@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.},
}

@article {pmid39216249,
year = {2024},
author = {Guo, D and Li, Z and Zhang, Y and Zhang, W and Wang, C and Zhang, DX and Liu, F and Gao, Z and Xu, B and Wang, N},
title = {The effect of lambda-cyhalothrin nanocapsules on the gut microbial communities and immune response of the bee elucidates the potential environmental impact of emerging nanopesticides.},
journal = {Journal of hazardous materials},
volume = {479},
number = {},
pages = {135650},
doi = {10.1016/j.jhazmat.2024.135650},
pmid = {39216249},
issn = {1873-3336},
abstract = {Emerging nanopesticides are gradually gaining widespread application in agriculture due to their excellent properties, but their potential risks to pollinating insects are not fully understood. In this study, lambda-cyhalothrin nanocapsules (LC-NCs) were constructed by electrostatic self-assembly method with iron mineralization optimization, and their effects on bee gut microbial communities and host immune-related factors were investigated. Microbiome sequencing revealed that LC-NCs increase the diversity of gut microbial communities and reduce the complexity of network features, disrupting the overall structure of the microbial communities. In addition, LC-NCs also had systemic effects on the immune response of bees, including increased activity of SOD and CAT enzymes and expression of their genes, as well as downregulation of Defensin1. Furthermore, we noticed that the immune system of the host was activated simultaneously with a rise in the abundance of beneficial bacteria in the gut. Our research emphasizes the importance of both the host and gut microbiota of holobiont in revealing the potential risks of LC-NCs to environmental indicators of honey bees, and provides references for exploring the interactions between host-microbiota systems under exogenous stress. At the same time, we hope that more research can focus on the potential impacts of nanopesticides on the ecological environment.},
}

@article {pmid39210412,
year = {2024},
author = {Barnes, CJ and Bünner, MS and Ramírez-Flores, MR and Nielsen, IB and Ramos-Madrigal, J and Zharikova, D and McLaughlin, CM and Gilbert, MT and Sawers, RJH},
title = {The ancestral environment of teosinte populations shapes their root microbiome.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {64},
pmid = {39210412},
issn = {2524-6372},
abstract = {BACKGROUND: The composition of the root microbiome affects the host's growth, with variation in the host genome associated with microbiome variation. However, it is not known whether this intra-specific variation of root microbiomes is a consequence of plants performing targeted manipulations of them to adapt to their local environment or varying passively with other traits. To explore the relationship between the genome, environment and microbiome, we sampled seeds from teosinte populations across its native range in Mexico. We then grew teosinte accessions alongside two modern maize lines in a common garden experiment. Metabarcoding was performed using universal bacterial and fungal primers to profile their root microbiomes.

RESULTS: The root microbiome varied between the two modern maize lines and the teosinte accessions. We further found that variation of the teosinte genome, the ancestral environment (temperature/elevation) and root microbiome were all correlated. Multiple microbial groups significantly varied in relative abundance with temperature/elevation, with an increased abundance of bacteria associated with cold tolerance found in teosinte accessions taken from high elevations.

CONCLUSIONS: Our results suggest that variation in the root microbiome is pre-conditioned by the genome for the local environment (i.e. non-random). Ultimately, these claims would be strengthened by confirming that these differences in the root microbiome impact host phenotype, for example, by confirming that the root microbiomes of high-elevation teosinte populations enhance cold tolerance.},
}

@article {pmid39209587,
year = {2024},
author = {Limborg, MT and Winther-Have, CS and Morueta-Holme, N and Gilbert, MTP and Rasmussen, JA},
title = {The overlooked biodiversity loss.},
journal = {Trends in ecology & evolution},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tree.2024.08.001},
pmid = {39209587},
issn = {1872-8383},
abstract = {As most life-forms exist as holobionts, reduction of host-level biodiversity drives parallel habitat losses to their host-adapted microorganisms. The holobiont concept helps us to understand how species are habitats for - often ignored - coevolved microorganisms also worthy of conservation. Indeed, loss of host-associated microbial biodiversity may accelerate the extinction risks of their host.},
}

@article {pmid39203380,
year = {2024},
author = {Bai, C and Wang, Q and Xu, J and Zhang, H and Huang, Y and Cai, L and Zheng, X and Yang, M},
title = {Impact of Nutrient Enrichment on Community Structure and Co-Occurrence Networks of Coral Symbiotic Microbiota in Duncanopsammia peltata: Zooxanthellae, Bacteria, and Archaea.},
journal = {Microorganisms},
volume = {12},
number = {8},
pages = {},
doi = {10.3390/microorganisms12081540},
pmid = {39203380},
issn = {2076-2607},
support = {2022YFC3102003//the National Key Research and Development Program of China/ ; 2022ZD01//the Fund of Fujian Key Laboratory of Island Monitoring and Ecological Development (Island Research Center, MNR)/ ; 2019017//the Scientific Research Foundation of the Third Institute of Oceanography, Ministry of Natural Resources of China/ ; 41976127//the National Natural Science Foundation of China/ ; 2023J06043//the Fujian Provincial Natural Science Funds for Distinguished Young Scholar/ ; },
abstract = {Symbiotic microorganisms in reef-building corals, including algae, bacteria, archaea, fungi, and viruses, play critical roles in the adaptation of coral hosts to adverse environmental conditions. However, their adaptation and functional relationships in nutrient-rich environments have yet to be fully explored. This study investigated Duncanopsammia peltata and the surrounding seawater and sediments from protected and non-protected areas in the summer and winter in Dongshan Bay. High-throughput sequencing was used to characterize community changes, co-occurrence patterns, and factors influencing symbiotic coral microorganisms (zooxanthellae, bacteria, and archaea) in different environments. The results showed that nutrient enrichment in the protected and non-protected areas was the greatest in December, followed by the non-protected area in August. In contrast, the August protected area had the lowest nutrient enrichment. Significant differences were found in the composition of the bacterial and archaeal communities in seawater and sediments from different regions. Among the coral symbiotic microorganisms, the main dominant species of zooxanthellae is the C1 subspecies (42.22-56.35%). The dominant phyla of bacteria were Proteobacteria, Cyanobacteria, Firmicutes, and Bacteroidota. Only in the August protected area did a large number (41.98%) of SAR324_cladeMarine_group_B exist. The August protected and non-protected areas and December protected and non-protected areas contained beneficial bacteria as biomarkers. They were Nisaea, Spiroplasma, Endozoicomonas, and Bacillus. No pathogenic bacteria appeared in the protected area in August. The dominant phylum in Archaea was Crenarchaeota. These symbiotic coral microorganisms' relative abundances and compositions vary with environmental changes. The enrichment of dissolved inorganic nitrogen in environmental media is a key factor affecting the composition of coral microbial communities. Co-occurrence analysis showed that nutrient enrichment under anthropogenic disturbances enhanced the interactions between coral symbiotic microorganisms. These findings improve our understanding of the adaptations of coral holobionts to various nutritional environments.},
}

@article {pmid39196422,
year = {2024},
author = {Toloza-Moreno, DL and Yockteng, R and Pérez-Zuñiga, JI and Salinas-Castillo, C and Caro-Quintero, A},
title = {Implications of Domestication in Theobroma cacao L. Seed-Borne Microbial Endophytes Diversity.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {108},
pmid = {39196422},
issn = {1432-184X},
mesh = {*Cacao/microbiology ; *Endophytes/genetics/classification/isolation & purification/physiology ; *Seeds/microbiology/growth & development ; *Bacteria/classification/genetics/isolation & purification ; *Domestication ; Microbiota ; Fungi/genetics/classification/isolation & purification ; Genotype ; Biodiversity ; },
abstract = {The study of plant-microbe interactions is a rapidly growing research field, with increasing attention to the role of seed-borne microbial endophytes in protecting the plant during its development from abiotic and biotic stresses. Recent evidence suggests that seed microbiota is crucial in establishing the plant microbial community, affecting its composition and structure, and influencing plant physiology and ecology. For Theobroma cacao L., the diversity and composition of vertically transmitted microbes have yet to be addressed in detail. We explored the composition and diversity of seed-borne endophytes in cacao pods of commercial genotypes (ICS95, IMC67), recently liberated genotypes from AGROSAVIA (TCS01, TCS19), and landraces from Tumaco (Colombia) (AC9, ROS1, ROS2), to evaluate microbial vertical transmission and establishment in various tissues during plant development. We observed a higher abundance of Pseudomonas and Pantoea genera in the landraces and AGROSAVIA genotypes, while the commercial genotypes presented a higher number of bacteria species but in low abundance. In addition, all the genotypes and plant tissues showed a high percentage of fungi of the genus Penicillium. These results indicate that domestication in cacao has increased bacterial endophyte diversity but has reduced their abundance. We isolated some of these seed-borne endophytes to evaluate their potential as growth promoters and found that Bacillus, Pantoea, and Pseudomonas strains presented high production of indole acetic acid and ACC deaminase activity. Our results suggest that cacao domestication could lead to the loss of essential bacteria for seedling establishment and development. This study improves our understanding of the relationship and interaction between perennial plants and seed-borne microbiota.},
}

*Cacao/microbiology
*Endophytes/genetics/classification/isolation & purification/physiology
*Seeds/microbiology/growth & development
*Bacteria/classification/genetics/isolation & purification
*Domestication
Microbiota
Fungi/genetics/classification/isolation & purification
Genotype
Biodiversity

@article {pmid39191812,
year = {2024},
author = {Feng, Y and Wei, R and Chen, Q and Shang, T and Zhou, N and Wang, Z and Chen, Y and Chen, G and Zhang, G and Dong, K and Zhong, Y and Zhao, H and Hu, F and Zheng, H},
title = {Host specificity and cophylogeny in the "animal-gut bacteria-phage" tripartite system.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {72},
pmid = {39191812},
issn = {2055-5008},
mesh = {Animals ; *Host Specificity ; *Bacteriophages/genetics/physiology ; *Gastrointestinal Microbiome ; Bees/virology/microbiology ; *Bacteria/virology/genetics/classification ; *Phylogeny ; Metagenomics/methods ; Metagenome ; },
abstract = {Cophylogeny has been identified between gut bacteria and their animal host and is highly relevant to host health, but little research has extended to gut bacteriophages. Here we use bee model to investigate host specificity and cophylogeny in the "animal-gut bacteria-phage" tripartite system. Through metagenomic sequencing upon different bee species, the gut phageome revealed a more variable composition than the gut bacteriome. Nevertheless, the bacteriome and the phageome showed a significant association of their dissimilarity matrices, indicating a reciprocal interaction between the two kinds of communities. Most of the gut phages were host generalist at the viral cluster level but host specialist at the viral OTU level. While the dominant gut bacteria Gilliamella and Snodgrassella exhibited matched phylogeny with bee hosts, most of their phages showed a diminished level of cophylogeny. The evolutionary rates of the bee, the gut bacteria and the gut phages showed a remarkably increasing trend, including synonymous and non-synonymous substitution and gene content variation. For all of the three codiversified tripartite members, however, their genes under positive selection and genes involving gain/loss during evolution simultaneously enriched the functions into metabolism of nutrients, therefore highlighting the tripartite coevolution that results in an enhanced ecological fitness for the whole holobiont.},
}

