@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.},
}

@article {pmid39382467,
year = {2024},
author = {Desikan, P and Rangnekar, A},
title = {Human holobionts: Metaorganisms hidden in plain sight?.},
journal = {The Indian journal of medical research},
volume = {159},
number = {6},
pages = {702-704},
doi = {10.25259/ijmr_1803_23},
pmid = {39382467},
issn = {0971-5916},
mesh = {Humans ; *Symbiosis ; Microbiota ; Biological Evolution ; },
}

Humans
*Symbiosis
Microbiota
Biological Evolution

@article {pmid39380028,
year = {2024},
author = {Bollati, E and Hughes, DJ and Suggett, DJ and Raina, JB and Kühl, M},
title = {Microscale sampling of the coral gastrovascular cavity reveals a gut-like microbial community.},
journal = {Animal microbiome},
volume = {6},
number = {1},
pages = {55},
pmid = {39380028},
issn = {2524-4671},
abstract = {Animal guts contain numerous microbes, which are critical for nutrient assimilation and pathogen defence. While corals and other Cnidaria lack a true differentiated gut, they possess semi-enclosed gastrovascular cavities (GVCs), where vital processes such as digestion, reproduction and symbiotic exchanges take place. The microbiome harboured in GVCs is therefore likely key to holobiont fitness, but remains severely understudied due to challenges of working in these small compartments. Here, we developed minimally invasive methodologies to sample the GVC of coral polyps and characterise the microbial communities harboured within. We used glass capillaries, low dead volume microneedles, or nylon microswabs to sample the gastrovascular microbiome of individual polyps from six species of corals, then applied low-input DNA extraction to characterise the microbial communities from these microliter volume samples. Microsensor measurements of GVCs revealed anoxic or hypoxic micro-niches, which persist even under prolonged illumination with saturating irradiance. These niches harboured microbial communities enriched in putatively microaerophilic or facultatively anaerobic taxa, such as Epsilonproteobacteria. Some core taxa found in the GVC of Lobophyllia hemprichii from the Great Barrier Reef were also detected in conspecific colonies held in aquaria, indicating that these associations are unlikely to be transient. Our findings suggest that the coral GVC is chemically and microbiologically similar to the gut of higher Metazoa. Given the importance of gut microbiomes in mediating animal health, harnessing the coral "gut microbiome" may foster novel active interventions aimed at increasing the resilience of coral reefs to the climate crisis.},
}

@article {pmid39379612,
year = {2024},
author = {Hermosilla-Albala, N and Silva, FE and Cuadros-Espinoza, S and Fontsere, C and Valenzuela-Seba, A and Pawar, H and Gut, M and Kelley, JL and Ruibal-Puertas, S and Alentorn-Moron, P and Faella, A and Lizano, E and Farias, I and Hrbek, T and Valsecchi, J and Gut, IG and Rogers, J and Farh, KK and Kuderna, LFK and Marques-Bonet, T and Boubli, JP},
title = {Whole genomes of Amazonian uakari monkeys reveal complex connectivity and fast differentiation driven by high environmental dynamism.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1283},
pmid = {39379612},
issn = {2399-3642},
mesh = {Animals ; *Genome ; Genetic Variation ; Rainforest ; Phylogeny ; Ecosystem ; Brazil ; Gene Flow ; Platyrrhini/genetics ; },
abstract = {Despite showing the greatest primate diversity on the planet, genomic studies on Amazonian primates show very little representation in the literature. With 48 geolocalized high coverage whole genomes from wild uakari monkeys, we present the first population-level study on platyrrhines using whole genome data. In a very restricted range of the Amazon rainforest, eight uakari species (Cacajao genus) have been described and categorized into the bald and black uakari groups, based on phenotypic and ecological differences. Despite a slight habitat overlap, we show that posterior to their split 0.92 Mya, bald and black uakaris have remained independent, without gene flow. Nowadays, these two groups present distinct genetic diversity and group-specific variation linked to pathogens. We propose differing hydrology patterns and effectiveness of geographic barriers have modulated the intra-group connectivity and structure of bald and black uakari populations. With this work we have explored the effects of the Amazon rainforest's dynamism on wild primates' genetics and increased the representation of platyrrhine genomes, thus opening the door to future research on the complexity and diversity of primate genomics.},
}

Animals
*Genome
Genetic Variation
Rainforest
Phylogeny
Ecosystem
Brazil
Gene Flow
Platyrrhini/genetics

@article {pmid39375799,
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 = {Blastocystis occurrence and subtype diversity in European wild boar (Sus scrofa) from the Iberian Peninsula.},
journal = {Veterinary research},
volume = {55},
number = {1},
pages = {133},
pmid = {39375799},
issn = {1297-9716},
support = {PI19CIII/00029//PI19CIII/00029/ ; },
abstract = {The ongoing increase in wild boar populations across Europe has fostered human-wildlife conflicts, including the transmission of emerging pathogens with zoonotic importance. Blastocystis is a ubiquitous, faecal-oral transmitted protist that can cause gastrointestinal illnesses and is observed in humans and animals worldwide. The role of wildlife in the epidemiology of Blastocystis is insufficiently understood. Thus, we investigated the occurrence and subtype diversity of Blastocystis in free-ranging wild boars from the Iberian Peninsula using conventional PCR and next-generation amplicon sequencing of a fragment of the ssu RNA gene. A total of 459 wild boar faecal samples were collected across Spain (n = 360) and Portugal (n = 99) between 2014 and 2021. Blastocystis was present in 15.3% (70/459; 95% CI 12.1-18.9) of the wild boars analysed, and its occurrence was significantly higher in Portugal (34.3%, 34/99; 95% CI 25.1-44.6) than in Spain (10.0%, 36/360; 95% CI 7.1-13.6). Seven Blastocystis subtypes (ST5, ST10b, ST13-ST15, ST24b, and ST43) were detected among the surveyed wild boar populations, with greater variability detected in Portuguese samples. ST5 was identified in all the Blastocystis-positive animals, whereas 14.3% of them harboured ST mixed colonisations. Our results demonstrate that Blastocystis ST5 is particularly adapted to infect wild boars. The additional identification of zoonotic STs reinforces the role of wild boars as spreaders of zoonotic infections with public health significance.},
}

