirochetes have not been reported as abundant in any other marine sponge except Clathrina clathrus. However, spirochetes are regularly the most dominant populations in marine corals and terrestrial invertebrates where they are predicted to serve as beneficial symbionts. Here, we interrogated eight metagenome-assembled genomes of the latrunculid-associated spirochetes and found that these symbionts are phylogenetically distinct from all invertebrate-associated spirochetes. The symbiosis between the spirochetes and their sponge host appears to have been established relatively recently.},
}

@article {pmid39568770,
year = {2024},
author = {Guéganton, M and Methou, P and Aubé, J and Noël, C and Rouxel, O and Cueff-Gauchard, V and Gayet, N and Durand, L and Pradillon, F and Cambon-Bonavita, MA},
title = {Symbiont Acquisition Strategies in Post-Settlement Stages of Two Co-Occurring Deep-Sea Rimicaris Shrimp.},
journal = {Ecology and evolution},
volume = {14},
number = {11},
pages = {e70369},
pmid = {39568770},
issn = {2045-7758},
abstract = {At deep-sea hydrothermal vents, deprived of light, most living communities are fueled by chemosynthetic microorganisms. These can form symbiotic associations with metazoan hosts, which are then called holobionts. Among these, two endemic co-occurring shrimp of the Mid-Atlantic Ridge (MAR), Rimicaris exoculata and Rimicaris chacei are colonized by dense and diversified chemosynthetic symbiotic communities in their cephalothoracic cavity and their digestive system. Although both shrimp harbor similar communities, they exhibit widely different population densities, distribution patterns at small scale and diet, as well as differences in post-settlement morphological modifications leading to the adult stage. These contrasting biological traits may be linked to their symbiotic development success. Consequently, key questions related to the acquisition of the symbiotic communities and the development of the three symbiotic organs are still open. Here we examined symbiotic development in juveniles of R. exoculata and R. chacei from TAG and Snake Pit using 16S metabarcoding to identify which symbiotic lineages are present at each juvenile stage. In addition, we highlighted the abundance and distribution of microorganisms at each stage using Fluorescence in situ Hybridization (FISH) and Scanning Electron Microscopy (SEM). For the first time, Candidatus Microvillispirillaceae family with Candidatus Rimicarispirillum spp. (midgut tube), Candidatus Foregutplasma rimicarensis and Candidatus BG2-rimicarensis (foregut) were identified in late juvenile stages. However, these lineages were absent in early juvenile stages, which coincides for the midgut tube with our observations of an immature tissue, devoid of microvilli. Conversely, symbiotic lineages from the cephalothoracic cavity were present from the earliest juvenile stages of both species and their overall diversities were similar to those of adults. These results suggest different symbiont acquisition dynamics between the cephalothoracic cavity and the digestive system, which may also involve distinct transmission mechanisms.},
}

@article {pmid39565113,
year = {2024},
author = {Nowak, VV and Hou, P and Owen, JG},
title = {Microbial communities associated with marine sponges from diverse geographic locations harbor biosynthetic novelty.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0072624},
doi = {10.1128/aem.00726-24},
pmid = {39565113},
issn = {1098-5336},
abstract = {Marine sponges are a prolific source of biologically active small molecules, many of which originate from sponge-associated bacteria. Identifying the producing bacteria is a key step in developing sustainable routes for the production of these metabolites. To facilitate the required computational analyses, we developed MetaSing, a reproducible singularity-based pipeline for assembly, identification of high-quality metagenome-assembled genomes (MAGs), and analysis of biosynthetic gene clusters (BGCs) from metagenomic short-read data. We applied this pipeline to metagenomic sequencing data from 16 marine sponges collected from New Zealand, Tonga, and the Mediterranean Sea. This analysis yielded 643 MAGs representing 510 species. Of the 2,670 BGCs identified across all samples, 70.8% were linked to a MAG. Comparison of BGCs to those identified from previously sequenced bacteria revealed high biosynthetic novelty in variety of underexplored phyla, including Poribacteria, Acidobacteriota, and Dadabacteria. Alongside the observation that each sample contains unique biosynthetic potential, this holds great promise for natural product discovery and for furthering the understanding of different sponge holobionts.IMPORTANCEDiscovery of new chemical compounds such as natural products is a crucial endeavor to combat the increasing resistance to antibiotics and other drugs. This manuscript demonstrates that microbial communities associated with marine sponges investigated in this work encode the potential to produce novel chemistry. Lesser studied bacterial taxa that are often difficult to cultivate are particularly rich in potential.},
}

@article {pmid39558079,
year = {2024},
author = {Sun, Y and Sheng, H and Rädecker, N and Lan, Y and Tong, H and Huang, L and Jiang, L and Diaz-Pulido, G and Zou, B and Zhang, Y and Kao, SJ and Qian, PY and Huang, H},
title = {Symbiodiniaceae algal symbionts of Pocillopora damicornis larvae provide more carbon to their coral host under elevated levels of acidification and temperature.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1528},
pmid = {39558079},
issn = {2399-3642},
support = {42206153//National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)/ ; 41906040//National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)/ ; },
abstract = {Climate change destabilizes the symbiosis between corals and Symbiodiniaceae. The effects of ocean acidification and warming on critical aspects of coral survical such as symbiotic interactions (i.e., carbon and nitrogen assimilation and exchange) during the planula larval stage remain understudied. By combining physiological and stable isotope techniques, here we show that photosynthesis and carbon and nitrogen assimilation (H[13]CO3[-] and [15]NH4[+]) in Pocillopora damicornis coral larvae is enhanced under acidification (1000 µatm) and elevated temperature (32 °C). Larvae maintain high survival and settlement rates under these treatment conditions with no observed decline in symbiont densities or signs of bleaching. Acidification and elevated temperature both enhance the net and gross photosynthesis of Symbiodiniaceae. This enhances light respiration and elevates C:N ratios within the holobiont. The increased carbon availability is primarily reflected in the [13]C enrichment of the host, indicating a greater contribution of the algal symbionts to the host metabolism. We propose that this enhanced mutualistic symbiotic nutrient cycling may bolster coral larvae's resistance to future ocean conditions. This research broadens our understanding of the early life stages of corals by emphasizing the significance of symbiotic interactions beyond those of adult corals.},
}

@article {pmid39553893,
year = {2024},
author = {Pfab, F and Detmer, AR and Moeller, HV and Nisbet, RM and Putnam, HM and Cunning, R},
title = {Heat stress and bleaching in corals: a bioenergetic model.},
journal = {Coral reefs (Online)},
volume = {43},
number = {6},
pages = {1627-1645},
pmid = {39553893},
issn = {1432-0975},
abstract = {UNLABELLED: The coral-dinoflagellate endosymbiosis is based on nutrient exchanges that impact holobiont energetics. Of particular concern is the breakdown or dysbiosis of this partnership that is seen in response to elevated temperatures, where loss of symbionts through coral bleaching can lead to starvation and mortality. Here we extend a dynamic bioenergetic model of coral symbioses to explore the mechanisms by which temperature impacts various processes in the symbiosis and to enable simulational analysis of thermal bleaching. Our model tests the effects of two distinct mechanisms for how increased temperature impacts the symbiosis: 1) accelerated metabolic rates due to thermodynamics and 2) damage to the photosynthetic machinery of the symbiont caused by heat stress. Model simulations show that the model can capture key biological responses to different levels of increased temperatures. Moderately increased temperatures increase metabolic rates and slightly decrease photosynthesis. The slightly decreased photosynthesis rates cause the host to receive less carbon and share more nitrogen with the symbiont. This results in temporarily increased symbiont growth and a higher symbiont/host ratio. In contrast, higher temperatures cause a breakdown of the symbiosis due to escalating feedback that involves further reduction in photosynthesis and insufficient energy supply for CO 2 concentration by the host. This leads to the accumulation of excess light energy and the generation of reactive oxygen species, eventually triggering symbiont expulsion and coral bleaching. Importantly, bleaching does not result from accelerated metabolic rates alone; it only occurs as a result of the photodamage mechanism due to its effect on nutrient cycling. Both higher light intensities and higher levels of DIN render corals more susceptible to heat stress. Conversely, heterotrophic feeding can increase the maximal temperature that can be tolerated by the coral. Collectively these results show that a bioenergetics model can capture many observed patterns of heat stress in corals, such as higher metabolic rates and higher symbiont/host ratios at moderately increased temperatures and symbiont expulsion at strongly increased temperatures.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00338-024-02561-1.},
}

@article {pmid39543733,
year = {2024},
author = {Köster, PC and Figueiredo, AM and Maloney, JG and Dashti, A and Bailo, B and Torres, RT and Fonseca, C and Mysterud, A and Habela, MÁ and Rivero-Juarez, A and Vicente, J and Serrano, E and Arnal, MC and de Luco, DF and Armenteros, JA and Balseiro, A and Cardona, GA and Carvalho, J and Hipólito, D and Fernandes, J and Palmeira, JD and Calero-Bernal, R and González-Barrio, D and Santin, M and Carmena, D},
title = {Correction: Blastocystis occurrence and subtype diversity in European wild boar (Sus scrofa) from the Iberian Peninsula.},
journal = {Veterinary research},
volume = {55},
number = {1},
pages = {152},
pmid = {39543733},
issn = {1297-9716},
}

@article {pmid39541453,
year = {2024},
author = {Bordenstein, SR and The Holobiont Biology Network, and , },
title = {The disciplinary matrix of holobiont biology.},
journal = {Science (New York, N.Y.)},
volume = {386},
number = {6723},
pages = {731-732},
doi = {10.1126/science.ado2152},
pmid = {39541453},
issn = {1095-9203},
mesh = {*Symbiosis ; Biology ; },
abstract = {Uniting life's seen and unseen realms guides a conceptual advance in research.},
}

*Symbiosis
Biology

@article {pmid39539714,
year = {2024},
author = {Hauptmann, AL and Johansen, J and Stæger, FF and Nielsen, DS and Mulvad, G and Hanghøj, K and Rasmussen, S and Hansen, T and Albrechtsen, A},
title = {Gut heavy metal and antibiotic resistome of humans living in the high Arctic.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1493803},
doi = {10.3389/fmicb.2024.1493803},
pmid = {39539714},
issn = {1664-302X},
abstract = {Contaminants, such as heavy metals (HMs), accumulate in the Arctic environment and the food web. The diet of the Indigenous Peoples of North Greenland includes locally sourced foods that are central to their nutritional, cultural, and societal health but these foods also contain high concentrations of heavy metals. While bacteria play an essential role in the metabolism of xenobiotics, there are limited studies on the impact of heavy metals on the human gut microbiome, and it is so far unknown if and how Arctic environmental contaminants impact the gut microbes of humans living in and off the Arctic environment. Using a multiomics approach including amplicon, metagenome, and metatranscriptome sequencing, we identified and assembled a near-complete (NC) genome of a mercury-resistant bacterial strain from the human gut microbiome, which expressed genes known to reduce mercury toxicity. At the overall ecological level studied through α- and β-diversity, there was no significant effect of heavy metals on the gut microbiota. Through the assembly of a high number of NC metagenome-assembled genomes (MAGs) of human gut microbes, we observed an almost complete overlap between heavy metal-resistant strains and antibiotic-resistant strains in which resistance genes were all located on the same genetic elements.},
}