Animals
*Host Specificity
*Bacteriophages/genetics/physiology
*Gastrointestinal Microbiome
Bees/virology/microbiology
*Bacteria/virology/genetics/classification
*Phylogeny
Metagenomics/methods
Metagenome

@article {pmid39189963,
year = {2024},
author = {Battilani, D and Gargiulo, R and Caniglia, R and Fabbri, E and Ramos-Madrigal, J and Fontsere, C and Ciucani, MM and Gopalakrishnan, S and Girardi, M and Fracasso, I and Mastroiaco, M and Ciucci, P and Vernesi, C},
title = {Beyond population size: whole-genome data reveal bottleneck legacies in the peninsular Italian wolf.},
journal = {The Journal of heredity},
volume = {},
number = {},
pages = {},
doi = {10.1093/jhered/esae041},
pmid = {39189963},
issn = {1465-7333},
abstract = {Preserving genetic diversity and adaptive potential while avoiding inbreeding depression is crucial for the long-term conservation of natural populations. Despite demographic increases, traces of past bottleneck events at the genomic level should be carefully considered for population management. From this perspective, the peninsular Italian wolf is a paradigmatic case. After being on the brink of extinction in the late 1960s, peninsular Italian wolves rebounded and recolonized most of the peninsula aided by conservation measures, including habitat and legal protection. Notwithstanding their demographic recovery, a comprehensive understanding of the genomic consequences of the historical bottleneck in Italian wolves is still lacking. To fill this gap, we sequenced whole genomes of thirteen individuals sampled in the core historical range of the species in Central Italy to conduct population genomic analyses, including a comparison with wolves from two highly-inbred wolf populations (i.e., Scandinavia and Isle Royale). We found that peninsular Italian wolves, despite their recent recovery, still exhibit relatively low genetic diversity, a small effective population size, signatures of inbreeding, and a non-negligible genetic load. Our findings indicate that the peninsular Italian wolf population is still susceptible to bottleneck legacies, which could lead to local inbreeding depression in case of population reduction or fragmentations. This study emphasizes the importance of considering key genetic parameters to design appropriate long-term conservation management plans.},
}

@article {pmid39189551,
year = {2024},
author = {Poupin, MJ and González, B},
title = {Embracing complexity in plant-microbiome systems.},
journal = {Environmental microbiology reports},
volume = {16},
number = {4},
pages = {e70000},
doi = {10.1111/1758-2229.70000},
pmid = {39189551},
issn = {1758-2229},
support = {ACT210052//Agencia Nacional de Investigación y Desarrollo PIA/ANILLOS/ ; NCN2021_010//Agencia Nacional de Investigación y Desarrollo-Millennium Science Initiative Program/ ; 1230472//Agencia Nacional de Investigación y Desarrollo - FONDECYT/ ; FB0002//Agencia NAcional de Investigación y Desarrollo - PIA/BASAL/ ; },
mesh = {*Microbiota ; *Plants/microbiology ; *Bacteria/genetics/classification ; Fungi/genetics/classification/physiology ; Archaea/classification/genetics ; Ecosystem ; },
abstract = {Despite recent advances in understanding the role of microorganisms in plant holobiont metabolism, physiology, and fitness, several relevant questions are yet to be answered, with implications for ecology, evolution, and sustainable agriculture. This article explores some of these questions and discusses emerging research areas in plant microbiomes. Firstly, it emphasizes the need to move beyond taxonomic characterization towards understanding microbial functions within plant ecosystems. Secondly, controlling methodological biases and enhancing OMICS technologies' standardization is imperative for a deeper comprehension of plant-microbiota interactions. Furthermore, while plant microbiota research has primarily centred on bacteria and fungi, other microbial players such as archaea, viruses, and microeukaryotes have been largely overlooked. Emerging evidence highlights their presence and potential roles, underscoring the need for thorough assessments. Future research should aim to elucidate the ecological microbial interactions, their impact on plant performance, and how the plant context shapes microbial community dynamics. Finally, a discussion is provided on how the multiple layers of abiotic and biotic factors influencing the spatiotemporal dynamics of plant-microbiome systems require in-depth attention. Examples illustrate how synthetic communities and computational methods such as machine learning and artificial intelligence provide alternatives to tackle these challenges and analyse the plant holobiont as a complex system.},
}

*Microbiota
*Plants/microbiology
*Bacteria/genetics/classification
Fungi/genetics/classification/physiology
Archaea/classification/genetics
Ecosystem

@article {pmid39187231,
year = {2024},
author = {Jefferson, T and Henley, EM and Erwin, PM and Lager, C and Perry, R and Chernikhova, D and Powell-Palm, MJ and Ushijima, B and Hagedorn, M},
title = {Evaluating the Coral Microbiome During Cryopreservation.},
journal = {Cryobiology},
volume = {},
number = {},
pages = {104960},
doi = {10.1016/j.cryobiol.2024.104960},
pmid = {39187231},
issn = {1090-2392},
abstract = {Coral reefs are threatened by various local and global stressors, including elevated ocean temperatures due to anthropogenic climate change. Coral cryopreservation could help secure the diversity of threatened corals. Recently, isochoric vitrification was used to demonstrate that coral fragments lived to 24 hr post-thaw; however, in this study, they were stressed post-thaw. The microbial portion of the coral holobiont has been shown to affect host fitness and the impact of cryopreservation treatment on coral microbiomes is unknown. Therefore, we examined the coral-associated bacterial communities pre- and post-cryopreservation treatments, with a view towards informing potential future stress reduction strategies. We characterized the microbiome of the Hawaiian finger coral, Porites compressa in the wild and at seven steps during the isochoric vitrification process. We observed significant changes in microbiome composition, including: 1) the natural wild microbiomes of P. compressa were dominated by Endozoicomonadaceae (76.5% relative abundance) and consistent between samples, independent of collection location across Kāne'ohe Bay; 2) Endozoicomonadaceae were reduced to <6.9% in captivity, and further reduced to <0.5% relative abundance after isochoric vitrification; and 3) Vibrionaceae dominated communities post-thaw (58.5 to 74.7% abundance). Thus, the capture and cryopreservation processes, are implicated as possible causal agents of dysbiosis characterized by the loss of putatively beneficial symbionts (Endozoicomonadaceae) and overgrowth of potential pathogens (Vibrionaceae). Offsetting these changes with probiotic restoration treatments may alleviate cryopreservation stress and improve post-thaw husbandry.},
}

@article {pmid39184395,
year = {2024},
author = {Gastaldi, M and Pankey, MS and Svendsen, G and Medina, A and Firstater, F and Narvarte, M and Lozada, M and Lesser, M},
title = {Holobiont dysbiosis or acclimatation? Shift in the microbial taxonomic diversity and functional composition of a cosmopolitan sponge subjected to chronic pollution in a Patagonian bay.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17707},
doi = {10.7717/peerj.17707},
pmid = {39184395},
issn = {2167-8359},
mesh = {Animals ; *Porifera/microbiology ; *Microbiota ; Argentina ; *Dysbiosis/microbiology ; Acclimatization ; Bays/microbiology ; Water Pollutants, Chemical/adverse effects/analysis ; },
abstract = {Dysbiosis and acclimatization are two starkly opposing outcomes of altered holobiont associations in response to environmental pollution. This study assesses whether shifts in microbial taxonomic composition and functional profiles of the cosmopolitan sponge Hymeniacidon perlevis indicate dysbiotic or acclimatized responses to water pollution. To do so, sponge and water samples were collected in a semi-enclosed environment (San Antonio Bay, Patagonia, Argentina) from variably polluted sites (i.e., eutrophication, heavy metal contamination). We found significant differences in the microbiome of H. perlevis with respect to the pollution history of the sites. Several indicators suggested that acclimatization, rather than dysbiosis, explained the microbiome response to higher pollution: 1) the distinction of the sponge microbiome from the water microbiome; 2) low similarity between the sponge and water microbiomes at the most polluted site; 3) the change in microbiome composition between sponges from the different sites; 4) a high similarity in the microbiome among sponge individuals within sites; 5) a similar ratio of common sponge microbes to opportunistic microbes between sponges at the most and least polluted sites; and 6) a distinctive functional profile of the sponge microbiome at the most polluted site. This profile indicated a more expansive metabolic repertoire, including the degradation of pollutants and the biosynthesis of secondary metabolites, suggesting a relevant role of these microbial communities in the adaptation of the holobiont to organic pollution. Our results shed light on the rearrangement of the H. perlevis microbiome that could allow it to successfully colonize sites with high anthropogenic impact while resisting dysbiosis.},
}

Animals
*Porifera/microbiology
*Microbiota
Argentina
*Dysbiosis/microbiology
Acclimatization
Bays/microbiology
Water Pollutants, Chemical/adverse effects/analysis

@article {pmid38922379,
year = {2024},
author = {Mikó, E and Sipos, A and Tóth, E and Lehoczki, A and Fekete, M and Sebő, É and Kardos, G and Bai, P},
title = {Guideline for designing microbiome studies in neoplastic diseases.},
journal = {GeroScience},
volume = {46},
number = {5},
pages = {4037-4057},
pmid = {38922379},
issn = {2509-2723},
support = {K142141//NKFIH/ ; FK128387//NKFIH/ ; FK146852//NKFIH/ ; TKP2021-EGA-20//NKFIH/ ; TKP2021-EGA-19//NFKIH/ ; POST-COVID2021-33//Magyar Tudományos Akadémia/ ; NKM2022-30//Magyar Tudományos Akadémia/ ; },
mesh = {Humans ; *Neoplasms/microbiology ; *Microbiota ; Research Design ; },
abstract = {Oncobiosis has emerged as a key contributor to the development, and modulator of the treatment efficacy of cancer. Hereby, we review the modalities through which the oncobiome can support the progression of tumors, and the emerging therapeutic opportunities they present. The review highlights the inherent challenges and limitations faced in sampling and accurately characterizing oncobiome. Additionally, the review underscores the critical need for the standardization of microbial analysis techniques and the consistent reporting of microbiome data. We provide a suggested metadata set that should accompany microbiome datasets from oncological settings so that studies remain comparable and decipherable.},
}

Humans
*Neoplasms/microbiology
*Microbiota
Research Design

@article {pmid39165397,
year = {2024},
author = {Jacob, M and Thomas, PK and Giebel, HA and Billerbeck, S and Simon, M and Striebel, M and Dlugosch, L},
title = {Cross-domain diversity effects: linking diatom species richness, intraspecific richness, and biomass production to host-associated bacterial diversity.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae046},
pmid = {39165397},
issn = {2730-6151},
abstract = {Interactions between bacteria and microalgae are important for the functioning of aquatic ecosystems, yet interactions based on the biodiversity of these two taxonomic domains have been scarcely studied. Specifically, it is unclear whether a positive biodiversity-productivity relationship in phytoplankton is largely facilitated by niche partitioning among the phytoplankton organisms themselves or whether associated bacterial communities play an additional role in modifying these diversity effects. Moreover, the effects of intraspecific diversity in phytoplankton communities on bacterial community diversity have not been tested. To address these points, we factorially manipulated both species and intraspecific richness of three diatoms to test the effects of diatom species/strain diversity on biomass production and bacterial diversity in algae-bacteria communities. The results show that diatom intraspecific diversity has significant positive effects on culture biomass and the diversity of the associated free-living bacterial community (0.2-3 μm size fraction), which are comparable in magnitude to species diversity effects. However, there were little to no effects of diatom diversity on host-associated bacterial diversity (>3 μm size fraction), or of bacterial diversity on biomass production. These results suggest a decoupling of bacterial diversity from the diatom diversity-productivity relationship and provide early insights regarding the relations between diversity across domains in aquatic ecosystems.},
}