@article {pmid39375020,
year = {2024},
author = {Garritano, AN and Zhang, Z and Jia, Y and Allen, MA and Hill, LJ and Kuzhiumparambil, U and Hinkley, C and Raina, JB and Peixoto, RS and Thomas, T},
title = {Simple Porifera holobiont reveals complex interactions between the host, an archaeon, a bacterium, and a phage.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae197},
pmid = {39375020},
issn = {1751-7370},
abstract = {The basal metazoan phylum, Porifera (sponges), is increasingly used as a model to investigate ecological and evolutionary features of microbe-animal symbioses. However, sponges often host complex microbiomes, which has hampered our understanding of their interactions with their microbial symbionts. Here, we describe the discovery and characterisation of the simplest sponge holobiont reported to date, consisting of the deep-sea glass sponge Aphrocalistes beatrix and two newly described microbial symbionts: an autotrophic ammonia-oxidising archaeon and a bacterial heterotroph. Omics analyses and metabolic modelling revealed the dependency of the ammonia-oxidising archaea on sponge-derived ammonia to drive primary production, which in turn supports the bacterium's growth by providing the dicarboxylate fumarate. Furthermore, virus-mediated archaeal lysis appears crucial to overcome the bacterium's vitamin B12 auxotrophy. These findings reveal that the exchange of vitamin B12 and dicarboxylate may be evolutionarily conserved features of symbiosis as they can also be found in interactions between free-living marine bacteria, and between microbes and plants or diatoms.},
}

@article {pmid39358872,
year = {2024},
author = {Hacquard, S and Martin, FM},
title = {The chemical language of plant-microbe-microbe associations: an introduction to a Virtual Issue.},
journal = {The New phytologist},
volume = {244},
number = {3},
pages = {739-742},
doi = {10.1111/nph.20124},
pmid = {39358872},
issn = {1469-8137},
support = {ANR-11-LABX-0002-01//Laboratory of Excellence ARBRE/ ; //Northwest Institute of Eco-Environment and Resources, Lanzhou, China/ ; //ERC Consolidator Grant MICROBIOSIS/ ; },
mesh = {*Plants/microbiology ; },
}

*Plants/microbiology

@article {pmid39358646,
year = {2024},
author = {Jiménez-Velásquez, S and Pacheco-Montealegre, ME and Torres-Higuera, L and Uribe-Gutiérrez, L and Burbano-David, D and Dávila-Mora, LL and Renjifo-Ibáñez, C and Caro-Quintero, A},
title = {Genus-targeted markers for the taxonomic identification and monitoring of coagulase-positive and coagulase-negative Staphylococcus species.},
journal = {World journal of microbiology & biotechnology},
volume = {40},
number = {11},
pages = {333},
pmid = {39358646},
issn = {1573-0972},
mesh = {*Staphylococcus/genetics/classification/isolation & purification/enzymology ; *Coagulase/metabolism/genetics ; *RNA, Ribosomal, 16S/genetics ; *DNA, Bacterial/genetics ; DNA Primers/genetics ; Phylogeny ; Staphylococcal Infections/microbiology ; Animals ; Genes, Bacterial/genetics ; Bacterial Proteins/genetics ; Sequence Analysis, DNA ; Multilocus Sequence Typing ; Bacterial Typing Techniques/methods ; Genetic Markers ; High-Throughput Nucleotide Sequencing ; },
abstract = {The Staphylococcus genus comprises multiple pathogenic and opportunistic species that represent a risk to public health. Epidemiological studies require accurate taxonomic classification of isolates with enough resolution to distinguish clonal complexes. Unfortunately, 16 S rRNA molecular analysis and phenotypic characterization cannot distinguish all species and do not offer enough resolution to assess intraspecific diversity. Other approaches, such as Multilocus Sequence Tagging, provide higher resolution; however, they have been developed for Staphylococcus aureus and a few other species. Here, we developed a set of genus-targeted primers using five orthologous genes (pta, tuf, tpi, groEs, and sarA) to identify all Staphylococcus species within the genus. The primers were initially evaluated using 20 strains from the Collection of Microorganisms of Interest in Animal Health from AGROSAVIA (CMISA), and their amplified sequences were compared to a set of 33 Staphylococcus species. This allowed the taxonomic identification of the strains even on close species and the establishment of intraspecies diversity. To enhance the scope and cost-effectiveness of the proposed strategy, we customized the primer sets for an Illumina paired-end amplicon protocol, enabling gene multiplexing. We assessed five genes across 177 strains, generating 880 paired-end libraries from the CMISA. This approach significantly reduced sequencing costs, as all libraries can be efficiently sequenced in a single MiSeq run at a fraction (one-fourth or less) of the cost associated with Sanger sequencing. In summary, this method can be used for precise identification and diversity analysis of Staphylococcus species, offering an advancement over traditional techniques in both resolution and cost-effectiveness.},
}

*Staphylococcus/genetics/classification/isolation & purification/enzymology
*Coagulase/metabolism/genetics
*RNA, Ribosomal, 16S/genetics
*DNA, Bacterial/genetics
DNA Primers/genetics
Phylogeny
Staphylococcal Infections/microbiology
Animals
Genes, Bacterial/genetics
Bacterial Proteins/genetics
Sequence Analysis, DNA
Multilocus Sequence Typing
Bacterial Typing Techniques/methods
Genetic Markers
High-Throughput Nucleotide Sequencing

@article {pmid39346007,
year = {2024},
author = {Eisenhofer, R and Alberdi, A and Woodcroft, BJ},
title = {Quantifying microbial DNA in metagenomes improves microbial trait estimation.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae111},
pmid = {39346007},
issn = {2730-6151},
abstract = {Shotgun metagenomics is a powerful tool for studying the genomic traits of microbial community members, such as genome size, gene content, etc. While such traits can be used to better understand the ecology and evolution of microbial communities, the accuracy of their estimations can be critically influenced by both known and unknown factors. One factor that can bias trait estimations is the proportion of eukaryotic and viral DNA in a metagenome, as some bioinformatic tools assume that all DNA reads in a metagenome are bacterial or archaeal. Here, we add to a recent debate about the influence of eukaryotic DNA in the estimation of average genome size from a global soil sample dataset using a new bioinformatic tool. Contrary to what was assumed, our reanalysis of this dataset revealed that soil samples can contain a substantial proportion of non-microbial DNA, which severely inflated the original estimates of average genome size. Correcting for this bias significantly improves the statistical support for the negative relationship between average bacterial genome size and soil pH. These results highlight that metagenomes can contain large quantities of non-microbial DNA and that new methods that correct for this can improve microbial trait estimation.},
}

@article {pmid39329334,
year = {2024},
author = {Navarro, B and Turina, M},
title = {Viroid and viroid-like elements in plants and plant-associated microbiota: a new layer of biodiversity for plant holobionts.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.20156},
pmid = {39329334},
issn = {1469-8137},
support = {P2022XX55J//European Union-NextGeneration EU, Missione 4, Componente 1, MUR Piano Nazionale di Ripresa e Resilienza (PNRR)/ ; },
abstract = {The functional relevance of plant-associated microorganisms is theoretically framed within the holobiont concept. The role of viruses in plant holobionts is being recognized both for their direct effects when hosted in plants (cryptic plant viruses) and for their indirect effects when infecting microorganisms associated with plants in tripartite interactions (e.g. mycoviruses and bacteriophages). We argue that viroids, the smallest infectious agents typically infecting only plant hosts, must also be included in plant holobiont studies. The same applies to the recently discovered large number of viroid-like elements infecting hosts of other life kingdoms that are closely associated with plants. Here we also describe in depth the diversity of such viroid-like elements and their initial functional characterization in plant-associated fungi.},
}