@article {pmid39536868,
year = {2024},
author = {Koll, R and Hauten, E and Theilen, J and Bang, C and Bouchard, M and Thiel, R and Möllmann, C and Woodhouse, JN and Fabrizius, A},
title = {Spatio-temporal plasticity of gill microbiota in estuarine fish.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {177505},
doi = {10.1016/j.scitotenv.2024.177505},
pmid = {39536868},
issn = {1879-1026},
abstract = {Coastal marine and estuarine systems are subject to enormous endogenous and exogenous pressures, particularly climate change, while at the same time being highly productive sources and nurseries for fish populations. Interactions between host and microbiome are increasingly recognized for their importance for fish health, with growing evidence indicating that increasing environmental pressures impact host resilience and favor the raise of opportunistic bacterial taxa. The microbial composition of the gill mucus reflects environmental conditions and represents an entry route for pathogens into the fish body. High-throughput sequencing of prokaryotic populations from 250 samples of two fish species with highly different habitat preferences, as well as seasonal and spatial distributions in the Elbe estuary system, allowed us to describe the variation of the microbiota along a salinity gradient and under fluctuating environmental conditions. The analysis of estuarine fish core microbiota in relation to variable bacterial components indicated dysbiotic states under sustained hypoxia and high nutrient loads largely driven by increased prevalence of facultatively aerobic (Acinetobacter) and anaerobic heterotrophs (Shewanella, Aeromonas). By correlating bacterial abundances with environmental and physiological parameters in a co-occurrence network approach, we describe plasticity in microbiota composition, identify potential biomarkers for fish health monitoring and reconstruct movement patterns of the fish. Our results can help to shape future minimal-invasive and cost-effective monitoring programs, and identify factors that need to be controlled in the estuary to promote fish and stock health.},
}

@article {pmid39536370,
year = {2024},
author = {Anthony, CJ and Lock, C and Pérez-Rosales, G and Rouzé, H and Paulino, L and Raymundo, LJ and Bentlage, B},
title = {Symbiodiniaceae phenotypic traits as bioindicators of acclimatization after coral transplantation.},
journal = {Marine pollution bulletin},
volume = {209},
number = {Pt B},
pages = {117250},
doi = {10.1016/j.marpolbul.2024.117250},
pmid = {39536370},
issn = {1879-3363},
abstract = {Coral-dinoflagellate symbiosis underpins coral reef resilience and influences conservation success, given the relationship's role in coral bleaching. Here, we transplanted Guam's dominant staghorn coral, Acropora pulchra, across four coral gardens and monitored their endosymbiotic dinoflagellates (family Symbiodiniaceae) for ∼15 months (May 2021-August 2022). Transplantation and predation resulted in temporary symbiotic destabilization, as signaled by increased cell roughness and decreased cell density. Eventually, the Symbiodiniaceae phenotypic profile mostly converged with the wild population, although cell density and red fluorescing photopigments remained modified. In March, corals paled, which allowed us to evaluate the Symbiodiniaceae assemblage's relationship with host color. Interestingly, cell density was not the most informative when predicting host color. Instead, fluorescence from antioxidant-associated pigments were most informative. We conclude that Symbiodiniaceae phenotypic traits respond differently depending on the condition, supporting their development as acclimatization bioindicators.},
}

@article {pmid39529628,
year = {2024},
author = {López-Rodríguez, MR and Gérikas Ribeiro, C and Rodríguez-Marconi, S and Parada-Pozo, G and Manrique-de-la-Cuba, M and Trefault, N},
title = {Stable dominance of parasitic dinoflagellates in Antarctic sponges.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e18365},
pmid = {39529628},
issn = {2167-8359},
mesh = {Antarctic Regions ; *Dinoflagellida/genetics/physiology ; Animals ; *Porifera/parasitology ; Symbiosis ; Seawater/parasitology/microbiology ; Biodiversity ; },
abstract = {BACKGROUND: Marine sponges are dominant components of Antarctic benthos and representative of the high endemism that characterizes this environment. All microbial groups are part of the Antarctic sponge holobionts, but microbial eukaryotes have been studied less, and their symbiotic role still needs to be better understood. Here, we characterize the dynamics of microbial eukaryotes associated with Antarctic sponges, focusing on dinoflagellates over three summer periods to better understand the members, interannual variations, and trophic and lifestyle strategies.

RESULTS: The analysis revealed that dinoflagellates dominate microeukaryotic communities in Antarctic sponges. The results also showed significant differences in the diversity and composition of dinoflagellate communities associated with sponges compared to those in seawater. Antarctic sponges were dominated by a single dinoflagellate family, Syndiniales Dino-Group-I-Clade 1, which was present in high abundance in Antarctic sponges compared to seawater communities. Despite minor differences, the top microeukaryotic amplicon sequence variants (ASVs) showed no significant interannual abundance changes, indicating general temporal stability within the studied sponge species. Our findings highlight the abundance and importance of parasitic groups, particularly the classes Coccidiomorphea, Gregarinomorphea, and Ichthyosporea, with the exclusive dominance of Syndiniales Dino-Group-I-Clade 1 within sponges.

CONCLUSIONS: The present study comprehensively characterizes the microbial eukaryotes associated with Antarctic sponges, showing a remarkable stability of parasitic dinoflagellates in Antarctic sponges. These findings underscore the significant role of parasites in these marine hosts, with implications for population dynamics of the microeukaryome and the holobiont response to a changing ocean.},
}

Antarctic Regions
*Dinoflagellida/genetics/physiology
Animals
*Porifera/parasitology
Symbiosis
Seawater/parasitology/microbiology
Biodiversity

@article {pmid39524434,
year = {2024},
author = {Hong, L and Wang, Q and Zhang, J and Chen, X and Liu, Y and Asiegbu, FO and Wu, P and Ma, X and Wang, K},
title = {Advances in the beneficial endophytic fungi for the growth and health of woody plants.},
journal = {Forestry research},
volume = {4},
number = {},
pages = {e028},
pmid = {39524434},
issn = {2767-3812},
abstract = {In recent years, the importance of microorganisms for plant survival has been increasingly recognized. Endophytic fungi, as part of holobiont, can confer growth advantages to plants. Most studies have shown that the endophytic fungi of forest trees can promote host plant growth, increase adversity resistance, and thus improve the survival competitiveness of forest trees. However, the beneficial examples of endophytic fungi on the growth and development of woody plants have not been systematically summarized. This review is focused on various aspects of beneficial endophytic fungi in forest trees (definition, classification, colonization mechanisms, etc.), with an emphasis on their beneficial roles in woody plant growth, protection against biotic and abiotic stresses, as well as the response of forest trees to endophytic fungi. In addition, this review lists a series of experiments on screening beneficial endophytic fungi from Chinese fir (Cunninghamia lanceolata) and verifying their beneficial functions, to explore the mutualistic relationships between them. This review not only provides a theoretical basis for the study of beneficial endophytic fungi in forest trees in the future but also sheds light on the molecular perspectives for a mechanistic understanding of their potential future significance for the sustainable utilization of forest resources and ecological environment protection.},
}

@article {pmid39517101,
year = {2024},
author = {Gantt, SE and Kemp, KM and Colin, PL and Hoadley, KD and LaJeunesse, TC and Warner, ME and Kemp, DW},
title = {Influence of reef habitat on coral microbial associations.},
journal = {Environmental microbiology reports},
volume = {16},
number = {6},
pages = {e70051},
doi = {10.1111/1758-2229.70051},
pmid = {39517101},
issn = {1758-2229},
support = {//University of Alabama at Birmingham/ ; IOS-1258058//National Science Foundation/ ; IOS-1258065//National Science Foundation/ ; IOS-1719675//National Science Foundation/ ; OCE-1635695//National Science Foundation/ ; OCE-1636022//National Science Foundation/ ; OCE-1719684//National Science Foundation/ ; },
mesh = {*Anthozoa/microbiology ; Animals ; *Coral Reefs ; *Symbiosis ; *Dinoflagellida/physiology/classification ; *Microbiota ; Bacteria/classification/isolation & purification/genetics ; Ecosystem ; Palau ; },
abstract = {Corals have complex symbiotic associations that can be influenced by the environment. We compare symbiotic dinoflagellate (family: Symbiodiniaceae) associations and the microbiome of five scleractinian coral species from three different reef habitats in Palau, Micronesia. Although pH and temperature corresponded with specific host-Symbiodiniaceae associations common to the nearshore and offshore habitats, bacterial community dissimilarity analyses indicated minimal influence of these factors on microbial community membership for the corals Coelastrea aspera, Psammocora digitata, and Pachyseris rugosa. However, coral colonies sampled close to human development exhibited greater differences in microbial community diversity compared to the nearshore habitat for the coral species Coelastrea aspera, Montipora foliosa, and Pocillopora acuta, and the offshore habitat for Coelastrea aspera, while also showing less consistency in Symbiodiniaceae associations. These findings indicate the influence that habitat location has on the bacterial and Symbiodiniaceae communities comprising the coral holobiont and provide important considerations for the conservation of coral reef communities, especially for island nations with increasing human populations and development.},
}

*Anthozoa/microbiology
Animals
*Coral Reefs
*Symbiosis
*Dinoflagellida/physiology/classification
*Microbiota
Bacteria/classification/isolation & purification/genetics
Ecosystem
Palau