@article {pmid39164135,
year = {2024},
author = {Cook, LSJ and Briscoe, AG and Fonseca, VG and Boenigk, J and Woodward, G and Bass, D},
title = {Microbial, holobiont, and Tree of Life eDNA/eRNA for enhanced ecological assessment.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2024.07.003},
pmid = {39164135},
issn = {1878-4380},
abstract = {Microbial environmental DNA and RNA (collectively 'eNA') originate from a diverse and abundant array of microbes present in environmental samples. These eNA signals, largely representing whole organisms, serve as a powerful complement to signals derived from fragments or remnants of larger organisms. Integrating microbial data into the toolbox of ecosystem assessments and biotic indices therefore has the potential to transform how we use eNA data to understand biodiversity dynamics and ecosystem functions, and to inform the next generation of environmental monitoring. Incorporating holobiont and Tree of Life approaches into eNA analyses offers further holistic insight into the range of ecological interactions between microbes and other organisms, paving the way for advancing our understanding of, and ultimately manipulating ecosystem properties pertinent to environmental management, conservation, wildlife health, and food production.},
}

@article {pmid39163656,
year = {2024},
author = {Sun, F and Yang, H and Zhang, X and Tan, F and Wang, G and Shi, Q},
title = {Significant response of coral-associated bacteria and their carbohydrate-active enzymes diversity to coral bleaching.},
journal = {Marine environmental research},
volume = {201},
number = {},
pages = {106694},
doi = {10.1016/j.marenvres.2024.106694},
pmid = {39163656},
issn = {1879-0291},
abstract = {Analysis of bacterial carbohydrate-active enzymes (CAZymes) contributes significantly to comprehending the response exhibited by coral symbionts to the external environment. This study explored the impact of bleaching on the bacteria and their CAZymes in coral Favites sp. through metagenomic sequencing. Notably, principal coordinates analysis (PCoA) unveiles substantial difference in bacterial communities between bleached and unbleached corals. Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidota, and Chloroflexi, exhibit noteworthy alterations during coral bleaching. CAZymes profiles in bleached coral disclosed a significant increase in Glycosyltransferases (GTs) abundance, suggesting an intensified biosynthesis of polysaccharides. Conversely, there is a marked reduction in other CAZymes abundance in bleached coral. Proteobacteria, Bacteroidota, Chlorobi, and Planctomycetota exhibit greater contributions to CAZymes in bleached corals, with Rhodobacterales, Cytophagales, Burkholderiales, Caulobacterales, and Hyphomicrobiales being the main contributors. While Acidobacteria, Actinobacteria, and Chloroflexi demonstrate higher contributions to CAZymes in unbleached corals. The changes in bacteria and their CAZymes reflect the ecological adaptability of coral holobionts when facing environmental stress. The alterations in CAZymes composition caused by bleaching events may have profound impacts on coral nutrient absorption and ecosystem stability. Therefore, understanding the dynamic changes in CAZymes is crucial for assessing the health and recovery potential of coral ecosystems.},
}

@article {pmid39151124,
year = {2024},
author = {Katirtzoglou, A and Hansen, SB and Sveier, H and Martin, MD and Brealey, JC and Limborg, MT},
title = {Genomic context determines the effect of DNA methylation on gene expression in the gut epithelium of Atlantic salmon (Salmo salar).},
journal = {Epigenetics},
volume = {19},
number = {1},
pages = {2392049},
doi = {10.1080/15592294.2024.2392049},
pmid = {39151124},
issn = {1559-2308},
mesh = {Animals ; *DNA Methylation ; *Salmo salar/genetics/metabolism ; *Epigenesis, Genetic ; Intestinal Mucosa/metabolism ; Transcription Initiation Site ; },
abstract = {The canonical view of DNA methylation, a pivotal epigenetic regulation mechanism in eukaryotes, dictates its role as a suppressor of gene activity, particularly within promoter regions. However, this view is being challenged as it is becoming increasingly evident that the connection between DNA methylation and gene expression varies depending on the genomic location and is therefore more complex than initially thought. We examined DNA methylation levels in the gut epithelium of Atlantic salmon (Salmo salar) using whole-genome bisulfite sequencing, which we correlated with gene expression data from RNA sequencing of the same gut tissue sample (RNA-seq). Assuming epigenetic signals might be pronounced between distinctive phenotypes, we compared large and small fish, finding 22 significant associations between 22 differentially methylated regions and 21 genes. We did not detect significant methylation differences between large and small fish. However, we observed a consistent signal of methylation levels around the transcription start sites (TSS), being negatively correlated with the expression levels of those genes. We found both negative and positive associations of methylation levels with gene expression further upstream or downstream of the TSS, revealing a more unpredictable pattern. The 21 genes showing significant methylation-expression correlations were involved in biological processes related to salmon health, such as growth and immune responses. Deciphering how DNA methylation affects the expression of such genes holds great potential for future applications. For instance, our results suggest the importance of genomic context in targeting epigenetic modifications to improve the welfare of aquaculture species like Atlantic salmon.},
}

Animals
*DNA Methylation
*Salmo salar/genetics/metabolism
*Epigenesis, Genetic
Intestinal Mucosa/metabolism
Transcription Initiation Site

@article {pmid39148013,
year = {2024},
author = {Hoenicka, H and Bein, S and Starczak, M and Graf, W and Hanelt, D and Gackowski, D},
title = {β-Aminobutyric acid promotes stress tolerance, physiological adjustments, as well as broad epigenetic changes at DNA and RNA nucleobases in field elms (Ulmus minor).},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {779},
pmid = {39148013},
issn = {1471-2229},
mesh = {*Epigenesis, Genetic ; *RNA, Plant/genetics ; Stress, Physiological/genetics ; Aminobutyrates/pharmacology ; DNA, Plant/genetics ; },
abstract = {BACKGROUND: β-Aminobutyric acid (BABA) has been successfully used to prime stress resistance in numerous plant species; however, its effectiveness in forest trees has been poorly explored thus far. This study aimed to investigate the influence of BABA on morphological, physiological, and epigenetic parameters in field elms under various growth conditions. Epigenetic changes were assessed in both DNA and RNA through the use of reversed-phase ultra-performance liquid chromatography (UPLC) coupled with sensitive mass spectrometry.

RESULTS: The presented results confirm the influence of BABA on the development, physiology, and stress tolerance in field elms. However, the most important findings are related to the broad epigenetic changes promoted by this amino acid, which involve both DNA and RNA. Our findings confirm, for the first time, that BABA influences not only well-known epigenetic markers in plants, such as 5-methylcytosine, but also several other non-canonical nucleobases, such as 5-hydroxymethyluracil, 5-formylcytosine, 5-hydroxymethylcytosine, N6-methyladenine, uracil (in DNA) and thymine (in RNA). The significant effect on the levels of N6-methyladenine, the main bacterial epigenetic marker, is particularly noteworthy. In this case, the question arises as to whether this effect is due to epigenetic changes in the microbiome, the plant genome, or both.

CONCLUSIONS: The plant phenotype is the result of complex interactions between the plant's DNA, the microbiome, and the environment. We propose that different types of epigenetic changes in the plant and microbiome may play important roles in the largely unknown memory process that enables plants to adapt faster to changing environmental conditions.},
}

*Epigenesis, Genetic
*RNA, Plant/genetics
Stress, Physiological/genetics
Aminobutyrates/pharmacology
DNA, Plant/genetics

@article {pmid39137959,
year = {2024},
author = {Saha, M and Dittami, SM and Chan, CX and Raina, JB and Stock, W and Ghaderiardakani, F and Valathuparambil Baby John, AM and Corr, S and Schleyer, G and Todd, J and Cardini, U and Bengtsson, MM and Prado, S and Skillings, D and Sonnenschein, EC and Engelen, AH and Wang, G and Wichard, T and Brodie, J and Leblanc, C and Egan, S},
title = {Progress and future directions for seaweed holobiont research.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.20018},
pmid = {39137959},
issn = {1469-8137},
support = {LT0028/2022-L//Human Frontier Science Programme/ ; ALTF 192-2021//European Molecular Biology Organization (EMBO) Postdoctoral Fellowship/ ; },
abstract = {In the marine environment, seaweeds (i.e. marine macroalgae) provide a wide range of ecological services and economic benefits. Like land plants, seaweeds do not provide these services in isolation, rather they rely on their associated microbial communities, which together with the host form the seaweed holobiont. However, there is a poor understanding of the mechanisms shaping these complex seaweed-microbe interactions, and of the evolutionary processes underlying these interactions. Here, we identify the current research challenges and opportunities in the field of seaweed holobiont biology. We argue that identifying the key microbial partners, knowing how they are recruited, and understanding their specific function and their relevance across all seaweed life history stages are among the knowledge gaps that are particularly important to address, especially in the context of the environmental challenges threatening seaweeds. We further discuss future approaches to study seaweed holobionts, and how we can apply the holobiont concept to natural or engineered seaweed ecosystems.},
}

@article {pmid39128929,
year = {2024},
author = {Nahor, O and Israel, Á and Barger, N and Rubin-Blum, M and Luzzatto-Knaan, T},
title = {Epiphytic microbiome associated with intertidal seaweeds in the Mediterranean Sea: comparative analysis of bacterial communities across seaweed phyla.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {18631},
pmid = {39128929},
issn = {2045-2322},
mesh = {Mediterranean Sea ; *Seaweed/microbiology/genetics ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification ; *RNA, Ribosomal, 16S/genetics ; Phylogeny ; Ecosystem ; },
abstract = {The complex interactions between epiphytic bacteria and marine macroalgae are still poorly understood, with limited knowledge about their community structure, interactions, and functions. This study focuses on comparing epiphytic prokaryotes community structure between three seaweed phyla; Chlorophyta, Rhodophyta, and Heterokontophyta in an easternmost rocky intertidal site of the Mediterranean Sea. By taking a snapshot approach and simultaneously collecting seaweed samples from the same habitat, we minimize environmental variations that could affect epiphytic bacterial assembly, thereby emphasizing host specificity. Through 16S rRNA gene amplicon sequencing, we identified that the microbial community composition was more similar within the same seaweed phylum host compared to seaweed host from other phyla. Furthermore, exclusive Amplicon Sequence Variants (ASVs) were identified for each algal phyla despite sharing higher taxonomic classifications across the other phyla. Analysis of niche breadth indices uncovers distinctive affinities and potential specialization among seaweed host phyla, with 39% of all ASVs identified as phylum specialists and 13% as generalists. Using taxonomy function prediction, we observed that the taxonomic variability does not significantly impact functional redundancy, suggesting resilience to disturbance. The study concludes that epiphytic bacteria composition is connected to host taxonomy, possibly influenced by shared morphological and chemical traits among genetically related hosts, implying a potential coevolutionary relationship between specific bacteria and their host seaweeds.},
}