@article {pmid39328926,
year = {2024},
author = {Duque-Granda, D and Vivero-Gómez, RJ and Junca, H and Cadavid-Restrepo, G and Moreno-Herrera, CX},
title = {Interaction and effects of temperature preference under a controlled environment on the diversity and abundance of the microbiome in Lutzomyia longipalpis (Diptera: Psychodidae).},
journal = {Biotechnology reports (Amsterdam, Netherlands)},
volume = {44},
number = {},
pages = {e00857},
pmid = {39328926},
issn = {2215-017X},
abstract = {Characterization of the temperature effects on the abundance and richness of the microbiota of Lutzomyia longipalpis, insect vector of Leishmania infantum in America, is an aspect of pivotal importance to understand the interactions between temperature, bacteria, and Leishmania infection. We developed and used a customized device with a temperature gradient (21-34 °C) to assess the temperature preferences of wild females of Lu. longipalpis collected in a rural area (Ricaurte, Cundinamarca, Colombia). Each replicate consisted of 50 females exposed to the gradient for an hour. At the end of the exposure time, insects were collected and separated by the temperature ranges selected varying from 21 °C to 34 °C. They were organized in 17 pools from which total DNA extracts were obtained, and samples were subjected to 16S rRNA amplicon sequencing analyzes. The most abundant phyla across the different temperature ranges were Proteobacteria (17.22-90.73 %), Firmicutes (5.99-77.21 %) and Actinobacteria (1.56-59.85 %). Results also showed an abundance (30 % to 57.36 %) of Pseudomonas (mainly at temperatures of 21-29 °C and 34 °C) that decreased to 6.55 %-13.20 % at temperatures of 31-33 °C, while Bacillus increase its abundance to 67.24 % at 29-33 °C. Serratia also had a greater representation (49.79 %), specifically in sand flies recovered at 25-27 °C. No significant differences were found at α-diversity level when comparing richness using the Shannon-Wiener, Simpson, and Chao1 indices, while β-diversity differences were found using the Bray-Curtis index (F-value of 3.5073, p-value < 0.013, R-squared of 0,4889), especially in the groups of Lu. longipalpis associated at higher temperatures (29-33 °C). It was also possible to detect the presence of endosymbionts such as Spiroplasma and Arsenophonus in the range of 29-33 °C. Rickettsia was only detected in Lu. longipalpis sand flies recovered between 25-27 °C. It was possible to characterize Lu. longipalpis microbiota in response to intraspecific temperature preferences and observe changes in bacterial communities and endosymbionts at different ranges of said environmental variable, which may be important in its vector competence and environmental plasticity to adapt to new climate change scenarios.},
}

@article {pmid39316562,
year = {2024},
author = {Kliver, S and Kovacic, I and Mak, S and Sinding, MS and Stagegaard, J and Petersen, B and Nesme, J and Gilbert, MTP},
title = {A chromosome phased diploid genome assembly of African hunting dog (Lycaon pictus).},
journal = {The Journal of heredity},
volume = {},
number = {},
pages = {},
doi = {10.1093/jhered/esae052},
pmid = {39316562},
issn = {1465-7333},
abstract = {The African hunting dog (Lycaon pictus, 2n=78) once ranged over most sub-Saharan ecosystems except its deserts and rainforests. However as a result of (still ongoing) population declines, today they remain only as small fragmented populations. Furthermore, the future of the species remains unclear, due to both anthropogenic pressure as well as interactions with domestic dogs, thus their preservation is a conservation priority. On the tree of life, the hunting dog is basal to Canis and Cuon and forms a crown group with them, making it a useful species for comparative genomic studies. Here, we present a diploid chromosome level assembly of an African hunting dog. Assembled according to VGP guidelines from a combination of PacBio HiFi reads and HiC data, it is phased at the level of individual chromosomes. The maternal (pseudo)haplotype (mat) of our assembly has a length of 2.38 Gbp, and 99.36 % of the sequence is encompassed by 39 chromosomal scaffolds. The rest is included in only 36 unplaced short scaffolds. At the contig level, mat consists of only 166 contigs with an N50 of 39 Mbp. BUSCO analysis showed 95.4 % completeness based on Сarnivora conservative genes (carnivora_odb10). When compared to other available genomes from subtribe Canina, the quality of the assembly is excellent, typically between the 1st and 3rd depending on the parameter used, and a significant improvement on previously published genomes for the species. We hope this assembly will play an important role in future conservation efforts and comparative studies of canid genomes.},
}

@article {pmid39314892,
year = {2024},
author = {Katirtzoglou, A and Rasmussen, JA and Schindler, DE and Limborg, MT},
title = {Intestinal microbial profiles of wild Alaskan rainbow trout (Oncorhynchus mykiss) characterized by 16S rRNA amplicon data.},
journal = {Data in brief},
volume = {57},
number = {},
pages = {110902},
pmid = {39314892},
issn = {2352-3409},
abstract = {Rainbow trout (Oncorhynchus mykiss) is a dominant aquaculture species of the Salmonidae family, native only to the North Pacific. Recently, the gut microbiome has been shown to reflect the health status and responses to environmental changes in farmed fish. In this analysis we investigated the microbiome composition of the intestinal tract in 20 wild-caught rainbow trout specimens sampled in Alaska, USA. The targeted 16S rRNA gene (V3-V4 region) was sequenced on the Illumina NovaSeq 6000 platform. After quality control, demultiplexing and adapter trimming reads were analyzed using the DADA2 pipeline to obtain Amplicon Sequencing Variants (ASVs) which were subsequently taxonomically assigned. We found two phyla dominating the gut ecosystem present in every sample, Firmicutes and Fusobacteria, followed by lower abundances of Cyanobacteria, Proteobacteria and Bacteroidetes. At the genus level, we found high relative abundances of Cetobacterium and Clostridium sensu stricto 1. Interestingly, we did not identify often dominant genera Mycoplasma, Pseudomonas or Weisella which were prevalent in numerous studies previously, in cultured rainbow trout. Wild fish are exposed to a plethora of unpredictable environmental challenges, ranging from fluctuating water temperatures to variable food availability, as opposed to controlled conditions in production facilities. Examining and comparing the gut ecosystem of wild and reared individuals holds great potential in optimizing management practices for commercially important species. Microbiome studies can provide novel ways to enhance the overall welfare of fish, strengthen disease prevention and increase sustainability in aquaculture production.},
}