@article {pmid39513573,
year = {2024},
author = {Brown, AL and Koskella, B and Boots, M},
title = {How host-microbiome/holobiont evolution depends on whether the microbiome affects host lifespan or fecundity.},
journal = {Journal of evolutionary biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jeb/voae127},
pmid = {39513573},
issn = {1420-9101},
support = {GBMF10578//Gordon and Betty Moore Foundation/ ; },
abstract = {There is overwhelming evidence that the microbiome can be important to host physiology and fitness. As such, there is interest in and some theoretical work on understanding when hosts and microbiomes (co)evolve so that microbes benefit hosts and hosts favour beneficial microbes. However, the outcome of evolution likely depends on how microbes benefit hosts. Here, we use adaptive dynamics to investigate how host and symbiont evolution depend on whether symbionts increase host lifespan or host reproduction in a simple model of host and symbiont dynamics. In addition, we investigate 2 ways hosts release (and transmit) symbionts: by releasing symbionts steadily during their lifetime or by releasing them at reproduction, potentially increasing symbionts' chances of infecting the host's offspring. The former is strict horizontal transmission, whereas the latter is also a form of indirect or "pseudovertical" transmission. Our first key result is that the evolution of symbionts that benefit host fecundity requires pseudovertical transmission, while the evolution of symbionts that benefit host lifespan does not. Furthermore, our second key result is that when investing in host benefits is costly to the free-living symbiont stage, intermediate levels of pseudovertical transmission are needed for selection to favour beneficial symbionts. This is true regardless of fitness effects because release at reproduction increases the free-living symbiont population, which increases competition for hosts. Consequently, hosts could evolve away from traits that favour beneficial symbionts. Generally, our work emphasizes the importance of different forms of vertical transmission and fitness benefits in host, microbiome, and holobiont evolution as highlighted by our prediction that the evolution of fecundity-increasing symbionts requires parent-to-offspring transmission.},
}

@article {pmid39511978,
year = {2024},
author = {Hecht, K and Kowalchuk, GA and Ford Denison, R and Kahmen, A and Xiong, W and Jousset, A and Ravanbakhsh, M},
title = {Deletion of ACC Deaminase in Symbionts Converts the Host Plant From Water Waster to Water Saver.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.15265},
pmid = {39511978},
issn = {1365-3040},
abstract = {Increasing drought events coupled with dwindling water reserves threaten global food production and security. This issue is exacerbated by the use of crops that overconsume water, undermining yield. We show here that microorganisms naturally associated with plant roots can undermine efficient water use, whereas modified bacteria can enhance it. We demonstrate that microbe-encoded genes shape drought tolerance, likely by modulating plant hormonal balance. Specifically, we built a minimal holobiont out of Arabidopsis thaliana and either the bacterium Pseudomonas putida UW4 or its isogenic AcdS[-] mutant, lacking the enzyme ACC deaminase. This enzyme breaks down the precursor of ethylene, a key regulator in plant response to drought. This single mutation profoundly affected plant physiology and shifted the plant from a 'water-spender' (with more growth under well-watered conditions) to a 'water-spender' phenotype. Under drought, plants associated with wild-type bacteria consumed soil water faster, leading to a shorter period of growth followed by death. In contrast, plants associated with the AcdS[-] mutant managed to maintain growth by reducing water consumption via stomatal closure, thus conserving soil water. This allowed plants to survive severe water deficiency. We conclude that plant-associated bacteria can modulate plant water use strategies, opening possibilities to engineer water-savvy crop-production systems.},
}

@article {pmid39509495,
year = {2024},
author = {Arafeh-Dalmau, N and Olguín-Jacobson, C and Earle, S and Bello, M and Lagger, C and Mora-Soto, A and Pantano, C and Palacios, M and Barbosa, RV and Fica-Rojas, E and Guajardo, E and Aburto-Oropeza, O and Eger, A and Dayton, P and Giraldo-Ospina, A and Cavanaugh, K and García-Pantoja, J and Montaño-Moctezuma, G and Possingham, H and Sala, E and Schoeman, D and Torres-Moye, G and Micheli, F},
title = {Protect kelp forests.},
journal = {Science (New York, N.Y.)},
volume = {386},
number = {6722},
pages = {629},
doi = {10.1126/science.adr4814},
pmid = {39509495},
issn = {1095-9203},
}

@article {pmid39505929,
year = {2024},
author = {Dantan, L and Carcassonne, P and Degrémont, L and Morga, B and Travers, MA and Petton, B and Mege, M and Maurouard, E and Allienne, JF and Courtay, G and Romatif, O and Pouzadoux, J and Lami, R and Intertaglia, L and Gueguen, Y and Vidal-Dupiol, J and Toulza, E and Cosseau, C},
title = {Microbial education plays a crucial role in harnessing the beneficial properties of microbiota for infectious disease protection in Crassostrea gigas.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {26914},
pmid = {39505929},
issn = {2045-2322},
support = {n°PFEA470020FA1000007//Fond Européen pour les Affaires Maritimes et la Pêche (FEAMP, GESTINNOV)/ ; n°PFEA470020FA1000007//Fond Européen pour les Affaires Maritimes et la Pêche (FEAMP, GESTINNOV)/ ; n°PFEA470020FA1000007//Fond Européen pour les Affaires Maritimes et la Pêche (FEAMP, GESTINNOV)/ ; n°PFEA470020FA1000007//Fond Européen pour les Affaires Maritimes et la Pêche (FEAMP, GESTINNOV)/ ; n°PFEA470020FA1000007//Fond Européen pour les Affaires Maritimes et la Pêche (FEAMP, GESTINNOV)/ ; n°PFEA470020FA1000007//Fond Européen pour les Affaires Maritimes et la Pêche (FEAMP, GESTINNOV)/ ; n°PFEA470020FA1000007//Fond Européen pour les Affaires Maritimes et la Pêche (FEAMP, GESTINNOV)/ ; n°PFEA470020FA1000007//Fond Européen pour les Affaires Maritimes et la Pêche (FEAMP, GESTINNOV)/ ; n°PFEA470020FA1000007//Fond Européen pour les Affaires Maritimes et la Pêche (FEAMP, GESTINNOV)/ ; n°PFEA470020FA1000007//Fond Européen pour les Affaires Maritimes et la Pêche (FEAMP, GESTINNOV)/ ; n°PFEA470020FA1000007//Fond Européen pour les Affaires Maritimes et la Pêche (FEAMP, GESTINNOV)/ ; n°PFEA470020FA1000007//Fond Européen pour les Affaires Maritimes et la Pêche (FEAMP, GESTINNOV)/ ; n°PFEA470020FA1000007//Fond Européen pour les Affaires Maritimes et la Pêche (FEAMP, GESTINNOV)/ ; n°PFEA470020FA1000007//Fond Européen pour les Affaires Maritimes et la Pêche (FEAMP, GESTINNOV)/ ; n°PFEA470020FA1000007//Fond Européen pour les Affaires Maritimes et la Pêche (FEAMP, GESTINNOV)/ ; ANR-19-CE20-0004//ANR DECICOMP/ ; ANR-19-CE20-0004//ANR DECICOMP/ ; ANR-19-CE20-0004//ANR DECICOMP/ ; ANR-19-CE20-0004//ANR DECICOMP/ ; ANR-19-CE20-0004//ANR DECICOMP/ ; ANR-19-CE20-0004//ANR DECICOMP/ ; ANR-19-CE20-0004//ANR DECICOMP/ ; ANR-19-CE20-0004//ANR DECICOMP/ ; ANR-19-CE20-0004//ANR DECICOMP/ ; ANR-19-CE20-0004//ANR DECICOMP/ ; ANR-19-CE20-0004//ANR DECICOMP/ ; ANR-19-CE20-0004//ANR DECICOMP/ ; ANR-19-CE20-0004//ANR DECICOMP/ ; ANR-19-CE20-0004//ANR DECICOMP/ ; ANR-10-LABX-41//Laboratoires d'Excellences (LABEX): TULIP/ ; ANR-10-LABX-41//Laboratoires d'Excellences (LABEX): TULIP/ ; ANR-10-LABX-41//Laboratoires d'Excellences (LABEX): TULIP/ ; ANR-10-LABX-41//Laboratoires d'Excellences (LABEX): TULIP/ ; ANR-10-LABX-41//Laboratoires d'Excellences (LABEX): TULIP/ ; ANR-10-LABX-41//Laboratoires d'Excellences (LABEX): TULIP/ ; ANR-10-LABX-41//Laboratoires d'Excellences (LABEX): TULIP/ ; ANR-10-LABX-41//Laboratoires d'Excellences (LABEX): TULIP/ ; ANR-10-LABX-41//Laboratoires d'Excellences (LABEX): TULIP/ ; ANR-10-LABX-41//Laboratoires d'Excellences (LABEX): TULIP/ ; ANR-10-LABX-04-01//Laboratoires d'Excellences (LABEX): CEMEB/ ; ANR-10-LABX-04-01//Laboratoires d'Excellences (LABEX): CEMEB/ ; ANR-10-LABX-04-01//Laboratoires d'Excellences (LABEX): CEMEB/ ; ANR-10-LABX-04-01//Laboratoires d'Excellences (LABEX): CEMEB/ ; ANR-10-LABX-04-01//Laboratoires d'Excellences (LABEX): CEMEB/ ; ANR-10-LABX-04-01//Laboratoires d'Excellences (LABEX): CEMEB/ ; ANR-10-LABX-04-01//Laboratoires d'Excellences (LABEX): CEMEB/ ; ANR-10-LABX-04-01//Laboratoires d'Excellences (LABEX): CEMEB/ ; ANR-10-LABX-04-01//Laboratoires d'Excellences (LABEX): CEMEB/ ; ANR-10-LABX-04-01//Laboratoires d'Excellences (LABEX): CEMEB/ ; ANR-10-LABX-04-01//Laboratoires d'Excellences (LABEX): CEMEB/ ; },
mesh = {Animals ; *Crassostrea/microbiology/immunology ; *Microbiota ; *Vibrio/immunology/pathogenicity ; Larva/microbiology/immunology ; Vibrio Infections/prevention & control/immunology/veterinary/microbiology ; Aquaculture/methods ; },
abstract = {The increase in marine diseases, particularly in economically important mollusks, is a growing concern. Among them, the Pacific oyster (Crassostrea gigas) production faces challenges from several diseases, such as the Pacific Oyster Mortality Syndrome (POMS) or vibriosis. The microbial education, which consists of exposing the host immune system to beneficial microorganisms during early life stages is a promising approach against diseases. This study explores the concept of microbial education using controlled and pathogen-free bacterial communities and assesses its protective effects against POMS and Vibrio aestuarianus infections, highlighting potential applications in oyster production. We demonstrate that it is possible to educate the oyster immune system by adding microorganisms during the larval stage. Adding culture based bacterial mixes to larvae protects only against the POMS disease while adding whole microbial communities from oyster donors protects against both POMS and vibriosis. The efficiency of immune protection depends both on oyster origin and on the composition of the bacterial mixes used for exposure. No preferential protection was observed when the oysters were stimulated with their sympatric strains. Furthermore, the added bacteria were not maintained into the oyster microbiota, but this bacterial addition induced long term changes in the microbiota composition and oyster immune gene expression. Our study reveals successful immune system education of oysters by introducing beneficial microorganisms during the larval stage. We improved the long-term resistance of oysters against critical diseases (POMS disease and Vibrio aestuarianus infections) highlighting the potential of microbial education in aquaculture.},
}