Mediterranean Sea
*Seaweed/microbiology/genetics
*Microbiota/genetics
*Bacteria/genetics/classification/isolation & purification
*RNA, Ribosomal, 16S/genetics
Phylogeny
Ecosystem

@article {pmid39120056,
year = {2024},
author = {Di Gesù, CM and Buffington, SA},
title = {The early life exposome and autism risk: a role for the maternal microbiome?.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2385117},
doi = {10.1080/19490976.2024.2385117},
pmid = {39120056},
issn = {1949-0984},
mesh = {Humans ; *Autism Spectrum Disorder/microbiology/etiology ; Female ; Pregnancy ; Exposome ; Gastrointestinal Microbiome ; Risk Factors ; Genetic Predisposition to Disease ; Animals ; Autistic Disorder/etiology/microbiology ; },
abstract = {Autism spectrum disorders (ASD) are highly heritable, heterogeneous neurodevelopmental disorders characterized by clinical presentation of atypical social, communicative, and repetitive behaviors. Over the past 25 years, hundreds of ASD risk genes have been identified. Many converge on key molecular pathways, from translational control to those regulating synaptic structure and function. Despite these advances, therapeutic approaches remain elusive. Emerging data unearthing the relationship between genetics, microbes, and immunity in ASD suggest an integrative physiology approach could be paramount to delivering therapeutic breakthroughs. Indeed, the advent of large-scale multi-OMIC data acquisition, analysis, and interpretation is yielding an increasingly mechanistic understanding of ASD and underlying risk factors, revealing how genetic susceptibility interacts with microbial genetics, metabolism, epigenetic (re)programming, and immunity to influence neurodevelopment and behavioral outcomes. It is now possible to foresee exciting advancements in the treatment of some forms of ASD that could markedly improve quality of life and productivity for autistic individuals. Here, we highlight recent work revealing how gene X maternal exposome interactions influence risk for ASD, with emphasis on the intrauterine environment and fetal neurodevelopment, host-microbe interactions, and the evolving therapeutic landscape for ASD.},
}

Humans
*Autism Spectrum Disorder/microbiology/etiology
Female
Pregnancy
Exposome
Gastrointestinal Microbiome
Risk Factors
Genetic Predisposition to Disease
Animals
Autistic Disorder/etiology/microbiology

@article {pmid39119491,
year = {2024},
author = {Passera, A and Escudero-Martinez, C},
title = {Editorial: Genome and metagenome interactions in the plant holobiont for plant health and productivity.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1463795},
doi = {10.3389/fpls.2024.1463795},
pmid = {39119491},
issn = {1664-462X},
}

@article {pmid39119209,
year = {2024},
author = {Clokie, MRJ and Sicheritz-Pontén, T},
title = {Editorial June 2024.},
journal = {PHAGE (New Rochelle, N.Y.)},
volume = {5},
number = {2},
pages = {43},
doi = {10.1089/phage.2024.0020},
pmid = {39119209},
issn = {2641-6549},
}

@article {pmid39110680,
year = {2024},
author = {Krishnakant Kushwaha, S and Wu, Y and Leonardo Avila, H and Anand, A and Sicheritz-Pontén, T and Millard, A and Amol Marathe, S and Nobrega, FL},
title = {Comprehensive blueprint of Salmonella genomic plasticity identifies hotspots for pathogenicity genes.},
journal = {PLoS biology},
volume = {22},
number = {8},
pages = {e3002746},
doi = {10.1371/journal.pbio.3002746},
pmid = {39110680},
issn = {1545-7885},
mesh = {*Salmonella/genetics/pathogenicity ; *Genome, Bacterial/genetics ; Virulence/genetics ; Humans ; Genomics/methods ; Multigene Family ; Phylogeny ; Plasmids/genetics ; Salmonella Infections/microbiology ; Prophages/genetics ; Evolution, Molecular ; },
abstract = {Understanding the dynamic evolution of Salmonella is vital for effective bacterial infection management. This study explores the role of the flexible genome, organised in regions of genomic plasticity (RGP), in shaping the pathogenicity of Salmonella lineages. Through comprehensive genomic analysis of 12,244 Salmonella spp. genomes covering 2 species, 6 subspecies, and 46 serovars, we uncover distinct integration patterns of pathogenicity-related gene clusters into RGP, challenging traditional views of gene distribution. These RGP exhibit distinct preferences for specific genomic spots, and the presence or absence of such spots across Salmonella lineages profoundly shapes strain pathogenicity. RGP preferences are guided by conserved flanking genes surrounding integration spots, implicating their involvement in regulatory networks and functional synergies with integrated gene clusters. Additionally, we emphasise the multifaceted contributions of plasmids and prophages to the pathogenicity of diverse Salmonella lineages. Overall, this study provides a comprehensive blueprint of the pathogenicity potential of Salmonella. This unique insight identifies genomic spots in nonpathogenic lineages that hold the potential for harbouring pathogenicity genes, providing a foundation for predicting future adaptations and developing targeted strategies against emerging human pathogenic strains.},
}

*Salmonella/genetics/pathogenicity
*Genome, Bacterial/genetics
Virulence/genetics
Humans
Genomics/methods
Multigene Family
Phylogeny
Plasmids/genetics
Salmonella Infections/microbiology
Prophages/genetics
Evolution, Molecular

@article {pmid39107841,
year = {2024},
author = {Murphy, RM and Sinotte, VM and Cuesta-Maté, A and Renelies-Hamilton, J and Lenz-Strube, M and Poulsen, M},
title = {Shaping the tripartite symbiosis: are termite microbiome functions directed by the environmentally acquired fungal cultivar?.},
journal = {Animal microbiome},
volume = {6},
number = {1},
pages = {44},
pmid = {39107841},
issn = {2524-4671},
abstract = {Microbiome assembly critically impacts the ability of hosts to access beneficial symbiont functions. Fungus-farming termites have co-evolved with a fungal cultivar as a primary food source and complex gut microbiomes, which collectively perform complementary degradation of plant biomass. A large subset of the bacterial community residing within termite guts are inherited (vertically transmitted) from parental colonies, while the fungal symbiont is, in most termite species, acquired from the environment (horizontally transmitted). It has remained unknown how the gut microbiota sustains incipient colonies prior to the acquisition of the fungal cultivar, and how, if at all, bacterial contributions are modulated by fungus garden establishment. Here, we test the latter by determining the composition and predicted functions of the gut microbiome using metabarcoding and shotgun metagenomics, respectively. We focus our functional predictions on bacterial carbohydrate-active enzyme and nitrogen cycling genes and verify compositional patterns of the former through enzyme activity assays. Our findings reveal that the vast majority of microbial functions are encoded in the inherited microbiome, and that the establishment of fungal gardens incurs only minor modulations of predicted bacterial capacities for carbohydrate and nitrogen metabolism. While we cannot rule out that other symbiont functions are gained post-fungus garden establishment, our findings suggest that fungus-farming termite hosts are equipped with a near-complete set of gut microbiome functions at the earliest stages of colony life. This inherited, incipient bacterial microbiome likely contributes to the high extent of functional specificity and coevolution observed between termite hosts, gut microbiomes, and the fungal cultivar.},
}

@article {pmid39095694,
year = {2024},
author = {He, X and Zou, J and Chen, Q and Qin, X and Liu, Y and Zeng, L and Su, H},
title = {Microbial and transcriptional response of Acropora valida and Turbinaria peltata to Vibrio coralliilyticus challenge: insights into corals disease resistance.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {288},
pmid = {39095694},
issn = {1471-2180},
mesh = {*Anthozoa/microbiology/genetics/immunology ; Animals ; *Vibrio/genetics ; *Disease Resistance/genetics ; Symbiosis/genetics ; Microbiota/genetics ; Coral Reefs ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: Coral diseases are significant drivers of global coral reef degradation, with pathogens dominated by Vibrio coralliilyticus playing a prominent role in the development of coral diseases. Coral phenotype, symbiotic microbial communities, and host transcriptional regulation have been well-established as factors involved in determining coral disease resistance, but the underlying mechanisms remain incompletely understood.

METHODS: This study employs high-throughput sequencing to analyse the symbiotic microbial and transcriptional response of the hosts in order to evaluate the disease resistance of Acropora valida and Turbinaria peltata exposed to Vibrio coralliilyticus.

RESULTS: A. valida exhibited pronounced bleaching and tissue loss within 7 h of pathogen infection, whereas T. peltata showed no signs of disease throughout the experiment. Microbial diversity analyses revealed that T. peltata had a more flexible microbial community and a higher relative abundance of potential beneficial bacteria compared to A. valida. Although Vibrio inoculation resulted in a more significant decrease in the Symbiodiniaceae density of A. valida compared to that of T. peltata, it did not lead to recombination of the coral host and Symbiodiniaceae in either coral species. RNA-seq analysis revealed that the interspecific differences in the transcriptional regulation of hosts after Vibrio inoculation. Differentially expressed genes in A. valida were mainly enriched in the pathways associated with energy supply and immune response, such as G protein-coupled receptor signaling, toll-like receptor signaling, regulation of TOR signaling, while these genes in T. peltata were mainly involved in the pathway related to immune homeostasis and ion transport, such as JAK-STAT signaling pathway and regulation of ion transport.