@article {pmid39313563,
year = {2024},
author = {Arnholdt-Schmitt, B and Noceda, C and Germano, TA and Aziz, S and Thiers, KLL and Oliveira, M and Bharadwaj, R and Mohanapriya, G and Sircar, D and Costa, JH},
title = {Validating alternative oxidase (AOX) gene family as efficient marker consortium for multiple-resilience in Xylella fastidiosa-infected Vitis holobionts.},
journal = {Plant cell reports},
volume = {43},
number = {10},
pages = {236},
pmid = {39313563},
issn = {1432-203X},
abstract = {AOX gene family in motion marks in-born efficiency of respiration adjustment; can serve for primer screening, genotype ranking, in vitro-plant discrimination and a SMART perspective for multiple-resilient plant holobiont selection. The bacteria Xylella fastidiosa (Xf) is a climate-dependent, global threat to many crops of high socio-economic value, including grapevine. Currently designed breeding strategies for Xf-tolerant or -resistant genotypes insufficiently address the danger of biodiversity loss by focusing on selected threats, neglecting future environmental conditions. Thus, breeding strategies should be validated across diverse populations and acknowledge temperature changes and drought by minimizing the metabolic-physiologic effects of multiple stress-induced oxygen shortages. This research hypothesizes that multiple-resilient plant holobionts achieve lifelong adaptive robustness through early molecular and metabolic responses in primary stress target cells, which facilitate efficient respiration adjustment and cell cycle down-regulation. To validate this concept open-access transcriptome data were analyzed of xylem tissues of Xf-tolerant and -resistant Vitis holobionts from diverse trials and genetic origins from early hours to longer periods after Xf-inoculation. The results indicated repetitive involvement of alternative oxidase (AOX) transcription in episodes of down-regulated transcripts of cytochrome c oxidase (COX) at various critical time points before disease symptoms emerged. The relation between transcript levels of COX and AOX ('relCOX/AOX') was found promising for plant discrimination and primer screening. Furthermore, transcript levels of xylem-harbored bacterial consortia indicated common regulation with Xf and revealed stress-induced early down-regulation and later enhancement. LPS priming promoted the earlier increase in bacterial transcripts after Xf-inoculation. This proof-of-principle study highlights a SMART perspective for AOX-assisted plant selection towards multiple-resilience that includes Xf-tolerance. It aims to support timely future plant diagnostics and in-field substitution, sustainable agro-management, which protects population diversity and strengthens both conventional breeding and high-tech, molecular breeding research. Furthermore, the results suggested early up-regulation of bacterial microbiota consortia in vascular-enriched tissues as a novel additional trait for future studies on Xf-tolerance.},
}

@article {pmid39311881,
year = {2024},
author = {Isaac, P and Mutusamy, P and Yin, LS and Jing Wei, Y and Mohd Salleh, F and Bin Abu Bakar, MAL and Parimannan, S and Rajandas, H},
title = {Complete genome sequence of Serratia marcescens D1_6, isolated from peat soil.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0029924},
doi = {10.1128/mra.00299-24},
pmid = {39311881},
issn = {2576-098X},
abstract = {We present a complete genome of Serratia marcescens D1_6 isolated from peat swamp forest. The complete genome for the isolate D1_6 was constructed using data from Oxford Nanopore Technologies and Illumina. The genome of D1_6 has a total length of 4,996,151 bp, comprising a chromosome and a plasmid.},
}

@article {pmid39304531,
year = {2024},
author = {Umar, M and Merlin, TS and Puthiyedathu, ST},
title = {Genomic insights into symbiosis and host adaptation of sponge-associated novel bacterium, Rossellomorea orangium sp. nov.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnae074},
pmid = {39304531},
issn = {1574-6968},
abstract = {Sponge-associated microorganisms play vital roles in marine sponge ecology. This study presents a genomic investigation of Rossellomorea sp. MCCB 382, isolated from Stelletta sp., reveals insights into its adaptations and symbiotic roles. Phylogenomic study and Overall Genomic Relatedness Index (OGRI) classify MCCB 382 as a novel species, Rossellomorea orangium sp. nov. The genome encodes numerous carbohydrate metabolism enzymes (CAZymes), likely aiding nutrient cycling in the sponge host. Unique eukaryotic-like protein domains hint at potential mechanisms of symbiosis. Defense mechanisms include CRISPR, restriction modification systems, DNA phosphorothioation, toxin-antitoxin systems, and heavy metal and multidrug resistance genes, indicating adaptation to challenging marine environments. Unlike obligate mutualists, MCCB 382 shows no genome reduction. Furthermore, the presence of mobile genetic elements, horizontal gene transfer, and prophages suggest genetic versatility, implying flexible metabolic potential and capacity for rapid adaptation and symbiosis shifts. MCCB 382 possesses six biosynthetic gene clusters for secondary metabolites, including both type II and III polyketide synthases (PKS), terpenes, (NRPS), NRPS-independent-siderophore, and lassopeptide. Further genome mining using BiGScape revealed four distinct gene cluster families, T2PKS, NRPS-independent-siderophore, lasso peptide, and terpene, presenting opportunities for novel compound elucidation. Our study reveals a symbiotic lifestyle of MCCB 382 with the host sponge, highlighting symbiont factors that aid in establishing and sustaining this relationship. This is the pioneering genomic characterisation of a novel Rossellomorea sp. within the sponge Stelletta sp. holobiont.},
}

@article {pmid39301440,
year = {2024},
author = {Morales, HE and Groombridge, JJ and Tollington, S and Henshaw, S and Tatayah, V and Ruhomaun, K and van Oosterhout, C and Gilbert, MTP and , and , and , and , },
title = {The genome sequence of the Mauritius parakeet, Alexandrinus eques (formerly Psittacula eques) (A.Newton & E. Newton, 1876).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {378},
pmid = {39301440},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Alexandrinus eques, formerly Psittacula eques (the Mauritius Parakeet; Chordata; Aves; Psittaciformes; Psittacidae). The genome sequence is 1203.8 megabases in span. Most of the assembly is scaffolded into 35 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 18.86 kilobases in length.},
}