Animals
*Crassostrea/microbiology/immunology
*Microbiota
*Vibrio/immunology/pathogenicity
Larva/microbiology/immunology
Vibrio Infections/prevention & control/immunology/veterinary/microbiology
Aquaculture/methods

@article {pmid39499397,
year = {2024},
author = {Hashemi, TS and Soltani, J and Samsampour, D and Seyahooei, MA and Ghasemi, M},
title = {Spatiotemporal diversity of bacterial endophyte microbiome of mandarin (Citrus reticulata) in the northern Persian Gulf and its HCN production and N2 fixation.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {39499397},
issn = {1874-9356},
abstract = {Endophytes are symbionts that live in healthy plants and potentially improve the health of plant holobionts. Here, we investigated the bacterial endophyte community of Citrus reticulata grown in the northern Persian Gulf. Bacteria were isolated seasonally from healthy trees (root, stem, bark, trunk, leaf, and crown tissues) in four regions of Hormozgan province (i.e., Ahmadi, Siyahoo, Sikhoran, Roudan), a subtropical hot region in Iran. A total of 742 strains from 17 taxa, 3 phyla, and 5 orders were found, most of which belonged to Actinobacteria (Actinobacteriales) as the dominant group, followed by Firmicutes (Bacillales), Proteobacteria (Sphingomonadales, Rhizobiales), and Cyanobacteria (Synechoccales). The genera included Altererythrobacter, Arthrobacter, Bacillus, Cellulosimicrobium, Curtobacterium, Kocuria, Kytococcus, Methylopila, Mycobacterium, Nocardioides, Okiabacterium, Paracraurococcus, and Psychrobacillus. The most frequently occurring species included Psychrobacillus psychrodurans, Kytococcus schroetri, and Bacillus cereus. In addition, the overall colonization frequency and variability of endophytes were higher on the trunks. The leaves showed the lowest species variability in all sampling periods. The frequency of endophyte colonization was also higher in summer. The Shannon-Wiener (H') and Simpson indices varied with all factors, i.e., region, season, and tissue type, with the maximum in Roudan. Furthermore, 52.9% of the strains were capable of nitrogen fixation, and 70% produced antagonistic hydrogen cyanide (HCN). Thus, C. reticulata harbors a variety of bioactive bacterial endophytes that could be beneficial for host fitness in such harsh environments.},
}

@article {pmid39498138,
year = {2024},
author = {Jain, S and Vaishnav, A and Choudhary, DK},
title = {Editorial: Climate impact on plant holobiont: mitigation strategies and sustainability, volume II.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1503816},
pmid = {39498138},
issn = {1664-302X},
}

@article {pmid39497183,
year = {2024},
author = {Prioux, C and Ferrier-Pages, C and Deter, J and Tignat-Perrier, R and Guilbert, A and Ballesta, L and Allemand, D and van de Water, JAJM},
title = {Insights into the occurrence of phylosymbiosis and co-phylogeny in the holobionts of octocorals from the Mediterranean Sea and Red Sea.},
journal = {Animal microbiome},
volume = {6},
number = {1},
pages = {62},
pmid = {39497183},
issn = {2524-4671},
abstract = {BACKGROUND: Corals are the foundational species of coral reefs and coralligenous ecosystems. Their success has been linked to symbioses with microorganisms, and a coral host and its symbionts are therefore considered a single entity, called the holobiont. This suggests that there may be evolutionary links between corals and their microbiomes. While there is evidence of phylosymbiosis in scleractinian hexacorals, little is known about the holobionts of Alcyonacean octocorals.

RESULTS: 16S rRNA gene amplicon sequencing revealed differences in the diversity and composition of bacterial communities associated with octocorals collected from the mesophotic zones of the Mediterranean and Red Seas. The low diversity and consistent dominance of Endozoicomonadaceae and/or Spirochaetaceae in the bacterial communities of Mediterranean octocorals suggest that these corals may have a shared evolutionary history with their microbiota. Phylosymbiotic signals were indeed detected and cophylogeny in associations between several bacterial strains, particularly those belonging to Endozoicomonadaceae or Spirochaetaceae, and coral species were identified. Conversely, phylosymbiotic patterns were not evident in Red Sea octocorals, likely due to the high bacterial taxonomic diversity in their microbiota, but cophylogeny in associations between certain coral and bacterial species was observed. Noteworthy were the associations with Endozoicomonadaceae, suggesting a plausible evolutionary link that warrants further investigations to uncover potential underlying patterns.

CONCLUSIONS: Overall, our findings emphasize the importance of Endozoicomonadaceae and Spirochaetaceae in coral symbiosis and the significance of exploring host-microbiome interactions in mesophotic ecosystems for a comprehensive understanding of coral-microbiome evolutionary history.},
}

@article {pmid39489036,
year = {2024},
author = {Hussain, M and Aizpurua, O and Pérez de Rozas, A and París, N and Guivernau, M and Jofré, A and Tous, N and Ng'ang'a, ZW and Alberdi, A and Rodríguez-Gallego, E and Kogut, MH and Tarradas, J},
title = {Positive impact of early-probiotic administration on performance parameters, intestinal health and microbiota populations in broiler chickens.},
journal = {Poultry science},
volume = {103},
number = {12},
pages = {104401},
doi = {10.1016/j.psj.2024.104401},
pmid = {39489036},
issn = {1525-3171},
abstract = {Minimizing the utilization of antibiotics in animal production is crucial to prevent the emergence of antimicrobial resistances. Thus, research on alternatives is needed to maintain productivity, sustainability, and animal health. To gain a comprehensive understanding of probiotics' modes of action on performance, intestinal microbiota, and gut health in poultry, 3 probiotic strains (Enterococcus faecalis CV1028 [EntF], Bacteroides fragilis GP1764 [BacF], and Ligilactobacillus salivarius CTC2197 [LacS]) were tested in 2 in vivo trials. Trial 1 comprised of a negative control group fed basal diet (BD) and 3 treatment groups that received BD with EntF, BacF and LacS. Trial 2 included a negative control group, a positive control group with Zinc-Bacitracin as antibiotic growth promoter (AGP), and 2 groups treated with a blend of probiotics (EntF+BacF+LacS) during 0 to 10 or 0 to 35 d, respectively. Wheat-soybean-rye based diets without exogenous enzymes were used as a challenge model to induce intestinal mild- or moderate-inflammatory process in the gut. In Trial 1, individually administered probiotics improved FCR at 8 d compared to Control, but these positive effects were lost in the following growing periods probably due to the high grade of challenging diet and a too low dose of probiotics. In Trial 2, both Probiotic treatments, administered only 10 or 35 d, significantly improved FCR to the same extent as of the Antibiotic group at the end of the trial. Although the performance between antibiotic and probiotic mixture showed similar values, microbiota analysis revealed different microbial composition at 7 d, but not at 21 d. This suggests that modes of action of the AGP and the tested probiotic blend differ on their effects on microbiome, and that the changes observed during the first days' posthatch are relevant on performance at the end of the study. Therefore, the probiotics administration only during the first 10 d posthatch was proven sufficient to induce similar performance improvements to those observed in birds fed antibiotic growth promoters throughout the whole experimental trial.},
}

@article {pmid39474739,
year = {2024},
author = {Sun, X and Cavill, EL and Margaryan, A and Lin, J and Thingaard, S and Said, TA and Gopalakrishnan, S and Gilbert, MTP},
title = {A Genomic Exploration of the Possible De-Extirpation of the Zanzibar Leopard.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17566},
doi = {10.1111/mec.17566},
pmid = {39474739},
issn = {1365-294X},
support = {681396//ERC Consolidator Award/ ; },
abstract = {The recently extirpated Zanzibar leopard was the only known African leopard (Panthera pardus spp.) population restricted exclusively to a major island habitat. Although its demise was driven through habitat change and conflict with humans, given its role as a keystone species for the Zanzibar Archipelago, its successful potential reintroduction might offer a means for helping preserve the natural biodiversity of its former habitat. Whether this is feasible, however, would be contingent on both whether closely related source populations can be identified on mainland Africa, and whether the Zanzibar form exhibited any special adaptations that might need to be considered when choosing such a source. In light of these questions, we genomically profiled two of the six known historic specimens, to explore whether they represent a realistic candidate for de-extirpation through reintroduction. Our analyses indicate that despite its geographical separation, the Zanzibar leopard shared a close genetic relationship with mainland East African individuals. Furthermore, although its uniqueness as an island population was emphasised by genomic signatures of high inbreeding and increased mutation load, the latter similar to the level of the critically endangered Amur leopard (P. p. orientalis), we find no evidence of functionally significant genetic diversity unique to Zanzibar. We therefore conclude that should attempts to restore leopards to Zanzibar be considered, then mainland East African leopards would provide a suitable gene pool.},
}

@article {pmid39472959,
year = {2024},
author = {Martin-Cuadrado, AB and Rubio-Portillo, E and Rosselló, F and Antón, J},
title = {The coral Oculina patagonica holobiont and its response to confinement, temperature, and Vibrio infections.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {222},
pmid = {39472959},
issn = {2049-2618},
mesh = {*Anthozoa/microbiology ; Animals ; *Coral Reefs ; *Microbiota ; *Vibrio/genetics/classification/physiology/isolation & purification ; Symbiosis ; Temperature ; Bacteria/classification/genetics/isolation & purification ; Metagenomics ; Rhodobacteraceae/genetics/classification/isolation & purification/physiology ; Fungi/classification/genetics/isolation & purification ; Vibrionaceae/genetics/classification/isolation & purification ; Vibrio Infections/microbiology ; Climate Change ; },
abstract = {BACKGROUND: Extensive research on the diversity and functional roles of the microorganisms associated with reef-building corals has been promoted as a consequence of the rapid global decline of coral reefs attributed to climate change. Several studies have highlighted the importance of coral-associated algae (Symbiodinium) and bacteria and their potential roles in promoting coral host fitness and survival. However, the complex coral holobiont extends beyond these components to encompass other entities such as protists, fungi, and viruses. While each constituent has been individually investigated in corals, a comprehensive understanding of their collective roles is imperative for a holistic comprehension of coral health and resilience.

RESULTS: The metagenomic analysis of the microbiome of the coral Oculina patagonica has revealed that fungi of the genera Aspergillus, Fusarium, and Rhizofagus together with the prokaryotic genera Streptomyces, Pseudomonas, and Bacillus were abundant members of the coral holobiont. This study also assessed changes in microeukaryotic, prokaryotic, and viral communities under three stress conditions: aquaria confinement, heat stress, and Vibrio infections. In general, stress conditions led to an increase in Rhodobacteraceae, Flavobacteraceae, and Vibrionaceae families, accompanied by a decrease in Streptomycetaceae. Concurrently, there was a significant decline in both the abundance and richness of microeukaryotic species and a reduction in genes associated with antimicrobial compound production by the coral itself, as well as by Symbiodinium and fungi.