CONCLUSIONS: Pathogenic challenges elicit different microbial and transcriptional shifts across coral species. This study offers novel insights into molecular mechanisms of coral resistance to disease.},
}

*Anthozoa/microbiology/genetics/immunology
Animals
*Vibrio/genetics
*Disease Resistance/genetics
Symbiosis/genetics
Microbiota/genetics
Coral Reefs
High-Throughput Nucleotide Sequencing

@article {pmid39089083,
year = {2024},
author = {Duret, M and Wallner, A and Buée, M and Aziz, A},
title = {Rhizosphere microbiome assembly, drivers and functions in perennial ligneous plant health.},
journal = {Microbiological research},
volume = {287},
number = {},
pages = {127860},
doi = {10.1016/j.micres.2024.127860},
pmid = {39089083},
issn = {1618-0623},
abstract = {Plants shape and interact continuously with their rhizospheric microbiota, which play a key role in plant health and resilience. However, plant-associated microbial community can be shaped by several factors including plant phenotype and cropping system. Thus, understanding the interplay between microbiome assembly during the onset of plant-pathogen interactions and long-lasting resistance traits in ligneous plants remains a major challenge. To date, such attempts were mainly investigated in herbaceous plants, due to their phenotypic characteristics and their short life cycle. However, only few studies have focused on the microbial structure, dynamic and their drivers in perennial ligneous plants. Ligneous plants coevolved in interaction with specific fungal and bacterial communities that differ from those of annual plants. The specificities of such ligneous plants in shaping their own functional microbial communities could be dependent on their high heterozygosis, physiological and molecular status associated to seasonality and their aging processes, root system and above-ground architectures, long-lasting climatic variations, and specific cultural practices. This article provides an overview of the specific characteristics of perennial ligneous plants that are likely to modulate symbiotic interactions in the rhizosphere, thus affecting the plant's fitness and systemic immunity. Plant and microbial traits contributing to the establishment of plant-microbiome interactions and the adaptation of this holobiont are also discussed.},
}

@article {pmid39090391,
year = {2024},
author = {Sun, PF and Lu, MR and Liu, YC and Shaw, BJP and Lin, CP and Chen, HW and Lin, YF and Hoh, DZ and Ke, HM and Wang, IF and Lu, MJ and Young, EB and Millett, J and Kirschner, R and Lin, YJ and Chen, YL and Tsai, IJ},
title = {An acidophilic fungus promotes prey digestion in a carnivorous plant.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {39090391},
issn = {2058-5276},
abstract = {Leaves of the carnivorous sundew plants (Drosera spp.) secrete mucilage that hosts microorganisms, but whether this microbiota contributes to prey digestion is unclear. We identified the acidophilic fungus Acrodontium crateriforme as the dominant species in the mucilage microbial communities, thriving in multiple sundew species across the global range. The fungus grows and sporulates on sundew glands as its preferred acidic environment, and its presence in traps increased the prey digestion process. A. crateriforme has a reduced genome similar to other symbiotic fungi. During A. crateriforme-Drosera spatulata coexistence and digestion of prey insects, transcriptomes revealed significant gene co-option in both partners. Holobiont expression patterns during prey digestion further revealed synergistic effects in several gene families including fungal aspartic and sedolisin peptidases, facilitating prey digestion in leaves, as well as nutrient assimilation and jasmonate signalling pathway expression. This study establishes that botanical carnivory is defined by adaptations involving microbial partners and interspecies interactions.},
}

@article {pmid39076113,
year = {2024},
author = {Ruggeri, M and Million, WC and Hamilton, L and Kenkel, CD},
title = {Microhabitat acclimatization alters sea anemone-algal symbiosis and thermal tolerance across the intertidal zone.},
journal = {Ecology},
volume = {},
number = {},
pages = {e4388},
doi = {10.1002/ecy.4388},
pmid = {39076113},
issn = {1939-9170},
support = {//USC Wrigley Institute for Environmental Studies/ ; //Wrigley Bakus Fellowship/ ; //Wrigley Summer Fellowship/ ; //Victoria J. Bertics Fellowship/ ; },
abstract = {Contemporary symbioses in extreme environments can give an insight into mechanisms that stabilize species interactions during environmental change. The intertidal sea anemone, Anthopleura elegantissima, engages in a nutritional symbiosis with microalgae similar to tropical coral, but withstands more intense environmental fluctuations during tidal inundations. In this study, we compare baseline symbiotic traits and their sensitivity to thermal stress within and among anemone aggregations across the intertidal using a laboratory-based tank experiment to better understand how fixed genotypic and plastic environmental effects contribute to the successful maintenance of this symbiosis in extreme habitats. High intertidal anemones had lower baseline symbiont-to-host cell ratios under control conditions, but their symbionts had higher baseline photosynthetic efficiency compared to low intertidal anemone symbionts. Symbiont communities were identical across all samples, suggesting that shifts in symbiont density and photosynthetic performance could be an acclimatory mechanism to maintain symbiosis in different environments. Despite lower baseline symbiont-to-host cell ratios, high intertidal anemones maintained greater symbiont-to-host cell ratios under heat stress compared with low intertidal anemones, suggesting greater thermal tolerance of high intertidal holobionts. However, the thermal tolerance of clonal anemones acclimatized to different zones was not explained by tidal height alone, indicating additional environmental variables contribute to physiological differences. Host genotype significantly influenced anemone weight, but only explained a minor proportion of variation among symbiotic traits and their response to thermal stress, further implicating environmental history as the primary driver of holobiont tolerance. These results indicate that this symbiosis is highly plastic and may be able to acclimatize to climate change over ecological timescales, defying the convention that symbiotic organisms are more susceptible to environmental stress.},
}

@article {pmid39072987,
year = {2024},
author = {Yan, G and Wei, T and Lan, Y and Xu, T and Qian, P},
title = {Different parts of the mussel Gigantidas haimaensis holobiont responded differently to deep-sea sampling stress.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.12881},
pmid = {39072987},
issn = {1749-4877},
support = {2019B030302004//Major Project of Basic and Applied Basic Research of Guangdong Province/ ; 2021HJ01//PI project of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; SMSEGL24SC01//Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; 16101822//HKSAR government/ ; C2013-22G//HKSAR government/ ; },
abstract = {Acute environmental changes cause stress during conventional deep-sea biological sampling without in situ fixation and affect gene expressions of samples collected. However, the degree of influence and underlying mechanisms are hardly investigated. Here, we conducted comparative transcriptomic analyses between in situ and onboard fixed gills and between in situ and onboard fixed mantles of deep-sea mussel Gigantidas haimaensis to assess the effects of incidental sampling stress. Results showed that transcription, translation, and energy metabolism were upregulated in onboard fixed gills and mantles, thereby mobilizing rapid gene expression to tackle the stress. Autophagy and phagocytosis that related to symbiotic interactions between the host and endosymbiont were downregulated in the onboard fixed gills. These findings demonstrated that symbiotic gill and nonsymbiotic mantle responded differently to sampling stress, and symbiosis in the gill was perturbed. Further comparative metatranscriptomic analysis between in situ and onboard fixed gills revealed that stress response genes, peptidoglycan biosynthesis, and methane fixation were upregulated in the onboard fixed endosymbiotic Gammaproteobacteria inside the gills, implying that energy metabolism of the endosymbiont was increased to cope with sampling stress. Furthermore, comparative analysis between the mussel G. haimaensis and the limpet Bathyacmaea lactea transcriptomes resultedidentified six transcription factor orthologs upregulated in both onboard fixed mussel mantles and limpets, including sharply increased early growth response protein 1 and Kruppel-like factor 5. They potentially play key roles in initiating the response of sampled deep-sea macrobenthos to sampling stress. Our results clearly show that in situ fixed biological samples are vital for studying deep-sea environmental adaptation.},
}

@article {pmid39071805,
year = {2024},
author = {Gilbert, SF},
title = {Inter-kingdom communication and the sympoietic way of life.},
journal = {Frontiers in cell and developmental biology},
volume = {12},
number = {},
pages = {1427798},
pmid = {39071805},
issn = {2296-634X},
abstract = {Organisms are now seen as holobionts, consortia of several species that interact metabolically such that they sustain and scaffold each other's existence and propagation. Sympoiesis, the development of the symbiotic relationships that form holobionts, is critical for our understanding the origins and maintenance of biodiversity. Rather than being the read-out of a single genome, development has been found to be sympoietic, based on multigenomic interactions between zygote-derived cells and symbiotic microbes. These symbiotic and sympoietic interactions are predicated on the ability of cells from different kingdoms of life (e.g., bacteria and animals) to communicate with one another and to have their chemical signals interpreted in a manner that facilitates development. Sympoiesis, the creation of an entity by the interactions of other entities, is commonly seen in embryogenesis (e.g., the creation of lenses and retinas through the interaction of brain and epidermal compartments). In holobiont sympoiesis, interactions between partners of different domains of life interact to form organs and biofilms, wherein each of these domains acts as the environment for the other. If evolution is forged by changes in development, and if symbionts are routinely involved in our development, then changes in sympoiesis can constitute an important factor in evolution.},
}

@article {pmid39066224,
year = {2024},
author = {Caetano-Anollés, G},
title = {Are Viruses Taxonomic Units? A Protein Domain and Loop-Centric Phylogenomic Assessment.},
journal = {Viruses},
volume = {16},
number = {7},
pages = {},
doi = {10.3390/v16071061},
pmid = {39066224},
issn = {1999-4915},
support = {ILLU-802-909 and ILLU-483-625//National Institute of Food and Agriculture/ ; Illinois Campus Cluster Program (ICCP), and Blue Waters supercomputing allocations//National Center for Supercomputing Applications/ ; },
abstract = {Virus taxonomy uses a Linnaean-like subsumption hierarchy to classify viruses into taxonomic units at species and higher rank levels. Virus species are considered monophyletic groups of mobile genetic elements (MGEs) often delimited by the phylogenetic analysis of aligned genomic or metagenomic sequences. Taxonomic units are assumed to be independent organizational, functional and evolutionary units that follow a 'natural history' rationale. Here, I use phylogenomic and other arguments to show that viruses are not self-standing genetically-driven systems acting as evolutionary units. Instead, they are crucial components of holobionts, which are units of biological organization that dynamically integrate the genetics, epigenetic, physiological and functional properties of their co-evolving members. Remarkably, phylogenomic analyses show that viruses share protein domains and loops with cells throughout history via massive processes of reticulate evolution, helping spread evolutionary innovations across a wider taxonomic spectrum. Thus, viruses are not merely MGEs or microbes. Instead, their genomes and proteomes conduct cellularly integrated processes akin to those cataloged by the GO Consortium. This prompts the generation of compositional hierarchies that replace the 'is-a-kind-of' by a 'is-a-part-of' logic to better describe the mereology of integrated cellular and viral makeup. My analysis demands a new paradigm that integrates virus taxonomy into a modern evolutionarily centered taxonomy of organisms.},
}

@article {pmid39047050,
year = {2024},
author = {Marzinelli, EM and Thomas, T and Vadillo Gonzalez, S and Egan, S and Steinberg, PD},
title = {Seaweeds as holobionts: Current state, challenges, and potential applications.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.13485},
pmid = {39047050},
issn = {1529-8817},
abstract = {Seaweeds play a strong ecological and economical role along the world's coastlines, where they support industries (e.g., aquaculture, bioproducts) and essential ecosystem services (e.g., biodiversity, fisheries, carbon capture). Evidence from wild and cultured seaweeds suggests that microorganisms play crucial roles in their health and functioning, prompting the need for considering seaweeds and their microbiome as a coherent entity or "holobiont." Here we show that the number of studies investigating seaweed hosts and their microbiome have increased in the last two decades. This likely reflects the increase in the appreciation of the importance of microbiomes for eukaryotic hosts, improved molecular approaches used to characterize their interactions, and increasing interest in commercial use of seaweeds. However, although increasing, most studies of seaweed holobionts have focused on (i) a few seaweed species of ecological or commercial significance, (ii) interactions involving only bacteria, and (iii) descriptive rather than experimental approaches. The relatively few experimental studies have mostly focused on manipulating abiotic factors to examine responses of seaweeds and their microbiome. Of the few studies that directly manipulated microorganisms to investigate their effects on seaweeds, most were done in laboratory or aquaria. We emphasize the need to move beyond the descriptions of patterns to experimental approaches for understanding causation and mechanisms. We argue that such experimental approaches are necessary for a better understanding of seaweed holobionts, for management actions for wild and cultivated seaweeds, and to better integrate studies of seaweed holobionts with the broader fields of seaweed ecology and biology, which are strongly experimental.},
}