@article {pmid39299961,
year = {2024},
author = {Soltani, J and Sheikh-Ahmadi, A},
title = {Genomic and Chemical Evidence on Biosynthesis of Taxane Diterpenoids in Alternaria Isolates from Cupressaceae.},
journal = {Current microbiology},
volume = {81},
number = {11},
pages = {367},
pmid = {39299961},
issn = {1432-0991},
mesh = {*Alternaria/genetics/metabolism ; *Taxoids/metabolism ; *Biosynthetic Pathways/genetics ; Endophytes/metabolism/genetics/isolation & purification/classification ; Bridged-Ring Compounds/metabolism ; Diterpenes/metabolism ; Paclitaxel/biosynthesis ; Fungal Proteins/genetics/metabolism ; Genomics ; Phylogeny ; },
abstract = {Alternaria species (Deuteromycetes, Ascomycota) as ubiquitous fungi and prolific producers of a variety of toxic compounds are a part of microbiomes of plants, humans, and animals, mainly causing disease, allergic reactions, and toxicosis. However, some species have also been reported as endophytic microorganisms with highly bioactive metabolites. Our previous results indicate that potentially endophytic Alternaria species from Cupressaceae produce bioactive metabolites that possibly contribute to plant holobiont's health. Here, a possible mechanism behind this bioactivity is elucidated. As some endophytic fungi are reported to produce cytotoxic taxane diterpenoids, eight potentially endophytic Alternaria isolates from our collection were analyzed for the presence of the key genes of the paclitaxel (Taxol) biosynthetic pathway, i.e., taxadin synthase (ts), 10-deacetylbaccatin III-10-O-acetyltransferase (dbat), and C-13-phenylpropanoid side-chain CoA acyltransferase (bapt). The presence of all genes, i.e., ts, dbat, and bapt, was detected by PCR in six isolates and dbat and bapt in two isolates. Chemical analyses of the fermentation broths by TLC and HPLC chromatography and IR spectroscopy indicated the synthesis of the final product, i.e., paclitaxel. So, we introduce the synthesis of taxane diterpenoids as a possible mechanism by which Alternaria occupies the plant niches and protects the plant holobiont in the presence of competing microorganisms.},
}

*Alternaria/genetics/metabolism
*Taxoids/metabolism
*Biosynthetic Pathways/genetics
Endophytes/metabolism/genetics/isolation & purification/classification
Bridged-Ring Compounds/metabolism
Diterpenes/metabolism
Paclitaxel/biosynthesis
Fungal Proteins/genetics/metabolism
Genomics
Phylogeny

@article {pmid39294150,
year = {2024},
author = {Wang, W and Song, W and Majzoub, ME and Feng, X and Xu, B and Tao, J and Zhu, Y and Li, Z and Qian, PY and Webster, NS and Thomas, T and Fan, L},
title = {Decoupling of strain- and intrastrain-level interactions of microbiomes in a sponge holobiont.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8205},
pmid = {39294150},
issn = {2041-1723},
support = {42376113//National Natural Science Foundation of China (National Science Foundation of China)/ ; 91951120//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42406103//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41776138//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31861143020//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; *Microbiota/genetics ; *Porifera/microbiology/virology ; *Symbiosis ; Genetic Variation ; Viruses/genetics/classification ; Phylogeny ; },
abstract = {Holobionts are highly organized assemblages of eukaryotic hosts, cellular microbial symbionts, and viruses, whose interactions and evolution involve complex biological processes. It is largely unknown which specific determinants drive similarity or individuality in genetic diversity between holobionts. Here, we combine short- and long-read sequencing and DNA-proximity-linkage technologies to investigate intraspecific diversity of the microbiomes, including host-resolved viruses, in individuals of a model marine sponge. We find strong impacts of the sponge host and the cellular hosts of viruses on strain-level organization of the holobiont, whereas substantial overlap in nucleotide diversity between holobionts suggests frequent exchanges of microbial cells and viruses at intrastrain level in the local sponge population. Immune-evasive arms races likely restricted virus-host co-evolution at the intrastrain level, generated holobiont-specific genome variations, and linked virus-host genetics through recombination. Our work shows that a decoupling of strain- and intrastrain-level interactions is a key factor in the genetic diversification of holobionts.},
}

Animals
*Microbiota/genetics
*Porifera/microbiology/virology
*Symbiosis
Genetic Variation
Viruses/genetics/classification
Phylogeny

@article {pmid39290662,
year = {2024},
author = {Thormar, EA and Hansen, SB and Jørgensen, LVG and Limborg, MT},
title = {Sampling fish gut microbiota - A genome-resolved metagenomic approach.},
journal = {Ecology and evolution},
volume = {14},
number = {9},
pages = {e70302},
pmid = {39290662},
issn = {2045-7758},
abstract = {Despite a surge in microbiota-focused studies in teleosts, few have reported functional data on whole metagenomes as it has proven difficult to extract high biomass microbial DNA from fish intestinal samples. The zebrafish is a promising model organism in functional microbiota research, yet studies on the functional landscape of the zebrafish gut microbiota through shotgun based metagenomics remain scarce. Thus, a consensus on an appropriate sampling method accurately representing the zebrafish gut microbiota, or any fish species is lacking. Addressing this, we systematically tested four methods of sampling the zebrafish gut microbiota: collection of faeces from the tank, the whole gut, intestinal content, and the application of ventral pressure to facilitate extrusion of gut material. Additionally, we included water samples as an environmental control to address the potential influence of the environmental microbiota on each sample type. To compare these sampling methods, we employed a combination of genome-resolved metagenomics and 16S metabarcoding techniques. We observed differences among sample types on all levels including sampling, bioinformatic processing, metagenome co-assemblies, generation of metagenome-assembled genomes (MAGs), functional potential, MAG coverage, and population level microdiversity. Comparison to the environmental control highlighted the potential impact of the environmental contamination on data interpretation. While all sample types tested are informative about the zebrafish gut microbiota, the results show that optimal sample type for studying fish microbiomes depends on the specific objectives of the study, and here we provide a guide on what factors to consider for designing functional metagenome-based studies on teleost microbiomes.},
}

@article {pmid39262445,
year = {2023},
author = {Borry, M and Forsythe, A and Andrades Valtueña, A and Hübner, A and Ibrahim, A and Quagliariello, A and White, AE and Kocher, A and Vågene, ÅJ and Bartholdy, BP and Spurīte, D and Ponce-Soto, GY and Neumann, G and Huang, IT and Light, I and Velsko, IM and Jackson, I and Frangenberg, J and Serrano, JG and Fumey, J and Özdoğan, KT and Blevins, KE and Daly, KG and Lopopolo, M and Moraitou, M and Michel, M and van Os, M and Bravo-Lopez, MJ and Sarhan, MS and Dagtas, ND and Oskolkov, N and Smith, OS and Lebrasseur, O and Rozwalak, P and Eisenhofer, R and Wasef, S and Ramachandran, SL and Vanghi, V and Warinner, C and Fellows Yates, JA},
title = {Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT.},
journal = {F1000Research},
volume = {12},
number = {},
pages = {926},
doi = {10.12688/f1000research.134798.2},
pmid = {39262445},
issn = {2046-1402},
mesh = {*Metagenomics/methods ; Humans ; *Metadata ; High-Throughput Nucleotide Sequencing/methods ; Software ; Metagenome ; Computational Biology/methods ; DNA, Ancient/analysis ; },
abstract = {BACKGROUND: Access to sample-level metadata is important when selecting public metagenomic sequencing datasets for reuse in new biological analyses. The Standards, Precautions, and Advances in Ancient Metagenomics community (SPAAM, https://spaam-community.org) has previously published AncientMetagenomeDir, a collection of curated and standardised sample metadata tables for metagenomic and microbial genome datasets generated from ancient samples. However, while sample-level information is useful for identifying relevant samples for inclusion in new projects, Next Generation Sequencing (NGS) library construction and sequencing metadata are also essential for appropriately reprocessing ancient metagenomic data. Currently, recovering information for downloading and preparing such data is difficult when laboratory and bioinformatic metadata is heterogeneously recorded in prose-based publications.