CONCLUSION: Our findings suggest that the interplay between microeukaryotic and prokaryotic components of the coral holobiont may be disrupted by stress conditions, such as confinement, increase of seawater temperature, or Vibrio infection, leading to a dysbiosis in the global microbial community that may increase coral susceptibility to diseases. Further, microeukaryotic community seems to exert influence on the prokaryotic community dynamics, possibly through predation or the production of secondary metabolites with anti-bacterial activity. Video Abstract.},
}

*Anthozoa/microbiology
Animals
*Coral Reefs
*Microbiota
*Vibrio/genetics/classification/physiology/isolation & purification
Symbiosis
Temperature
Bacteria/classification/genetics/isolation & purification
Metagenomics
Rhodobacteraceae/genetics/classification/isolation & purification/physiology
Fungi/classification/genetics/isolation & purification
Vibrionaceae/genetics/classification/isolation & purification
Vibrio Infections/microbiology
Climate Change

@article {pmid39455736,
year = {2024},
author = {Gupta, S and Vera-Ponce de León, A and Kodama, M and Hoetzinger, M and Clausen, CG and Pless, L and Verissimo, ARA and Stengel, B and Calabuig, V and Kvingedal, R and Skugor, S and Westereng, B and Harvey, TN and Nordborg, A and Bertilsson, S and Limborg, MT and Mørkøre, T and Sandve, SR and Pope, PB and Hvidsten, TR and La Rosa, SL},
title = {The need for high-resolution gut microbiome characterization to design efficient strategies for sustainable aquaculture production.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1391},
pmid = {39455736},
issn = {2399-3642},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Aquaculture/methods ; *Salmo salar/microbiology ; *Animal Feed ; Mannans/metabolism ; Dietary Supplements ; Bacteria/genetics/classification/metabolism ; Dietary Fiber/metabolism ; Diet/veterinary ; },
abstract = {Microbiome-directed dietary interventions such as microbiota-directed fibers (MDFs) have a proven track record in eliciting responses in beneficial gut microbes and are increasingly being promoted as an effective strategy to improve animal production systems. Here we used initial metataxonomic data on fish gut microbiomes as well as a wealth of a priori mammalian microbiome knowledge on α-mannooligosaccharides (MOS) and β-mannan-derived MDFs to study effects of such feed supplements in Atlantic salmon (Salmo salar) and their impact on its gut microbiome composition and functionalities. Our multi-omic analysis revealed that the investigated MDFs (two α-mannans and an acetylated β-galactoglucomannan), at a dose of 0.2% in the diet, had negligible effects on both host gene expression, and gut microbiome structure and function under the studied conditions. While a subsequent trial using a higher (4%) dietary inclusion of β-mannan significantly shifted the gut microbiome composition, there were still no biologically relevant effects on salmon metabolism and physiology. Only a single Burkholderia-Caballeronia-Paraburkholderia (BCP) population demonstrated consistent and significant abundance shifts across both feeding trials, although with no evidence of β-mannan utilization capabilities or changes in gene transcripts for producing metabolites beneficial to the host. In light of these findings, we revisited our omics data to predict and outline previously unreported and potentially beneficial endogenous lactic acid bacteria that should be targeted with future, conceivably more suitable, MDF strategies for salmon.},
}

Animals
*Gastrointestinal Microbiome
*Aquaculture/methods
*Salmo salar/microbiology
*Animal Feed
Mannans/metabolism
Dietary Supplements
Bacteria/genetics/classification/metabolism
Dietary Fiber/metabolism
Diet/veterinary

@article {pmid39453088,
year = {2024},
author = {Donneschi, A and Recchia, M and Romeo, C and Pozzi, P and Salogni, C and Maisano, AM and Santucci, G and Scali, F and Faccini, S and Boniotti, MB and D'Incau, M and Maes, D and Alborali, GL},
title = {Infectious Agents Associated with Abortion Outbreaks in Italian Pig Farms from 2011 to 2021.},
journal = {Veterinary sciences},
volume = {11},
number = {10},
pages = {},
doi = {10.3390/vetsci11100496},
pmid = {39453088},
issn = {2306-7381},
support = {PRC2017007//Ministero della Salute/ ; },
abstract = {The present study retrospectively analyzed the infectious agents associated with 829 abortion outbreaks occurring from 2011 to 2021 in northern Italy. Foetuses were subjected to necropsies, and organ samples were analyzed by direct PCR to screen for six swine pathogens. In 42.0% of the examined outbreaks, at least one infectious agent was found. Porcine reproductive and respiratory syndrome virus (PRRSV) (24.9%) and porcine circovirus-2 (PCV2) (11.5%) were the most frequently detected among the known abortion-inducing pathogens. Chlamydia spp. (5.6%), porcine parvovirus (PPV) (4.0%), and Leptospira spp. (2.6%) were less common. Although its role in swine reproductive disorders is still unclear, PCV3 was detected in 19.6% of the cases. Coinfections were detected in 25.0% of positive outbreaks, and the most frequent coinfection was represented by PRRSV and PCV2 (32.2%), followed by PRRSV and PCV3 (23%). PCV2 prevalence showed a slight but consistent reduction during the study period, while PCV3 increased in frequency. Our data suggest an overall reduction in abortion outbreaks during the study period. PRRSV was confirmed as the main abortion agent detected in the examined area, while PCV2 prevalence showed a decline. Conversely, PCV3 detection has been increasing, supporting its potential role as an abortion agent. Our results highlight the importance of implementing a consistent and standardized sampling procedure, as well as a thorough diagnostic protocol, to reduce the incidence of inconclusive diagnoses.},
}

@article {pmid39452359,
year = {2024},
author = {González-Román, P and Hernández-Oaxaca, D and Bustamante-Brito, R and Rogel, MA and Martínez-Romero, E},
title = {On the Origins of Symbiotic Fungi in Carmine Cochineals and Their Function in the Digestion of Plant Polysaccharides.},
journal = {Insects},
volume = {15},
number = {10},
pages = {},
doi = {10.3390/insects15100783},
pmid = {39452359},
issn = {2075-4450},
abstract = {The cochineal insect Dactylopius coccus Costa (Hemiptera) has cultural and economic value because it produces carminic acid that is used commercially. In this study, distinct fungi were cultured from dissected tissue and identified as Penicillium, Coniochaeta, Arthrinium, Cladosporium, Microascus, Aspergillus, and Periconia. Fungi were microscopically observed inside cochineals in the gut, fat body, and ovaries. Since cochineals spend their lives attached to cactus leaves and use the sap as feed, they can obtain fungi from cacti plants. Indeed, we obtained Penicillium, Aspergillus, and Cladosporium fungi from cacti that were identical to those inside cochineals, supporting their plant origin. Fungi could be responsible for the degrading activities in the insect guts, since cellulase, pectinase, and amylase enzymatic activities in insect guts decreased in fungicide-treated cochineals. Our findings set the basis for the further study of the interactions between insects, fungi, and their host plants.},
}

@article {pmid39444680,
year = {2024},
author = {Khara, A and Chakraborty, A and Modlinger, R and Synek, J and Roy, A},
title = {Comparative metagenomic study unveils new insights on bacterial communities in two pine-feeding Ips beetles (Coleoptera: Curculionidae: Scolytinae).},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1400894},
pmid = {39444680},
issn = {1664-302X},
abstract = {BACKGROUND: Climate change has recently boosted the severity and frequency of pine bark beetle attacks. The bacterial community associated with these beetles acts as "hidden players," enhancing their ability to infest and thrive on defense-rich pine trees. There is limited understanding of the environmental acquisition of these hidden players and their life stage-specific association with different pine-feeding bark beetles. There is inadequate knowledge on novel bacterial introduction to pine trees after the beetle infestation. Hence, we conducted the first comparative bacterial metabarcoding study revealing the bacterial communities in the pine trees before and after beetle feeding and in different life stages of two dominant pine-feeding bark beetles, namely Ips sexdentatus and Ips acuminatus. We also evaluated the bacterial association between wild and lab-bred beetles to measure the deviation due to inhabiting a controlled environment.

RESULTS: Significant differences in bacterial amplicon sequence variance (ASVs) abundance existed among different life stages within and between the pine beetles. However, Pseudomonas, Serratia, Pseudoxanthomonas, Taibaiella, and Acinetobacter served as core bacteria. Interestingly, I. sexdentatus larvae correspond to significantly higher bacterial diversity and community richness and evenness compared to other developmental stages, while I. acuminatus adults displayed higher bacterial richness with no significant variation in the diversity and evenness between the life stages. Both wild and lab-bred I. sexdentatus beetles showed a prevalence of the bacterial family Pseudomonadaceae. In addition, wild I. sexdentatus showed dominance of Yersiniaceae, whereas Erwiniaceae was abundant in lab-bred beetles. Alternatively, Acidobacteriaceae, Corynebacteriaceae, and Microbacteriaceae were highly abundant bacterial families in lab-bred, whereas Chitinophagaceae and Microbacteriaceae were highly abundant in wild I. accuminatus. We validated the relative abundances of selected bacterial taxa estimated by metagenomic sequencing with quantitative PCR.