@article {pmid39026872,
year = {2024},
author = {Ostridge, HJ and Fontsere, C and Lizano, E and Soto, DC and Schmidt, JM and Saxena, V and Alvarez-Estape, M and Barratt, CD and Gratton, P and Bocksberger, G and Lester, JD and Dieguez, P and Agbor, A and Angedakin, S and Assumang, AK and Bailey, E and Barubiyo, D and Bessone, M and Brazzola, G and Chancellor, R and Cohen, H and Coupland, C and Danquah, E and Deschner, T and Dotras, L and Dupain, J and Egbe, VE and Granjon, AC and Head, J and Hedwig, D and Hermans, V and Hernandez-Aguilar, RA and Jeffery, KJ and Jones, S and Junker, J and Kadam, P and Kaiser, M and Kalan, AK and Kambere, M and Kienast, I and Kujirakwinja, D and Langergraber, KE and Lapuente, J and Larson, B and Laudisoit, A and Lee, KC and Llana, M and Maretti, G and Martín, R and Meier, A and Morgan, D and Neil, E and Nicholl, S and Nixon, S and Normand, E and Orbell, C and Ormsby, LJ and Orume, R and Pacheco, L and Preece, J and Regnaut, S and Robbins, MM and Rundus, A and Sanz, C and Sciaky, L and Sommer, V and Stewart, FA and Tagg, N and Tédonzong, LR and van Schijndel, J and Vendras, E and Wessling, EG and Willie, J and Wittig, RM and Yuh, YG and Yurkiw, K and Vigilant, L and Piel, A and Boesch, C and Kühl, HS and Dennis, MY and Marques-Bonet, T and Arandjelovic, M and Andrés, AM},
title = {Local genetic adaptation to habitat in wild chimpanzees.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39026872},
issn = {2692-8205},
support = {/WT_/Wellcome Trust/United Kingdom ; DP2 MH119424/MH/NIMH NIH HHS/United States ; R01 MH132818/MH/NIMH NIH HHS/United States ; },
abstract = {How populations adapt to their environment is a fundamental question in biology. Yet we know surprisingly little about this process, especially for endangered species such as non-human great apes. Chimpanzees, our closest living relatives, are particularly interesting because they inhabit diverse habitats, from rainforest to woodland-savannah. Whether genetic adaptation facilitates such habitat diversity remains unknown, despite having wide implications for evolutionary biology and conservation. Using 828 newly generated exomes from wild chimpanzees, we find evidence of fine-scale genetic adaptation to habitat. Notably, adaptation to malaria in forest chimpanzees is mediated by the same genes underlying adaptation to malaria in humans. This work demonstrates the power of non-invasive samples to reveal genetic adaptations in endangered populations and highlights the importance of adaptive genetic diversity for chimpanzees.},
}

@article {pmid39037435,
year = {2024},
author = {Liu, X and Liu, S and Yu, Z and Guo, X and Zhang, R and Sun, H and Zhang, Y},
title = {Cognatishimia coralii sp. nov., a marine bacterium isolated from seawater surrounding corals.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {74},
number = {7},
pages = {},
doi = {10.1099/ijsem.0.006467},
pmid = {39037435},
issn = {1466-5034},
mesh = {*Anthozoa/microbiology ; *Phylogeny ; *Seawater/microbiology ; *Base Composition ; *RNA, Ribosomal, 16S/genetics ; *DNA, Bacterial/genetics ; *Fatty Acids/analysis ; Animals ; China ; *Bacterial Typing Techniques ; *Sequence Analysis, DNA ; *Coral Reefs ; Ubiquinone/analogs & derivatives ; Nucleic Acid Hybridization ; },
abstract = {Coral reefs are declining due to the rising seawater temperature. Bacteria within and surrounding corals play key roles in maintaining the homeostasis of the coral holobiont. Research on coral-related bacteria could provide benefits for coral reef restoration. During the isolation of coral-associated bacteria, a Gram-stain-negative, motile bacterium (D5M38[T]) was isolated from seawater surrounding corals in Daya Bay, Shenzhen, PR China. Phylogenetic analysis revealed that strain D5M38[T] represents a novel species in the genus Cognatishimia. The temperature range for strain D5M38[T] growth was 10-40 °C, and the optimum temperature was 37 °C. The salinity range for the growth of this isolate was from 0 to 4.0 %, with an optimal salinity level of 0.5 %. The pH range necessary for strain D5M38[T] growth was between pH 5.0 and 9.0, with an optimal pH being 7.5. The predominant fatty acid was summed feature 8 (65.0 %). The major respiratory quinone was Q-10. The DNA G+C content was 56.8 %. The genome size was 3.88 Mb. The average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) values between strain D5M38[T] and its two closest neighbours, Cognatishimia activa LMG 29900[T] and Cognatishimia maritima KCTC 23347[T], were 73.2/73.6%, 73.2/73.6% and 19.7/19.5%, respectively. Strain D5M38[T] was clearly distinct from its closest neighbours C. activa LMG 29900[T] and C. maritima KCTC 23347[T], with 16S rRNA gene sequence similarity values of 97.5 and 97.3 %, respectively. The phylogenetic analysis, along with the ANI, AAI, and dDDH values, demonstrated that strain D5M38[T] is a member of the genus Cognatishimia, and is distinct from the other two recognized species within this genus. The physiological, biochemical and chemotaxonomic characteristics also supported the species novelty of strain D5M38[T]. Thus, strain D5M38[T] is considered to be classified as representing a novel species in the genus Cognatishimia, for which the name Cognatishimia coralii sp. nov. is proposed. The type strain is D5M38[T] (=MCCC 1K08692[T]=KCTC 8160[T]).},
}

*Anthozoa/microbiology
*Phylogeny
*Seawater/microbiology
*Base Composition
*RNA, Ribosomal, 16S/genetics
*DNA, Bacterial/genetics
*Fatty Acids/analysis
Animals
China
*Bacterial Typing Techniques
*Sequence Analysis, DNA
*Coral Reefs
Ubiquinone/analogs & derivatives
Nucleic Acid Hybridization

@article {pmid39036359,
year = {2024},
author = {Rolli, E and Ghitti, E and Mapelli, F and Borin, S},
title = {Polychlorinated biphenyls modify Arabidopsis root exudation pattern to accommodate degrading bacteria, showing strain and functional trait specificity.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1429096},
pmid = {39036359},
issn = {1664-462X},
abstract = {INTRODUCTION: The importance of plant rhizodeposition to sustain microbial growth and induce xenobiotic degradation in polluted environments is increasingly recognized.

METHODS: Here the "cry-for-help" hypothesis, consisting in root chemistry remodeling upon stress, was investigated in the presence of polychlorinated biphenyls (PCBs), highly recalcitrant and phytotoxic compounds, highlighting its role in reshaping the nutritional and signaling features of the root niche to accommodate PCB-degrading microorganisms.

RESULTS: Arabidopsis exposure to 70 µM PCB-18 triggered plant-detrimental effects, stress-related traits, and PCB-responsive gene expression, reproducing PCB phytotoxicity. The root exudates of plantlets exposed for 2 days to the pollutant were collected and characterized through untargeted metabolomics analysis by liquid chromatography-mass spectrometry. Principal component analysis disclosed a different root exudation fingerprint in PCB-18-exposed plants, potentially contributing to the "cry-for-help" event. To investigate this aspect, the five compounds identified in the exudate metabolomic analysis (i.e., scopoletin, N-hydroxyethyl-β-alanine, hypoxanthine, L-arginyl-L-valine, and L-seryl-L-phenylalanine) were assayed for their influence on the physiology and functionality of the PCB-degrading strains Pseudomonas alcaliphila JAB1, Paraburkholderia xenovorans LB400, and Acinetobacter calcoaceticus P320. Scopoletin, whose relative abundance decreased in PCB-18-stressed plant exudates, hampered the growth and proliferation of strains JAB1 and P320, presumably due to its antimicrobial activity, and reduced the beneficial effect of Acinetobacter P320, which showed a higher degree of growth promotion in the scopoletin-depleted mutant f6'h1 compared to Arabidopsis WT plants exposed to PCB. Nevertheless, scopoletin induced the expression of the bph catabolic operon in strains JAB1 and LB400. The primary metabolites hypoxanthine, L-arginyl-L-valine, and L-seryl-L-phenylalanine, which increased in relative abundance upon PCB-18 stress, were preferentially used as nutrients and growth-stimulating factors by the three degrading strains and showed a variable ability to affect rhizocompetence traits like motility and biofilm formation.

DISCUSSION: These findings expand the knowledge on PCB-triggered "cry-for-help" and its role in steering the PCB-degrading microbiome to boost the holobiont fitness in polluted environments.},
}

@article {pmid39030686,
year = {2024},
author = {Wallace, BA and Varona, NS and Hesketh-Best, PJ and Stiffler, AK and Silveira, CB},
title = {Globally distributed bacteriophage genomes reveal mechanisms of tripartite phage-bacteria-coral interactions.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae132},
pmid = {39030686},
issn = {1751-7370},
abstract = {Reef-building corals depend on an intricate community of microorganisms for functioning and resilience. The infection of coral-associated bacteria by bacteriophages can modify bacteria-host interactions, yet very little is known about phage functions in the holobiont. This gap stems from methodological limitations that have prevented the recovery of high-quality viral genomes and bacterial host assignment from coral samples. Here, we introduce a size fractionation approach that increased bacterial and viral recovery in coral metagenomes by 9-fold and 2-fold, respectively, and enabled the assembly and binning of bacterial and viral genomes at relatively low sequencing coverage. We combined these viral genomes with those derived from 677 publicly available metagenomes, viromes, and bacterial isolates from stony corals to build a global coral virus database of over 20 000 viral genomic sequences spanning four viral realms. The tailed bacteriophage families Kyanoviridae and Autographiviridae were the most abundant, replacing groups formerly referred to as Myoviridae and Podoviridae, respectively. Prophage and CRISPR spacer linkages between these viruses and 626 bacterial metagenome-assembled genomes and bacterial isolates showed that most viruses infected Alphaproteobacteria, the most abundant class, and less abundant taxa like Halanaerobiia and Bacteroidia. A host-phage-gene network identified keystone viruses with the genomic capacity to modulate bacterial metabolic pathways and direct molecular interactions with eukaryotic cells. This study reveals the genomic basis of nested symbioses between bacteriophage, bacteria, and the coral host and its endosymbiotic algae.},
}