METHODS: Through a series of community-based hackathon events, AncientMetagenomeDir was updated to provide standardised library-level metadata of existing and new ancient metagenomic samples. In tandem, the companion tool 'AMDirT' was developed to facilitate rapid data filtering and downloading of ancient metagenomic data, as well as improving automated metadata curation and validation for AncientMetagenomeDir.

RESULTS: AncientMetagenomeDir was extended to include standardised metadata of over 6000 ancient metagenomic libraries. The companion tool 'AMDirT' provides both graphical- and command-line interface based access to such metadata for users from a wide range of computational backgrounds. We also report on errors with metadata reporting that appear to commonly occur during data upload and provide suggestions on how to improve the quality of data sharing by the community.

CONCLUSIONS: Together, both standardised metadata reporting and tooling will help towards easier incorporation and reuse of public ancient metagenomic datasets into future analyses.},
}

*Metagenomics/methods
Humans
*Metadata
High-Throughput Nucleotide Sequencing/methods
Software
Metagenome
Computational Biology/methods
DNA, Ancient/analysis

@article {pmid39256870,
year = {2024},
author = {Kløve, S and Stinson, SE and Romme, FO and Butt, J and Graversen, KB and Lund, MAV and Fonvig, CE and Waterboer, T and Perez-Perez, GI and Hansen, T and Holm, JC and Andersen, SB},
title = {Helicobacter pylori seropositivity associates with hyperglycemia, but not obesity, in Danish children and adolescents.},
journal = {BMC medicine},
volume = {22},
number = {1},
pages = {379},
pmid = {39256870},
issn = {1741-7015},
abstract = {BACKGROUND: Helicobacter pylori colonizes the human stomach and may affect the inflammatory response, hormone production related to energy regulation, and gastrointestinal microbiota composition. Previous studies have explored a potential association between H. pylori infection and pediatric obesity with varying results. Considering the immunomodulatory effects of early-life infection with H. pylori that can confer beneficial effects, we hypothesized that we would find an inverse relationship between H. pylori seropositivity and obesity among Danish children and adolescents.

METHODS: We assessed H. pylori seroprevalence in 713 subjects from an obesity clinic cohort and 990 subjects from a population-based cohort, aged 6 to 19 years, and examined its association with obesity and other cardiometabolic risk factors.

RESULTS: No association was found between H. pylori and body mass index standard deviation score (BMI SDS). H. pylori seropositivity was, however, significantly associated with higher fasting plasma glucose levels and the prevalence of hyperglycemia.

CONCLUSION: While we did not find an association between H. pylori seropositivity and BMI SDS, we observed a significant association with higher fasting plasma glucose levels and increased prevalence of hyperglycemia, suggesting that H. pylori infection may contribute to impaired glucose regulation in Danish children and adolescents.},
}

@article {pmid39256139,
year = {2024},
author = {Pepke, ML and Hansen, SB and Limborg, MT},
title = {Telomere dynamics as mediators of gut microbiota-host interactions.},
journal = {Trends in cell biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tcb.2024.08.003},
pmid = {39256139},
issn = {1879-3088},
abstract = {The highly proliferative gut tissue exhibits rapid telomere shortening with systemic effects on the host organism. Recent studies have demonstrated a bidirectionality in interactions between intestinal telomere length dynamics and the composition and activity of the gut microbiome thus linking processes of inflammation, dysbiosis and aging across different vertebrate species.},
}

@article {pmid39253787,
year = {2024},
author = {Cheng, S and Gong, X and Xue, W and Kardol, P and Delgado-Baquerizo, M and Ling, N and Chen, X and Liu, M},
title = {Evolutionarily conserved core microbiota as an extended trait in nitrogen acquisition strategy of herbaceous species.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.20118},
pmid = {39253787},
issn = {1469-8137},
support = {42077047//National Foundation of Sciences in China/ ; lzujbky-2022-ct04//Fundamental Research Funds for the Central University of China/ ; 2021YFD1700202//National Key R&D program/ ; },
abstract = {Microbiota have co-evolved with plants over millions of years and are intimately linked to plants, ranging from symbiosis to pathogenesis. However, our understanding of the existence of a shared core microbiota across phylogenetically diverse plants remains limited. A common garden field experiment was conducted to investigate the rhizosphere microbial communities of phylogenetically contrasting herbaceous families. Through a combination of metagenomic sequencing, analysis of plant economic traits, and soil biochemical properties, we aimed to elucidate the eco-evolutionary role of the core rhizosphere microbiota in light of plant economic strategies. We identified a conserved core microbiota consisting of 278 taxa that was closely associated with the phylogeny of the plants studied. This core microbiota actively participated in multiple nitrogen metabolic processes and showed a strong correlation with the functional potential of rhizosphere nitrogen cycling, thereby serving as an extended trait in the plant nitrogen acquisition. Furthermore, our examination of simulated species loss revealed the crucial role of the core microbiota in maintaining the rhizosphere community's network stability. Our study highlighted that the core microbiota, which exhibited a phylogenetically conserved association with plants, potentially represented an extension of the plant phenotype and played an important role in nitrogen acquisition. These findings held implications for the utilization of microbiota-mediated plant functions.},
}