CONCLUSION: Our study sheds new insights into bacterial associations in pine beetles under the influence of various drivers such as environment, host, and life stages. We documented that lab-breeding considerably influences beetle bacterial community assembly. Furthermore, beetle feeding alters bacteriome at the microhabitat level. Nevertheless, our study revisited pine-feeding bark beetle symbiosis under the influence of different drivers and revealed intriguing insight into bacterial community assembly, facilitating future functional studies.},
}

@article {pmid39418324,
year = {2024},
author = {Freudenthal, J and Dumack, K and Schaffer, S and Schlegel, M and Bonkowski, M},
title = {Algae-fungi symbioses and bacteria-fungi co-exclusion drive tree species-specific differences in canopy bark microbiomes.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae206},
pmid = {39418324},
issn = {1751-7370},
abstract = {With over 3 trillion trees, forest ecosystems comprise nearly one-third of the terrestrial surface of the Earth. Very little attention has been given to the exploration of the above-ground plant microbiome of trees, its complex trophic interactions, and variations among tree species. To address this knowledge gap, we applied a primer-independent shotgun metatranscriptomic approach to assess the entire living canopy bark microbiome comprising prokaryotic and eukaryotic primary producers, decomposers, and various groups of consumers. With almost 1500 genera, we found a high microbial diversity on three tree species with distinct bark textures: oak (Quercus robur), linden (Tilia cordata), both with rough bark, and maple (Acer pseudoplatanus) with smooth bark. Core co-occurrence network analysis revealed a rich food web dominated by algal primary producers, and bacterial and fungal decomposers, sustaining a diverse community of consumers, including protists, microscopic metazoans and predatory bacteria. Whereas maple accommodated a depauperate microbiome, oak and linden accommodated a richer microbiome mainly differing in their relative community composition: Bacteria exhibited an increased dominance on linden, whereas co-occurring algae and fungi dominated on oak, highlighting the importance of algal-fungal lichen symbioses even at the microscopic scale. Further, due to bacteria-fungi co-exclusion, bacteria on bark are not the main beneficiaries of algae-derived carbon compounds as it is known from aquatic systems.},
}

@article {pmid39414857,
year = {2024},
author = {Villela, LB and da Silva-Lima, AW and Moreira, APB and Aiube, YRA and Ribeiro, FV and Villela, HDM and Majzoub, ME and Amario, M and de Moura, RL and Thomas, T and Peixoto, RS and Salomon, PS},
title = {Bacterial and Symbiodiniaceae communities' variation in corals with distinct traits and geographical distribution.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {24319},
pmid = {39414857},
issn = {2045-2322},
support = {310057/2022-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
mesh = {Animals ; *Anthozoa/microbiology ; *Microbiota ; *Coral Reefs ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; Brazil ; Symbiosis ; Phylogeny ; Dinoflagellida/genetics/physiology ; High-Throughput Nucleotide Sequencing ; Ecosystem ; },
abstract = {Coral microbiomes play crucial roles in holobiont homeostasis and adaptation. The host's ability to populate broad ecological niches and to cope with environmental changes seems to be related to the flexibility of the coral microbiome. By means of high-throughput DNA sequencing we characterized simultaneously both bacterial (16S rRNA) and Symbiodiniaceae (ITS2) communities of four reef-building coral species (Mussismilia braziliensis, Mussismilia harttii, Montastraea cavernosa, and Favia gravida) that differ in geographic distribution and niche specificity. Samples were collected in a marginal reef system (Abrolhos, Brazil) in four sites of contrasting irradiance and turbidity. Biological filters governed by the host are important in shaping corals' microbiome structure. More structured associated microbial communities by reef site tend to occur in coral species with broader geographic and depth ranges, especially for Symbiodiniaceae, whereas the endemic and habitat-specialist host, M. braziliensis, has relatively more homogenous bacterial communities with more exclusive members. Our findings lend credence to the hypothesis that higher microbiome flexibility renders corals more adaptable to diverse environments, a trend that should be investigated in more hosts and reef areas.},
}

Animals
*Anthozoa/microbiology
*Microbiota
*Coral Reefs
*RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification
Brazil
Symbiosis
Phylogeny
Dinoflagellida/genetics/physiology
High-Throughput Nucleotide Sequencing
Ecosystem

@article {pmid39407340,
year = {2024},
author = {Chemel, M and Peru, E and Binsarhan, M and Logares, R and Lartaud, F and Galand, PE},
title = {Cold-water coral mortality under ocean warming is associated with pathogenic bacteria.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {76},
pmid = {39407340},
issn = {2524-6372},
support = {ANR-20-CE02-0006//Agence Nationale de la Recherche/ ; ANR-20-CE02-0006//Agence Nationale de la Recherche/ ; },
abstract = {Cold-water corals form vast reefs that are highly valuable habitats for diverse deep-sea communities. However, as the deep ocean is warming, it is essential to assess the resilience of cold-water corals to future conditions. The effects of elevated temperatures on the cold-water coral Lophelia pertusa (now named Desmophyllum pertusum) from the north-east Atlantic Ocean were experimentally investigated at the holobiont level, the coral host, and its microbiome. We show that at temperature increases of + 3 and + 5 °C, L. pertusa exhibits significant mortality concomitant with changes in its microbiome composition. In addition, a metagenomic approach revealed the presence of gene markers for bacterial virulence factors suggesting that coral death was due to infection by pathogenic bacteria. Interestingly, different coral colonies had different survival rates and, colony-specific microbiome signatures, indicating strong colony-specific variability in their response to warming waters. These results suggest that L. pertusa can only survive a long-term temperature increase of < 3 °C. Therefore, regional variations in deep-sea temperature increase should be considered in future estimates of the global distribution of cold-water corals.},
}

@article {pmid39322283,
year = {2024},
author = {Narechania, A and Bobo, D and Deitz, K and DeSalle, R and Planet, PJ and Mathema, B},
title = {Rapid SARS-CoV-2 surveillance using clinical, pooled, or wastewater sequence as a sensor for population change.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.278594.123},
pmid = {39322283},
issn = {1549-5469},
abstract = {The COVID-19 pandemic has highlighted the critical role of genomic surveillance for guiding policy and control. Timeliness is key, but sequence alignment and phylogeny slow most surveillance techniques. Millions of SARS-CoV-2 genomes have been assembled. Phylogenetic methods are ill equipped to handle this sheer scale. We introduce a pangenomic measure that examines the information diversity of a k-mer library drawn from a country's complete set of clinical, pooled, or wastewater sequence. Quantifying diversity is central to ecology. Hill numbers, or the effective number of species in a sample, provide a simple metric for comparing species diversity across environments. The more diverse the sample, the higher the Hill number. We adopt this ecological approach and consider each k-mer an individual and each genome a transect in the pangenome of the species. Structured in this way, Hill numbers summarize the temporal trajectory of pandemic variants, collapsing each day's assemblies into genome equivalents. For pooled or wastewater sequence, we instead compare days using survey sequence divorced from individual infections. Across data from the UK, USA, and South Africa, we trace the ascendance of new variants of concern as they emerge in local populations well before these variants are named and added to phylogenetic databases. Using data from San Diego wastewater, we monitor these same population changes from raw, unassembled sequence. This history of emerging variants senses all available data as it is sequenced, intimating variant sweeps to dominance or declines to extinction at the leading edge of the COVID-19 pandemic.},
}

@article {pmid39402236,
year = {2024},
author = {Vera-Ponce de León, A and Hensen, T and Hoetzinger, M and Gupta, S and Weston, B and Johnsen, SM and Rasmussen, JA and Clausen, CG and Pless, L and Veríssimo, ARA and Rudi, K and Snipen, L and Karlsen, CR and Limborg, MT and Bertilsson, S and Thiele, I and Hvidsten, TR and Sandve, SR and Pope, PB and La Rosa, SL},
title = {Genomic and functional characterization of the Atlantic salmon gut microbiome in relation to nutrition and health.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {39402236},
issn = {2058-5276},
support = {300846//Norges Forskningsråd (Research Council of Norway)/ ; 757922//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 12/RC/2273-P2//Science Foundation Ireland (SFI)/ ; },
abstract = {To ensure sustainable aquaculture, it is essential to understand the path 'from feed to fish', whereby the gut microbiome plays an important role in digestion and metabolism, ultimately influencing host health and growth. Previous work has reported the taxonomic composition of the Atlantic salmon (Salmo salar) gut microbiome; however, functional insights are lacking. Here we present the Salmon Microbial Genome Atlas consisting of 211 high-quality bacterial genomes, recovered by cultivation (n = 131) and gut metagenomics (n = 80) from wild and farmed fish both in freshwater and seawater. Bacterial genomes were taxonomically assigned to 14 different orders, including 35 distinctive genera and 29 previously undescribed species. Using metatranscriptomics, we functionally characterized key bacterial populations, across five phyla, in the salmon gut. This included the ability to degrade diet-derived fibres and release vitamins and other exometabolites with known beneficial effects, which was supported by genome-scale metabolic modelling and in vitro cultivation of selected bacterial species coupled with untargeted metabolomic studies. Together, the Salmon Microbial Genome Atlas provides a genomic and functional resource to enable future studies on salmon nutrition and health.},
}

@article {pmid39400157,
year = {2024},
author = {Gan, B and Wang, K and Zhang, B and Jia, C and Lin, X and Zhao, J and Ding, S},
title = {Dynamic microbiome diversity shaping the adaptation of sponge holobionts in coastal waters.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0144824},
doi = {10.1128/spectrum.01448-24},
pmid = {39400157},
issn = {2165-0497},
abstract = {UNLABELLED: The microbial communities associated with sponges contribute to the adaptation of hosts to environments, which are essential for the trophic transformation of benthic-marine coupling. However, little is known about the symbiotic microbial community interactions and adaptative strategies of high- and low-microbial abundance (HMA and LMA) sponges, which represent two typical ecological phenotypes. Here, we compared the 1-year dynamic patterns of microbiomes with the HMA sponge Spongia officinalis and two LMA sponge species Tedania sp. and Haliclona simulans widespread on the coast of China. Symbiotic bacterial communities with the characteristic HMA-LMA dichotomy presented higher diversity and stability in S. officinalis than in Tedania sp. and H. simulans, while archaeal communities showed consistent diversity across all sponges throughout the year. Dissolved oxygen, dissolved inorganic phosphorus, dissolved organic phosphorus, and especially temperature were the major factors affecting the seasonal changes in sponge microbial communities. S. officinalis-associated microbiome had higher diversity, stronger stability, and closer interaction, which adopted a relatively isolated strategy to cope with environmental changes, while Tedania sp. and H. simulans were more susceptible and shared more bacterial Amplicon Sequence Variants (ASVs) with surrounding waters, with an open way facing the uncertainty of the environment. Meta-analysis of the microbiome in composition, diversity, and ecological function from 13 marine sponges further supported that bacterial communities associated with HMA and LMA sponges have evolved two distinct environmental adaptation strategies. We propose that the different adaptive ways of sponges responding to the environment may be responsible for their successful evolution and their competence in global ocean change.