@article {pmid39030648,
year = {2024},
author = {Moretti, LG and Crusciol, CAC and Leite, MFA and Momesso, L and Bossolani, JW and Costa, OYA and Hungria, M and Kuramae, EE},
title = {Diverse bacterial consortia: key drivers of rhizosoil fertility modulating microbiome functions, plant physiology, nutrition, and soybean grain yield.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {50},
pmid = {39030648},
issn = {2524-6372},
support = {2016/23699-8; 2018/14892-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 151120/2020-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
abstract = {Soybean cultivation in tropical regions relies on symbioses with nitrogen-fixing Bradyrhizobium and plant growth-promoting bacteria (PGPBs), reducing environmental impacts of N fertilizers and pesticides. We evaluate the effects of soybean inoculation with different bacterial consortia combined with PGPBs or microbial secondary metabolites (MSMs) on rhizosoil chemistry, plant physiology, plant nutrition, grain yield, and rhizosphere microbial functions under field conditions over three growing seasons with four treatments: standard inoculation of Bradyrhizobium japonicum and Bradyrhizobium diazoefficiens consortium (SI); SI plus foliar spraying with Bacillus subtilis (SI + Bs); SI plus foliar spraying with Azospirillum brasilense (SI + Az); and SI plus seed application of MSMs enriched in lipo-chitooligosaccharides extracted from B. diazoefficiens and Rhizobium tropici (SI + MSM). Rhizosphere microbial composition, diversity, and function was assessed by metagenomics. The relationships between rhizosoil chemistry, plant nutrition, grain yield, and the abundance of microbial taxa and functions were determined by generalized joint attribute modeling. The bacterial consortia had the most significant impact on rhizosphere soil fertility, which in turn affected the bacterial community, plant physiology, nutrient availability, and production. Cluster analysis identified microbial groups and functions correlated with shifts in rhizosoil chemistry and plant nutrition. Bacterial consortia positively modulated specific genera and functional pathways involved in biosynthesis of plant secondary metabolites, amino acids, lipopolysaccharides, photosynthesis, bacterial secretion systems, and sulfur metabolism. The effects of the bacterial consortia on the soybean holobiont, particularly the rhizomicrobiome and rhizosoil fertility, highlight the importance of selecting appropriate consortia for desired outcomes. These findings have implications for microbial-based agricultural practices that enhance crop productivity, quality, and sustainability.},
}

@article {pmid39030484,
year = {2024},
author = {Siegieda, D and Panek, J and Frąc, M},
title = {Ecological processes of bacterial microbiome assembly in healthy and dysbiotic strawberry farms.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {692},
pmid = {39030484},
issn = {1471-2229},
support = {BIOSTRATEG3/344433/16/NCBR/2018//Narodowe Centrum Badań i Rozwoju/ ; },
mesh = {*Fragaria/microbiology ; *Microbiota ; *Soil Microbiology ; *Rhizosphere ; *Bacteria/classification/genetics ; Plant Roots/microbiology ; Plant Shoots/microbiology ; Farms ; },
abstract = {The bacterial microbiome plays crucial role in plants' resistance to diseases, nutrient uptake and productivity. We examined the microbiome characteristics of healthy and unhealthy strawberry farms, focusing on soil (bulk soil, rhizosphere soil) and plant (roots and shoots). The relative abundance of most abundant taxa were correlated with the chemical soil properties and shoot niche revealed the least amount of significant correlations between the two. While alpha and beta diversities did not show differences between health groups, we identified a number of core taxa (16-59) and marker bacterial taxa for each healthy (Unclassified Tepidisphaerales, Ohtaekwangia, Hydrocarboniphaga) and dysbiotic (Udaeobacter, Solibacter, Unclassified Chitinophagales, Unclassified Nitrosomonadaceae, Nitrospira, Nocardioides, Tardiphaga, Skermanella, Pseudomonas, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Curtobacterium) niche. We also revealed selective pressure of strawberry rhizosphere soil and roots plants in unhealthy plantations increased stochastic ecological processes of bacterial microbiome assembly in shoots. Our findings contribute to understanding sustainable agriculture and plant-microbiome interactions.},
}

*Fragaria/microbiology
*Microbiota
*Soil Microbiology
*Rhizosphere
*Bacteria/classification/genetics
Plant Roots/microbiology
Plant Shoots/microbiology
Farms

@article {pmid39030351,
year = {2024},
author = {Gong, S and Liang, J and Xu, L and Wang, Y and Li, J and Jin, X and Yu, K and Zhang, Y},
title = {Diel transcriptional responses of coral-Symbiodiniaceae holobiont to elevated temperature.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {882},
pmid = {39030351},
issn = {2399-3642},
mesh = {*Anthozoa/genetics/physiology ; Animals ; *Symbiosis ; Circadian Rhythm/genetics ; Transcription, Genetic ; Hot Temperature ; Dinoflagellida/genetics/physiology ; Temperature ; },
abstract = {Coral exhibits diel rhythms in behavior and gene transcription. However, the influence of elevated temperature, a key factor causing coral bleaching, on these rhythms remains poorly understood. To address this, we examined physiological, metabolic, and gene transcription oscillations in the Acropora tenuis-Cladocopium sp. holobiont under constant darkness (DD), light-dark cycle (LD), and LD with elevated temperature (HLD). Under LD, the values of photosystem II efficiency, reactive oxygen species leakage, and lipid peroxidation exhibited significant diel oscillations. These oscillations were further amplified during coral bleaching under HLD. Gene transcription analysis identified 24-hour rhythms for specific genes in both coral and Symbiodiniaceae under LD. Notably, these rhythms were disrupted in coral and shifted in Symbiodiniaceae under HLD. Importantly, we identified over 20 clock or clock-controlled genes in this holobiont. Specifically, we suggested CIPC (CLOCK-interacting pacemaker-like) gene as a core clock gene in coral. We observed that the transcription of two abundant rhythmic genes encoding glycoside hydrolases (CBM21) and heme-binding protein (SOUL) were dysregulated by elevated temperature. These findings indicate that elevated temperatures disrupt diel gene transcription rhythms in the coral-Symbiodiniaceae holobiont, affecting essential symbiosis processes, such as carbohydrate utilization and redox homeostasis. These disruptions may contribute to the thermal bleaching of coral.},
}

*Anthozoa/genetics/physiology
Animals
*Symbiosis
Circadian Rhythm/genetics
Transcription, Genetic
Hot Temperature
Dinoflagellida/genetics/physiology
Temperature

@article {pmid38999024,
year = {2024},
author = {Schwarcz, S and Nyerges, P and Bíró, TI and Janka, E and Bai, P and Mikó, E},
title = {Cytostatic Bacterial Metabolites Interfere with 5-Fluorouracil, Doxorubicin and Paclitaxel Efficiency in 4T1 Breast Cancer Cells.},
journal = {Molecules (Basel, Switzerland)},
volume = {29},
number = {13},
pages = {},
pmid = {38999024},
issn = {1420-3049},
support = {FK128387, K142141, TKP2021-EGA-19, TKP-EGA-20//NKFIH/ ; POST-COVID2021-33//Grant from the Hungarian Academy of Sciences/ ; ÚNKP-23-3-II-DE-151, ÚNKP-23-3-I-DE-184, ÚNKP-23-4-II-DE-172//ÚNKP-23/ ; },
mesh = {*Paclitaxel/pharmacology ; *Fluorouracil/pharmacology ; *Doxorubicin/pharmacology ; *Breast Neoplasms/drug therapy/metabolism/pathology ; Female ; *Cytostatic Agents/pharmacology ; *Cell Proliferation/drug effects ; Cell Line, Tumor ; Humans ; Mice ; Animals ; Bacteria/drug effects/metabolism ; Antineoplastic Agents/pharmacology ; Indoles/pharmacology ; },
abstract = {The microbiome is capable of modulating the bioavailability of chemotherapy drugs, mainly due to metabolizing these agents. Multiple cytostatic bacterial metabolites were recently identified that have cytostatic effects on cancer cells. In this study, we addressed the question of whether a set of cytostatic bacterial metabolites (cadaverine, indolepropionic acid and indoxylsulfate) can interfere with the cytostatic effects of the chemotherapy agents used in the management of breast cancer (doxorubicin, gemcitabine, irinotecan, methotrexate, rucaparib, 5-fluorouracil and paclitaxel). The chemotherapy drugs were applied in a wide concentration range to which a bacterial metabolite was added in a concentration within its serum reference range, and the effects on cell proliferation were assessed. There was no interference between gemcitabine, irinotecan, methotrexate or rucaparib and the bacterial metabolites. Nevertheless, cadaverine and indolepropionic acid modulated the Hill coefficient of the inhibitory curve of doxorubicin and 5-fluorouracil. Changes to the Hill coefficient implicate alterations to the kinetics of the binding of the chemotherapy agents to their targets. These effects have an unpredictable significance from the clinical or pharmacological perspective. Importantly, indolepropionic acid decreased the IC50 value of paclitaxel, which is a potentially advantageous combination.},
}

*Paclitaxel/pharmacology
*Fluorouracil/pharmacology
*Doxorubicin/pharmacology
*Breast Neoplasms/drug therapy/metabolism/pathology
Female
*Cytostatic Agents/pharmacology
*Cell Proliferation/drug effects
Cell Line, Tumor
Humans
Mice
Animals
Bacteria/drug effects/metabolism
Antineoplastic Agents/pharmacology
Indoles/pharmacology

@article {pmid38996487,
year = {2024},
author = {Sandoval-Velasco, M and Dudchenko, O and Rodríguez, JA and Pérez Estrada, C and Dehasque, M and Fontsere, C and Mak, SST and Khan, R and Contessoto, VG and Oliveira Junior, AB and Kalluchi, A and Zubillaga Herrera, BJ and Jeong, J and Roy, RP and Christopher, I and Weisz, D and Omer, AD and Batra, SS and Shamim, MS and Durand, NC and O'Connell, B and Roca, AL and Plikus, MV and Kusliy, MA and Romanenko, SA and Lemskaya, NA and Serdyukova, NA and Modina, SA and Perelman, PL and Kizilova, EA and Baiborodin, SI and Rubtsov, NB and Machol, G and Rath, K and Mahajan, R and Kaur, P and Gnirke, A and Garcia-Treviño, I and Coke, R and Flanagan, JP and Pletch, K and Ruiz-Herrera, A and Plotnikov, V and Pavlov, IS and Pavlova, NI and Protopopov, AV and Di Pierro, M and Graphodatsky, AS and Lander, ES and Rowley, MJ and Wolynes, PG and Onuchic, JN and Dalén, L and Marti-Renom, MA and Gilbert, MTP and Aiden, EL},
title = {Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample.},
journal = {Cell},
volume = {187},
number = {14},
pages = {3541-3562.e51},
doi = {10.1016/j.cell.2024.06.002},
pmid = {38996487},
issn = {1097-4172},
mesh = {Animals ; *Mammoths/genetics ; *Genome/genetics ; Female ; *Skin ; Elephants/genetics ; Chromatin/genetics ; Fossils ; DNA, Ancient/analysis ; Mice ; Humans ; X Chromosome/genetics ; },
abstract = {Analyses of ancient DNA typically involve sequencing the surviving short oligonucleotides and aligning to genome assemblies from related, modern species. Here, we report that skin from a female woolly mammoth (†Mammuthus primigenius) that died 52,000 years ago retained its ancient genome architecture. We use PaleoHi-C to map chromatin contacts and assemble its genome, yielding 28 chromosome-length scaffolds. Chromosome territories, compartments, loops, Barr bodies, and inactive X chromosome (Xi) superdomains persist. The active and inactive genome compartments in mammoth skin more closely resemble Asian elephant skin than other elephant tissues. Our analyses uncover new biology. Differences in compartmentalization reveal genes whose transcription was potentially altered in mammoths vs. elephants. Mammoth Xi has a tetradic architecture, not bipartite like human and mouse. We hypothesize that, shortly after this mammoth's death, the sample spontaneously freeze-dried in the Siberian cold, leading to a glass transition that preserved subfossils of ancient chromosomes at nanometer scale.},
}