@article {pmid39245169,
year = {2024},
author = {Brulin, L and Ducrocq, S and Estellé, J and Even, G and Martel, S and Merlin, S and Audebert, C and Croiseau, P and Sanchez, MP},
title = {The fecal microbiota of Holstein cows is heritable and genetically correlated to dairy performances.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2024-25003},
pmid = {39245169},
issn = {1525-3198},
abstract = {The fecal microbiota of ruminants constitutes a diversified community that has been phenotypically associated with a variety of host phenotypes, such as production and health. To gain a better understanding of the complex and interconnected factors that drive the fecal bacterial community, we have aimed to estimate the genetic parameters of the diversity and composition of the fecal microbiota, including heritabilities, genetic correlations among taxa, and genetic correlations between fecal microbiota features and host phenotypes. To achieve this, we analyzed a large population of 1,875 Holstein cows originating from 144 French commercial herds and routinely recorded for production, somatic cell score, and fertility traits. Fecal samples were collected from the animals and subjected to 16S rRNA gene sequencing, with reads classified into Amplicon Sequence Variants (ASVs). The estimated α- and β-diversity indices (i.e., Observed Richness, Shannon index, Bray-Curtis and Jaccard dissimilarity matrices) and the abundances of ASVs, genera, families and phyla, normalized by centered-log ratio (CLR), were considered as phenotypes. Genetic parameters were calculated using either univariate or bivariate animal models. Heritabilities estimates, ranging from 0.08 to 0.31 for taxa abundances and β-diversity indices, highlight the influence of the host genetics on the composition of the fecal microbiota. Furthermore, genetic correlations estimated within the microbial community and between microbiota features and host traits reveal the complex networks linking all components of the fecal microbiota together and to their host, thus strengthening the holobiont concept. By estimating the heritabilities of microbiota-associated phenotypes, our study quantifies the impact of the host genetics on the fecal microbiota composition. In addition, genetic correlations between taxonomic groups and between taxa abundances and host performance suggest potential applications for selective breeding to improve host traits or promote a healthier microbiota.},
}

@article {pmid39242500,
year = {2024},
author = {Zhang, Y and Zhang, Y and Tang, X and Guo, X and Yang, Q and Sun, H and Wang, H and Ling, J and Dong, J},
title = {A transcriptome-wide analysis provides novel insights into how Metabacillus indicus promotes coral larvae metamorphosis and settlement.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {840},
pmid = {39242500},
issn = {1471-2164},
support = {2022YFC3103602//National Key Research and Development Program of China/ ; 2022YFC3102003//National Key Research and Development Program of China/ ; 2022YFC3102004//National Key Research and Development Program of China/ ; 41976147//National Natural Science Foundation of China/ ; U2106208//National Natural Science Foundation of China-Shandong Joint Fund/ ; 2020B1212060058//Science and Technology Planning Project of Guangdong Province, China/ ; },
mesh = {Animals ; *Anthozoa/genetics/growth & development/microbiology ; *Metamorphosis, Biological/genetics ; *Larva/growth & development ; *Gene Expression Profiling ; Transcriptome ; Bacillaceae/genetics/growth & development ; Coral Reefs ; },
abstract = {BACKGROUND: Coral reefs experience frequent and severe disturbances that can overwhelm their natural resilience. In such cases, ecological restoration is essential for coral reef recovery. Sexual reproduction has been reported to present the simplest and most cost-effective means for coral reef restoration. However, larval settlement and post-settlement survival represent bottlenecks for coral recruitment in sexual reproduction. While bacteria play a significant role in triggering coral metamorphosis and settlement in many coral species, the underlying molecular mechanisms remain largely unknown. In this study, we employed a transcriptome-level analysis to elucidate the intricate interactions between bacteria and coral larvae that are crucial for the settlement process.

RESULTS: High Metabacillus indicus strain cB07 inoculation densities resulted in the successful induction of metamorphosis and settlement of coral Pocillopora damicoris larvae. Compared with controls, inoculated coral larvae exhibited a pronounced increase in the abundance of strain cB07 during metamorphosis and settlement, followed by a significant decrease in total lipid contents during the settled stage. The differentially expressed genes (DEGs) during metamorphosis were significantly enriched in amino acid, protein, fatty acid, and glucose related metabolic pathways. In settled coral larvae induced by strain cB07, there was a significant enrichment of DEGs with essential roles in the establishment of a symbiotic relationship between coral larvae and their symbiotic partners. The photosynthetic efficiency of strain cB07 induced primary polyp holobionts was improved compared to those of the negative controls. In addition, coral primary polyps induced by strain cB07 showed significant improvements in energy storage and survival.

CONCLUSIONS: Our findings revealed that strain cB07 can promote coral larval settlement and enhance post-settlement survival and fitness. Manipulating coral sexual reproduction with strain cB07 can overcome the current recruitment bottleneck. This innovative approach holds promise for future coral reef restoration efforts.},
}

Animals
*Anthozoa/genetics/growth & development/microbiology
*Metamorphosis, Biological/genetics
*Larva/growth & development
*Gene Expression Profiling
Transcriptome
Bacillaceae/genetics/growth & development
Coral Reefs

@article {pmid39228372,
year = {2024},
author = {Alexandre, PA and Rodríguez-Ramilo, ST and Mach, N and Reverter, A},
title = {Combining genomics and semen microbiome increases the accuracy of predicting bull prolificacy.},
journal = {Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie},
volume = {},
number = {},
pages = {},
doi = {10.1111/jbg.12899},
pmid = {39228372},
issn = {1439-0388},
support = {//CSIRO-INRAE linkage Travel Grant/ ; },
abstract = {Commercial livestock producers need to prioritize genetic progress for health and efficiency traits to address productivity, welfare, and environmental concerns but face challenges due to limited pedigree information in extensive multi-sire breeding scenarios. Utilizing pooled DNA for genotyping and integrating seminal microbiome information into genomic models could enhance predictions of male fertility traits, thus addressing complexities in reproductive performance and inbreeding effects. Using the Angus Australia database comprising genotypes and pedigree data for 78,555 animals, we simulated percentage of normal sperm (PNS) and prolificacy of sires, resulting in 713 sires and 27,557 progeny in the final dataset. Publicly available microbiome data from 45 bulls was used to simulate data for the 713 sires. By incorporating both genomic and microbiome information our models were able to explain a larger proportion of phenotypic variation in both PNS (0.94) and prolificacy (0.56) compared to models using a single data source (e.g., 0.36 and 0.41, respectively, using only genomic information). Additionally, models containing both genomic and microbiome data revealed larger phenotypic differences between animals in the top and bottom quartile of predictions, indicating potential for improved productivity and sustainability in livestock farming systems. Inbreeding depression was observed to affect fertility traits, which makes the incorporation of microbiome information on the prediction of fertility traits even more actionable. Crucially, our inferences demonstrate the potential of the semen microbiome to contribute to the improvement of fertility traits in cattle and pave the way for the development of targeted microbiome interventions to improve reproductive performance in livestock.},
}