IMPORTANCE: During long-term evolution, sponge holobionts, among the oldest symbiotic relationships between microbes and metazoans, developed two distinct phenotypes with high- and low-microbial abundance (HMA and LMA). Despite sporadic studies indicating that the characteristic microbial assemblages present in HMA and LMA sponges, the adaptation strategies of symbionts responding to environments are still unclear. This deficiency limits our understanding of the selection of symbionts and the ecological functions during the evolutionary history and the adaptative assessment of HMA and LMA sponges in variable environments. Here, we explored symbiotic communities with two distinct phenotypes in a 1-year dynamic environment and combined with the meta-analysis of 13 sponges. The different strategies of symbionts in adapting to the environment were basically drawn: microbes with LMA were more acclimated to environmental changes, forming relatively loose-connected communities, while HMA developed relatively tight-connected and more similar communities beyond the divergence of species and geographical location.},
}

@article {pmid39396843,
year = {2024},
author = {González, A and Fullaondo, A and Odriozola, A},
title = {Host genetics-associated mechanisms in colorectal cancer.},
journal = {Advances in genetics},
volume = {112},
number = {},
pages = {83-122},
doi = {10.1016/bs.adgen.2024.08.003},
pmid = {39396843},
issn = {0065-2660},
mesh = {*Colorectal Neoplasms/genetics ; Humans ; DNA Methylation/genetics ; Epigenesis, Genetic ; Microsatellite Instability ; Cell Transformation, Neoplastic/genetics ; CpG Islands/genetics ; Genetic Predisposition to Disease/genetics ; },
abstract = {Colorectal cancer (CRC) represents the second leading cause of cancer incidence and the third leading cause of cancer deaths worldwide. There is currently a lack of understanding of the onset of CRC, hindering the development of effective prevention strategies, early detection methods and the selection of appropriate therapies. This article outlines the key aspects of host genetics currently known about the origin and development of CRC. The organisation of the colonic crypts is described. It discusses how the transformation of a normal cell to a cancer cell occurs and how that malignant cell can populate an entire colonic crypt, promoting colorectal carcinogenesis. Current knowledge about the cell of origin of CRC is discussed, and the two morphological pathways that can give rise to CRC, the classical and alternative pathways, are presented. Due to the molecular heterogeneity of CRC, each of these pathways has been associated with different molecular mechanisms, including chromosomal and microsatellite genetic instability, as well as the CpG island methylator phenotype. Finally, different CRC classification systems are described based on genetic, epigenetic and transcriptomic alterations, allowing diagnosis and treatment personalisation.},
}

*Colorectal Neoplasms/genetics
Humans
DNA Methylation/genetics
Epigenesis, Genetic
Microsatellite Instability
Cell Transformation, Neoplastic/genetics
CpG Islands/genetics
Genetic Predisposition to Disease/genetics

@article {pmid39396842,
year = {2024},
author = {González, A and Badiola, I and Fullaondo, A and Rodríguez, J and Odriozola, A},
title = {Personalised medicine based on host genetics and microbiota applied to colorectal cancer.},
journal = {Advances in genetics},
volume = {112},
number = {},
pages = {411-485},
doi = {10.1016/bs.adgen.2024.08.004},
pmid = {39396842},
issn = {0065-2660},
mesh = {Humans ; *Colorectal Neoplasms/genetics/microbiology ; *Precision Medicine/methods ; *Gastrointestinal Microbiome/genetics ; Biomarkers, Tumor/genetics ; Prognosis ; },
abstract = {Colorectal cancer (CRC) ranks second in incidence and third in cancer mortality worldwide. This situation, together with the understanding of the heterogeneity of the disease, has highlighted the need to develop a more individualised approach to its prevention, diagnosis and treatment through personalised medicine. This approach aims to stratify patients according to risk, predict disease progression and determine the most appropriate treatment. It is essential to identify patients who may respond adequately to treatment and those who may be resistant to treatment to avoid unnecessary therapies and minimise adverse side effects. Current research is focused on identifying biomarkers such as specific mutated genes, the type of mutations and molecular profiles critical for the individualisation of CRC diagnosis, prognosis and treatment guidance. In addition, the study of the intestinal microbiota as biomarkers is being incorporated due to the growing scientific evidence supporting its influence on this disease. This article comprehensively addresses the use of current and emerging diagnostic, prognostic and predictive biomarkers in precision medicine against CRC. The effects of host genetics and gut microbiota composition on new approaches to treating this disease are discussed. How the gut microbiota could mitigate the side effects of treatment is reviewed. In addition, strategies to modulate the gut microbiota, such as dietary interventions, antibiotics, and transplantation of faecal microbiota and phages, are discussed to improve CRC prevention and treatment. These findings provide a solid foundation for future research and improving the care of CRC patients.},
}

Humans
*Colorectal Neoplasms/genetics/microbiology
*Precision Medicine/methods
*Gastrointestinal Microbiome/genetics
Biomarkers, Tumor/genetics
Prognosis

@article {pmid39396841,
year = {2024},
author = {González, A and Fullaondo, A and Odriozola, I and Odriozola, A},
title = {Microbiota and beneficial metabolites in colorectal cancer.},
journal = {Advances in genetics},
volume = {112},
number = {},
pages = {367-409},
doi = {10.1016/bs.adgen.2024.08.002},
pmid = {39396841},
issn = {0065-2660},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/metabolism ; *Gastrointestinal Microbiome ; Fatty Acids, Volatile/metabolism ; Polyphenols/metabolism ; Animals ; },
abstract = {Colorectal cancer (CRC) is the third most common cancer and the second leading cause of cancer-related death worldwide. In recent years, the impact of the gut microbiota on the development of CRC has become clear. The gut microbiota is the community of microorganisms living in the gut symbiotic relationship with the host. These microorganisms contribute to the development of CRC through various mechanisms that are not yet fully understood. Increasing scientific evidence suggests that metabolites produced by the gut microbiota may influence CRC development by exerting protective and deleterious effects. This article reviews the metabolites produced by the gut microbiota, which are derived from the intake of complex carbohydrates, proteins, dairy products, and phytochemicals from plant foods and are associated with a reduced risk of CRC. These metabolites include short-chain fatty acids (SCFAs), indole and its derivatives, conjugated linoleic acid (CLA) and polyphenols. Each metabolite, its association with CRC risk, the possible mechanisms by which they exert anti-tumour functions and their relationship with the gut microbiota are described. In addition, other gut microbiota-derived metabolites that are gaining importance for their role as CRC suppressors are included.},
}

Humans
*Colorectal Neoplasms/microbiology/metabolism
*Gastrointestinal Microbiome
Fatty Acids, Volatile/metabolism
Polyphenols/metabolism
Animals

@article {pmid39396840,
year = {2024},
author = {González, A and Fullaondo, A and Odriozola, A},
title = {Host genetics and microbiota data analysis in colorectal cancer research.},
journal = {Advances in genetics},
volume = {112},
number = {},
pages = {31-81},
doi = {10.1016/bs.adgen.2024.08.007},
pmid = {39396840},
issn = {0065-2660},
mesh = {*Colorectal Neoplasms/genetics/microbiology ; Humans ; *Computational Biology/methods ; Precision Medicine ; Gastrointestinal Microbiome/genetics ; Microbiota/genetics ; Data Analysis ; },
abstract = {Colorectal cancer (CRC) is a heterogeneous disease with a complex aetiology influenced by a myriad of genetic and environmental factors. Despite advances in CRC research, it is a major burden of disease, with the second highest incidence and third leading cause of cancer deaths worldwide. To individualise diagnosis, prognosis, and treatment of CRC, developing new strategies combining precision medicine and bioinformatic procedures is promising. Precision medicine is based on omics technologies and aims to individualise the management of CRC based on patient host genetic characteristics and microbiota. Bioinformatics is central to the application of personalised medicine because it enables the analysis of large datasets generated by these technologies. At the level of host genetics, bioinformatics allows the identification of mutations, genes, molecular pathways, biomarkers and drugs relevant to colorectal carcinogenesis. At the microbiota level, bioinformatics is fundamental to analysing microbial communities' composition and functionality and developing biomarkers and personalised microbiota-based therapies. This paper explores the host and microbiota genetic data analysis in CRC research.},
}

*Colorectal Neoplasms/genetics/microbiology
Humans
*Computational Biology/methods
Precision Medicine
Gastrointestinal Microbiome/genetics
Microbiota/genetics
Data Analysis

@article {pmid39396839,
year = {2024},
author = {González, A and Fullaondo, A and Odriozola, I and Odriozola, A},
title = {Microbiota and other detrimental metabolites in colorectal cancer.},
journal = {Advances in genetics},
volume = {112},
number = {},
pages = {309-365},
doi = {10.1016/bs.adgen.2024.08.006},
pmid = {39396839},
issn = {0065-2660},
mesh = {*Colorectal Neoplasms/microbiology/metabolism ; Humans ; *Gastrointestinal Microbiome ; Diet ; Bile Acids and Salts/metabolism ; Polycyclic Aromatic Hydrocarbons/metabolism ; Animals ; },
abstract = {Increasing scientific evidence demonstrates that gut microbiota plays an essential role in the onset and development of Colorectal cancer (CRC). However, the mechanisms by which these microorganisms contribute to cancer development are complex and far from completely clarified. Specifically, the impact of gut microbiota-derived metabolites on CRC is undeniable, exerting both protective and detrimental effects. This paper examines the effects and mechanisms by which important bacterial metabolites exert detrimental effects associated with increased risk of CRC. Metabolites considered include heterocyclic amines and polycyclic aromatic hydrocarbons, heme iron, secondary bile acids, ethanol, and aromatic amines. It is necessary to delve deeper into the mechanisms of action of these metabolites in CRC and identify the microbiota members involved in their production. Furthermore, since diet is the main factor capable of modifying the intestinal microbiota, conducting studies that include detailed descriptions of dietary interventions is crucial. All this knowledge is essential for developing precision nutrition strategies to optimise a protective intestinal microbiota against CRC.},
}

*Colorectal Neoplasms/microbiology/metabolism
Humans
*Gastrointestinal Microbiome
Diet
Bile Acids and Salts/metabolism
Polycyclic Aromatic Hydrocarbons/metabolism
Animals

@article {pmid39396838,
year = {2024},
author = {González, A and Odriozola, I and Fullaondo, A and Odriozola, A},
title = {Microbiota and detrimental protein derived metabolites in colorectal cancer.},
journal = {Advances in genetics},
volume = {112},
number = {},
pages = {255-308},
doi = {10.1016/bs.adgen.2024.06.001},
pmid = {39396838},
issn = {0065-2660},
mesh = {*Colorectal Neoplasms/microbiology/metabolism/etiology ; Humans ; *Gastrointestinal Microbiome ; Fermentation ; Risk Factors ; Diet ; Animals ; },
abstract = {Colorectal cancer (CRC) is the third leading cancer in incidence and the second leading cancer in mortality worldwide. There is growing scientific evidence to support the crucial role of the gut microbiota in the development of CRC. The gut microbiota is the complex community of microorganisms that inhabit the host gut in a symbiotic relationship. Diet plays a crucial role in modulating the risk of CRC, with a high intake of red and processed meat being a risk factor for the development of CRC. The production of metabolites derived from protein fermentation by the gut microbiota is considered a crucial element in the interaction between red and processed meat consumption and the development of CRC. This paper examines several metabolites derived from the bacterial fermentation of proteins associated with an increased risk of CRC. These metabolites include ammonia, polyamines, trimethylamine N-oxide (TMAO), N-nitroso compounds (NOC), hydrogen sulphide (H2S), phenolic compounds (p-cresol) and indole compounds (indolimines). These compounds are depicted and reviewed for their association with CRC risk, possible mechanisms promoting carcinogenesis and their relationship with the gut microbiota. Additionally, this paper analyses the evidence related to the role of red and processed meat intake and CRC risk and the factors and pathways involved in bacterial proteolytic fermentation in the large intestine.},
}

*Colorectal Neoplasms/microbiology/metabolism/etiology
Humans
*Gastrointestinal Microbiome
Fermentation
Risk Factors
Diet
Animals

@article {pmid39396837,
year = {2024},
author = {Orozco-Castaño, C and Mejia-Garcia, A and Zambrano, Y and Combita, AL and Parra-Medina, R and Bonilla, DA and González, A and Odriozola, A},
title = {Construction of an immune gene expression meta signature to assess the prognostic risk of colorectal cancer patients.},
journal = {Advances in genetics},
volume = {112},
number = {},
pages = {207-254},
doi = {10.1016/bs.adgen.2024.08.005},
pmid = {39396837},
issn = {0065-2660},
mesh = {Humans ; *Colorectal Neoplasms/genetics/immunology ; Prognosis ; *Biomarkers, Tumor/genetics ; *Gene Expression Regulation, Neoplastic ; *Transcriptome ; Gene Expression Profiling ; Proportional Hazards Models ; Male ; Female ; },
abstract = {Despite recent advancements in colorectal cancer (CRC) treatment, particularly with the introduction of immunotherapy and checkpoint inhibitors, the efficacy of these therapies remains limited to a subset of patients. To address this challenge, our study aimed to develop a prognostic biomarker based on immune-related genes to predict better outcomes in CRC patients and aid in treatment decision-making. We comprehensively analysed immune gene expression signatures associated with CRC prognosis to construct an immune meta-signature with prognostic potential. Utilising data from The Cancer Genome Atlas (TCGA), we employed Cox regression to identify immune-related genes with prognostic significance from multiple studies. Subsequently, we compared the expression levels of immune genes, levels of immune cell infiltration, and various immune-related molecules between high-risk and low-risk patient groups. Functional analysis using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses provided insights into the biological pathways associated with the identified prognostic genes. Finally, we validated our findings using a separate CRC cohort from the Gene Expression Omnibus (GEO). Integration of the prognostic genes revealed significant disparities in survival outcomes. Differential expression analysis identified a set of immune-associated genes, which were further refined using LASSO penalisation and Cox regression. Univariate Cox regression analyses confirmed the autonomy of the gene signature as a prognostic indicator for CRC patient survival. Our risk prediction model effectively stratified CRC patients based on their prognosis, with the high-risk group showing enrichment in pro-oncogenic terms and pathways. Immune infiltration analysis revealed an augmented presence of certain immunosuppressive subsets in the high-risk group. Finally, we validated the performance of our prognostic model by applying the risk score equation to a different CRC patient dataset, confirming its prognostic potential in this new cohort. Overall, our study presents a novel immune-related gene signature with promising implications for predicting cancer progression and prognosis, thereby enabling more personalised management strategies for CRC patients.},
}

Humans
*Colorectal Neoplasms/genetics/immunology
Prognosis
*Biomarkers, Tumor/genetics
*Gene Expression Regulation, Neoplastic
*Transcriptome
Gene Expression Profiling
Proportional Hazards Models
Male
Female

@article {pmid39396836,
year = {2024},
author = {González, A and Fullaondo, A and Odriozola, A},
title = {Microbiota-associated mechanisms in colorectal cancer.},
journal = {Advances in genetics},
volume = {112},
number = {},
pages = {123-205},
doi = {10.1016/bs.adgen.2024.05.002},
pmid = {39396836},
issn = {0065-2660},
mesh = {*Colorectal Neoplasms/microbiology ; Humans ; *Gastrointestinal Microbiome ; Animals ; Bacteria/classification ; },
abstract = {Colorectal cancer (CRC) is one of the most common cancers worldwide, ranking third in terms of incidence and second as a cause of cancer-related death. There is growing scientific evidence that the gut microbiota plays a key role in the initiation and development of CRC. Specific bacterial species and complex microbial communities contribute directly to CRC pathogenesis by promoting the neoplastic transformation of intestinal epithelial cells or indirectly through their interaction with the host immune system. As a result, a protumoural and immunosuppressive environment is created conducive to CRC development. On the other hand, certain bacteria in the gut microbiota contribute to protection against CRC. In this chapter, we analysed the relationship of the gut microbiota to CRC and the associations identified with specific bacteria. Microbiota plays a key role in CRC through various mechanisms, such as increased intestinal permeability, inflammation and immune system dysregulation, biofilm formation, genotoxin production, virulence factors and oxidative stress. Exploring the interaction between gut microbiota and tumourigenesis is essential for developing innovative therapeutic approaches in the fight against CRC.},
}

*Colorectal Neoplasms/microbiology
Humans
*Gastrointestinal Microbiome
Animals
Bacteria/classification

@article {pmid39388223,
year = {2024},
author = {Alcaraz, CM and Séneca, J and Kunert, M and Pree, C and Sudo, M and Petersen, JM},
title = {Sulfur-oxidizing symbionts colonize the digestive tract of their Lucinid hosts.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae200},
pmid = {39388223},
issn = {1751-7370},
abstract = {Like many marine invertebrates, marine lucinid clams have an intimate relationship with beneficial sulfur-oxidizing bacteria located within specialized gill cells known as bacteriocytes. Most previous research has focused on the symbionts in the gills of these (and other) symbiotic bivalves, often assuming that the symbionts only persistently colonize the gills, at least in the adult stage. We used 16S rRNA gene sequencing and digital polymerase chain reaction with symbiont-specific primers targeting the soxB gene on the foot, mantle, visceral mass, and gills of the lucinid clam Loripes orbiculatus. We also used fluorescence in situ hybridization with symbiont-specific probes to examine symbiont distribution at the level of the whole holobiont. Despite 40 years of research on these symbioses, we detected previously unknown populations of symbiont cells in several organs, including the digestive tract. As in the well-studied gills, symbionts in the digestive tract may be housed within host cells. A 14-month starvation experiment without hydrogen sulfide to power symbiont metabolism caused a larger reduction in symbiont numbers in the gills compared to the visceral mass, raising the possibility that symbionts in the digestive tract are persistent and may have a distinct physiology and role in the symbiosis compared with the gill symbionts. Our results highlight the unexpectedly complex relationships between marine lucinid clams and their symbionts and challenge the view that chemosynthetic symbionts are restricted to the gills of these hosts.},
}

@article {pmid39392666,
year = {2024},
author = {Zhang, N and Qian, Z and He, J and Shen, X and Lei, X and Sun, C and Fan, J and Felton, GW and Shao, Y},
title = {Gut bacteria of lepidopteran herbivores facilitate digestion of plant toxins.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {42},
pages = {e2412165121},
doi = {10.1073/pnas.2412165121},
pmid = {39392666},
issn = {1091-6490},
support = {32022081//MOST | National Natural Science Foundation of China (NSFC)/ ; CARS-18-ZJ0302//MOA | Earmarked Fund for China Agriculture Research System/ ; LZ22C170001//MOST | NSFC | NSFC-Zhejiang Joint Fund | | Natural Science Foundation of Zhejiang Province (ZJNSF)/ ; },
mesh = {Animals ; *Herbivory ; *Gastrointestinal Microbiome/physiology ; Bombyx/metabolism/microbiology ; Morus ; Symbiosis ; Lepidoptera/microbiology ; Spodoptera/microbiology ; Bacteria/metabolism/genetics/classification ; Digestion ; },
abstract = {Lepidopterans commonly feed on plant material, being the most significant insect herbivores in nature. Despite plant resistance to herbivory, such as producing toxic secondary metabolites, herbivores have developed mechanisms encoded in their genomes to tolerate or detoxify plant defensive compounds. Recent studies also highlight the role of gut microbiota in mediating detoxification in herbivores; however, convincing evidence supporting the significant contribution of gut symbionts is rare in Lepidoptera. Here, we show that the growth of various lepidopteran species was inhibited by a mulberry-derived secondary metabolite, 1-deoxynojirimycin (DNJ); as expected, the specialist silkworm Bombyx mori grew well, but interestingly, gut microbiota of early-instar silkworms was affected by the DNJ level, and several bacterial species responded positively to enriched DNJ. Among these, a bacterial strain isolated from the silkworm gut (Pseudomonas fulva ZJU1) can degrade and utilize DNJ as the sole energy source, and after inoculation into nonspecialists (e.g., beet armyworm Spodoptera exigua), P. fulva ZJU1 increased host resistance to DNJ and significantly promoted growth. We used genomic and transcriptomic analyses to identify genes potentially involved in DNJ degradation, and CRISPR-Cas9-mediated mutagenesis verified the function of ilvB, a key binding protein, in metabolizing DNJ. Furthermore, the ilvB deletion mutant, exhibiting normal bacterial growth, could no longer enhance nonspecialist performance, supporting a role in DNJ degradation in vivo. Therefore, our study demonstrated causality between the gut microbiome and detoxification of plant chemical defense in Lepidoptera, facilitating a mechanistic understanding of host-microbe relationships across this complex, abundant insect group.},
}

Animals
*Herbivory
*Gastrointestinal Microbiome/physiology
Bombyx/metabolism/microbiology
Morus
Symbiosis
Lepidoptera/microbiology
Spodoptera/microbiology
Bacteria/metabolism/genetics/classification
Digestion

@article {pmid39391863,
year = {2024},
author = {Martin Bideguren, G and Razgour, O and Alberdi, A},
title = {Quantitative Synthesis of Microbe-Driven Acclimation and Adaptation in Wild Vertebrates.},
journal = {Evolutionary applications},
volume = {17},
number = {10},
pages = {e70025},
pmid = {39391863},
issn = {1752-4571},
abstract = {Microorganisms associated with animals harbour a unique set of functional traits pivotal for the normal functioning of their hosts. This realisation has led researchers to hypothesise that animal-associated microbial communities may boost the capacity of their hosts to acclimatise and adapt to environmental changes, two eco-evolutionary processes with significant applied relevance. Aiming to assess the importance of microorganisms for wild vertebrate conservation, we conducted a quantitative systematic review to evaluate the scientific evidence for the contribution of gut microorganisms to the acclimation and adaptation capacity of wild vertebrate hosts. After screening 1974 publications, we scrutinised the 109 studies that met the inclusion criteria based on 10 metrics encompassing study design, methodology and reproducibility. We found that the studies published so far were not able to resolve the contribution of gut microorganisms due to insufficient study design and research methods for addressing the hypothesis. Our findings underscore the limited application to date of microbiome knowledge in vertebrate conservation and management, highlighting the need for a paradigm shift in research approaches. Considering these results, we advocate for a shift from observational studies to experimental manipulations, where fitness or related indicators are measured, coupled with an update in molecular techniques used to analyse microbial functions. In addition, closer collaboration with conservation managers and practitioners from the inception of the project is needed to encourage meaningful application of microbiome knowledge in adaptive wildlife conservation management.},
}