@article {pmid39228291,
year = {2024},
author = {Martin, EJ and Speak, SA and Urban, L and Morales, HE and van Oosterhout, C},
title = {Sonification of Genomic Data to Represent Genetic Load in Zoo Populations.},
journal = {Zoo biology},
volume = {},
number = {},
pages = {},
doi = {10.1002/zoo.21859},
pmid = {39228291},
issn = {1098-2361},
support = {//E.J.M. was funded by East of Scotland Bioscience Doctoral Training Partnership (EASTBIO) funded by UKRI Biotechnology and Biological Sciences Research Council (BBSRC) Grant Number BB/M010996/1. C.v.O. was funded by the Royal Society International Collaboration Awards (ICA\R1\201194) and the Earth and Life Systems Alliance (ELSA), S.A.S. was funded by a NERC ARIES PhD studentship (T209447) at the UEA and a Research Training Support Grant (RTSG; 100162318RA1). H.M. was funded by an EMBO fellowship (grant 1111-2018) and the European Union's Horizon 2020 research and innovation program under Marie Skłodowska-Curie (grant 840519)./ ; },
abstract = {Maintaining a diverse gene pool is important in the captive management of zoo populations, especially in endangered species such as the pink pigeon (Nesoenas mayeri). However, due to the limited number of breeding individuals and relaxed natural selection, the loss of variation and accumulation of harmful variants is inevitable. Inbreeding results in a loss of fitness (i.e., inbreeding depression), principally because related parents are more likely to transmit a copy of the same recessive deleterious genetic variant to their offspring. Genomics-informed captive breeding can manage harmful variants by artificial selection, reducing the genetic load by avoiding the inheritance of two copies of the same harmful variant. To explain this concept in an interactive way to zoo visitors, we developed a sonification game to represent the fitness impacts of harmful variants by detuning notes in a familiar musical melody (i.e., Beethoven's Für Elise). Conceptually, zoo visitors play a game aiming to create the most optimal pink pigeon offspring in terms of inbreeding depression. They select virtual crosses between pink pigeon individuals and listen for the detuning of the melody, which represents the realised load of the resultant offspring. Here we present the sonification algorithm and the results of an online survey to see whether participants could identify the most and least optimal offspring from three potential pink pigeon offspring. Of our 98 respondents, 85 (86.7%) correctly identified the least optimal offspring, 73 (74.5%) correctly identified the most optimal, and 62 (63.3%) identified both the most and least optimal offspring using only the sonification.},
}

@article {pmid39221442,
year = {2024},
author = {Morales, HE and Norris, K and Henshaw, S and Tatayah, V and Ruhomaun, K and van Oosterhout, C and Groombridge, JJ and Gilbert, MTP and , and , and , and , },
title = {The genome sequence of the Mauritius kestrel, Falco punctatus (Temminck, 1821).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {312},
pmid = {39221442},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Falco punctatus (the Mauritius kestrel; Chordata; Aves; Falconiformes; Falconidae). The genome sequence is 1,279.3 megabases in span. Most of the assembly is scaffolded into 23 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 17.34 kilobases in length.},
}

@article {pmid39217744,
year = {2024},
author = {Pylak, M and Oszust, K and Panek, J and Siegieda, D and Cybulska, J and Zdunek, A and Orzeł, A and Frąc, M},
title = {Impact of microbial-based biopreparations on soil quality, plant health, and fruit chemistry in raspberry cultivation.},
journal = {Food chemistry},
volume = {462},
number = {},
pages = {140943},
doi = {10.1016/j.foodchem.2024.140943},
pmid = {39217744},
issn = {1873-7072},
abstract = {Application of microbial-based biopreparations as a pre-harvest strategy offers a method to obtain sustainable agricultural practices and could be an important approach for advancing food science, promoting sustainability, and meeting global food market demands. The impact of a bacterial-fungal biopreparation mixture on soil-plant-microbe interactions, fruit chemical composition and yield of 7 raspberry clones was investigated by examining the structural and functional profiles of microbial communities within leaves, fruits, and soil. Biopreparation addition caused the enhancement of the microbiological utilization of specific compounds, such as d-mannitol, relevant in plant-pathogen interactions and overall plant health. The biopreparation treatment positively affected the nitrogen availability in soil (9-160%). The analysis of plant stress marker enzymes combined with the evaluation of fruit quality and chemical properties highlight changes inducted by the pre-harvest biopreparation application. Chemical analyses highlight biopreparations' role in soil and fruit quality improvement, promoting sustainable agriculture. This effect was dependent on tested clones, showing increase of soluble solid content in fruits, concentration of polyphenols or the sensory quality of the fruits. The results of the next-generation sequencing indicated increase in the effective number of bacterial species after biopreparation treatment. The network analysis showed stimulating effect of biopreparation on microbial communities by enhancing microbial interactions (increasing the number of network edges up to 260%) of and affecting the proportions of mutual relationships between both bacteria and fungi. These findings show the potential of microbial-based biopreparation in enhancing raspberry production whilst promoting sustainable practices and maintaining environmental homeostasis and giving inshght in holistic understanding of microbial-based approaches for advancing food science monitoring.},
}

@article {pmid39216737,
year = {2024},
author = {Chen, J and Yu, X and Yu, K and Chen, B and Qin, Z and Liao, Z and Ma, Y and Xu, L and Wang, Y},
title = {Potential adaptation of scleractinian coral Pocillopora damicornis during hypo-salinity stress caused by extreme pre-flood rainfall over South China.},
journal = {Environmental research},
volume = {},
number = {},
pages = {119848},
doi = {10.1016/j.envres.2024.119848},
pmid = {39216737},
issn = {1096-0953},
abstract = {Global warming intensifies the water cycle, resulting in significant increases in precipitation and river runoff, which brings severe hypo-salinity stress to nearshore coral reefs. Ecological investigations have found that some corals exhibit remarkable adaptability to hypo-salinity stress during mass-bleaching events. However, the exact cause of this phenomenon remains unclear. To elucidate the potential molecular mechanism leading to high tolerance to hypo-salinity stress, Pocillopora damicornis was used as a research object in this study. We compared the differences in transcriptional responses and symbiotic microbiomes between bleaching and unbleaching P. damicornis during hypo-salinity stress caused by extreme pre-flood rainfall over South China in 2022. The results showed that: (1) Under hypo-salinity stress, the coral genes related to immune defense and cellular stress were significantly upregulated in bleaching corals, indicating more severe immune damage and stress, and the Symbiodiniaceae had no significant gene enrichment. Conversely, metabolic genes related to glycolysis/gluconeogenesis were significantly downregulated in unbleaching corals, whereas Symbiodiniaceae genes related to oxidative phosphorylation were significantly upregulated to meet the energy requirements of coral holobiont; (2) C1d was the dominant Symbiodiniaceae subclade in all samples, with no significant difference between the two groups; (3) The symbiotic bacterial community structure was reorganized under hypo-salinity stress. The abundance of opportunistic bacteria increased significantly in bleaching coral, whereas the relative abundance of probiotics was higher in unbleaching coral. This may be due to severe immune damage, making the coral more susceptible to opportunistic infection and bleaching. These results suggest that long-term hypo-salinity acclimation in the Pearl River Estuary enhances the tolerance of some corals to hypo-salinity stress. Corals with higher tolerance may reduce energy consumption by slowing down their metabolism, improve the energy metabolism of Symbiodiniaceae to meet the energy requirements of the coral holobiont, and alter the structure of symbiotic bacterial communities to avoid bleaching.},
}