Animals
*Mammoths/genetics
*Genome/genetics
Female
*Skin
Elephants/genetics
Chromatin/genetics
Fossils
DNA, Ancient/analysis
Mice
Humans
X Chromosome/genetics

@article {pmid38993286,
year = {2022},
author = {Reynoso-García, J and Miranda-Santiago, AE and Meléndez-Vázquez, NM and Acosta-Pagán, K and Sánchez-Rosado, M and Díaz-Rivera, J and Rosado-Quiñones, AM and Acevedo-Márquez, L and Cruz-Roldán, L and Tosado-Rodríguez, EL and Figueroa-Gispert, MDM and Godoy-Vitorino, F},
title = {A complete guide to human microbiomes: Body niches, transmission, development, dysbiosis, and restoration.},
journal = {Frontiers in systems biology},
volume = {2},
number = {},
pages = {},
pmid = {38993286},
issn = {2674-0702},
abstract = {Humans are supra-organisms co-evolved with microbial communities (Prokaryotic and Eukaryotic), named the microbiome. These microbiomes supply essential ecosystem services that play critical roles in human health. A loss of indigenous microbes through modern lifestyles leads to microbial extinctions, associated with many diseases and epidemics. This narrative review conforms a complete guide to the human holobiont-comprising the host and all its symbiont populations- summarizes the latest and most significant research findings in human microbiome. It pretends to be a comprehensive resource in the field, describing all human body niches and their dominant microbial taxa while discussing common perturbations on microbial homeostasis, impacts of urbanization and restoration and humanitarian efforts to preserve good microbes from extinction.},
}

@article {pmid38989465,
year = {2024},
author = {Nanetti, E and Scicchitano, D and Palladino, G and Interino, N and Corlatti, L and Pedrotti, L and Zanetti, F and Pagani, E and Esposito, E and Brambilla, A and Grignolio, S and Marotti, I and Turroni, S and Fiori, J and Rampelli, S and Candela, M},
title = {The Alpine ibex (Capra ibex) gut microbiome, seasonal dynamics, and potential application in lignocellulose bioconversion.},
journal = {iScience},
volume = {27},
number = {7},
pages = {110194},
pmid = {38989465},
issn = {2589-0042},
abstract = {Aiming to shed light on the biology of wild ruminants, we investigated the gut microbiome seasonal dynamics of the Alpine ibex (Capra ibex) from the Central Italian Alps. Feces were collected in spring, summer, and autumn during non-invasive sampling campaigns. Samples were analyzed by 16S rRNA amplicon sequencing, shotgun metagenomics, as well as targeted and untargeted metabolomics. Our findings revealed season-specific compositional and functional profiles of the ibex gut microbiome that may allow the host to adapt to seasonal changes in available forage, by fine-tuning the holobiont catabolic layout to fully exploit the available food. Besides confirming the importance of the host-associated microbiome in providing the phenotypic plasticity needed to buffer dietary changes, we obtained species-level genome bins and identified minimal gut microbiome community modules of 11-14 interacting strains as a possible microbiome-based solution for the bioconversion of lignocellulose to high-value compounds, such as volatile fatty acids.},
}

@article {pmid38986611,
year = {2024},
author = {Odriozola, I and Rasmussen, JA and Gilbert, MTP and Limborg, MT and Alberdi, A},
title = {A practical introduction to holo-omics.},
journal = {Cell reports methods},
volume = {},
number = {},
pages = {100820},
doi = {10.1016/j.crmeth.2024.100820},
pmid = {38986611},
issn = {2667-2375},
abstract = {Holo-omics refers to the joint study of non-targeted molecular data layers from host-microbiota systems or holobionts, which is increasingly employed to disentangle the complex interactions between the elements that compose them. We navigate through the generation, analysis, and integration of omics data, focusing on the commonalities and main differences to generate and analyze the various types of omics, with a special focus on optimizing data generation and integration. We advocate for careful generation and distillation of data, followed by independent exploration and analyses of the single omic layers to obtain a better understanding of the study system, before the integration of multiple omic layers in a final model is attempted. We highlight critical decision points to achieve this aim and flag the main challenges to address complex biological questions regarding the integrative study of host-microbiota relationships.},
}

@article {pmid38981551,
year = {2024},
author = {Roik, A and Wall, M and Dobelmann, M and Nietzer, S and Fiesinger, A and Reverter, M and Brefeld, D and Schupp, PJ and Jackson, M and Rutsch, M and Strahl, J},
title = {Trade-off in a reef-building coral after six years of thermal acclimation.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {174589},
doi = {10.1016/j.scitotenv.2024.174589},
pmid = {38981551},
issn = {1879-1026},
abstract = {There is growing evidence that reef-building corals can acclimate to novel and challenging thermal conditions. However, potential trade-offs that accompany acclimation remain largely unexplored. We investigated physiological trade-offs in colonies of a globally abundant coral species (Pocillopora acuta) that were acclimated ex situ to an elevated temperature of 31 °C (i.e., 1 °C above their bleaching threshold) for six years. By comparing them to conspecifics maintained at a cooler temperature, we found that the energy storage of corals was prioritized over skeletal growth at the elevated temperature. This was associated with the formation of higher density skeletons, lower calcification rates and consequently lower skeletal extension rates, which entails ramifications for future reef-building processes, structural complexity and reef community composition. Furthermore, symbionts were physiologically compromised at 31 °C and had overall lower energy reserves, likely due to greater exploitation by their host, resulting in an overall lower stress resilience of the holobiont. Our study shows how biological trade-offs of thermal acclimation unfold, helping to refine our picture of future coral reef trajectories. Importantly, our observations in this six-year study do not align with observations of short-term studies, where elevated temperatures were often associated with the depletion of energy reserves, highlighting the importance of studying acclimation of organisms at relevant biological scales.},
}

@article {pmid38979873,
year = {2024},
author = {Chávez-González, JD and Flores-Núñez, VM and Merino-Espinoza, IU and Partida-Martínez, LP},
title = {Desert plants, arbuscular mycorrhizal fungi and associated bacteria: Exploring the diversity and role of symbiosis under drought.},
journal = {Environmental microbiology reports},
volume = {16},
number = {4},
pages = {e13300},
doi = {10.1111/1758-2229.13300},
pmid = {38979873},
issn = {1758-2229},
support = {//CONAHCYT (Consejo Nacional de Humanidades Ciencias y Tecnologias)/ ; A1-S-9889//Consejo Nacional de Ciencia y Tecnología/ ; IDEAGTO/CONV/014/2022//IDEA GTO/ ; },
mesh = {*Mycorrhizae/physiology/classification/genetics ; *Symbiosis ; *Droughts ; *Desert Climate ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Agave/microbiology ; Biodiversity ; Plant Roots/microbiology ; },
abstract = {Desert plants, such as Agave tequilana, A. salmiana and Myrtillocactus geometrizans, can survive harsh environmental conditions partly due to their symbiotic relationships with microorganisms, including arbuscular mycorrhizal fungi (AMF). Interestingly, some of these fungi also harbour endosymbiotic bacteria. Our research focused on investigating the diversity of these AMFs and their associated bacteria in these plants growing in arid soil. We found that agaves have a threefold higher AMF colonization than M. geometrizans. Metabarcoding techniques revealed that the composition of AMF communities was primarily influenced by the plant host, while the bacterial communities were more affected by the specific plant compartment or niche they inhabited. We identified both known and novel endofungal bacterial taxa, including Burkholderiales, and confirmed their presence within AMF spores using multiphoton microscopy. Our study also explored the effects of drought on the symbiosis between A. tequilana and AMF. We discovered that the severity of drought conditions could modulate the strength of this symbiosis and its outcomes for the plant holobiont. Severe drought conditions prevented the formation of this symbiosis, while moderate drought conditions promoted it, thereby conferring drought tolerance in A. tequilana. This research sheds light on the diversity of AMF and associated bacteria in Crassulacean Acid Metabolism (CAM) plants and underscores the crucial role of drought as a factor modulating the symbiosis between A. tequilana and AMF. Further research is needed to understand the role of endofungal bacteria in this response.},
}

*Mycorrhizae/physiology/classification/genetics
*Symbiosis
*Droughts
*Desert Climate
*Soil Microbiology
*Bacteria/classification/genetics/isolation & purification/metabolism
Agave/microbiology
Biodiversity
Plant Roots/microbiology

@article {pmid38974189,
year = {2024},
author = {Cham, AK and Adams, AK and Wadl, PA and Ojeda-Zacarías, MDC and Rutter, WB and Jackson, DM and Shoemaker, DD and Yencho, GC and Olukolu, BA},
title = {Metagenome-enabled models improve genomic predictive ability and identification of herbivory-limiting genes in sweetpotato.},
journal = {Horticulture research},
volume = {11},
number = {7},
pages = {uhae135},
pmid = {38974189},
issn = {2662-6810},
abstract = {Plant-insect interactions are often influenced by host- or insect-associated metagenomic community members. The relative abundance of insects and the microbes that modulate their interactions were obtained from sweetpotato (Ipomoea batatas) leaf-associated metagenomes using quantitative reduced representation sequencing and strain/species-level profiling with the Qmatey software. Positive correlations were found between whitefly (Bemisia tabaci) and its endosymbionts (Candidatus Hamiltonella defensa, Candidatus Portiera aleyrodidarum, and Rickettsia spp.) and negative correlations with nitrogen-fixing bacteria that implicate nitric oxide in sweetpotato-whitefly interaction. Genome-wide associations using 252 975 dosage-based markers, and metagenomes as a covariate to reduce false positive rates, implicated ethylene and cell wall modification in sweetpotato-whitefly interaction. The predictive abilities (PA) for whitefly and Ocypus olens abundance were high in both populations (68%-69% and 33.3%-35.8%, respectively) and 69.9% for Frankliniella occidentalis. The metagBLUP (gBLUP) prediction model, which fits the background metagenome-based Cao dissimilarity matrix instead of the marker-based relationship matrix (G-matrix), revealed moderate PA (35.3%-49.1%) except for O. olens (3%-10.1%). A significant gain in PA after modeling the metagenome as a covariate (gGBLUP, ≤11%) confirms quantification accuracy and that the metagenome modulates phenotypic expression and might account for the missing heritability problem. Significant gains in PA were also revealed after fitting allele dosage (≤17.4%) and dominance effects (≤4.6%). Pseudo-diploidized genotype data underperformed for dominance models. Including segregation-distorted loci (SDL) increased PA by 6%-17.1%, suggesting that traits associated with fitness cost might benefit from the inclusion of SDL. Our findings confirm the holobiont theory of host-metagenome co-evolution and underscore its potential for breeding within the context of G × G × E interactions.},
}

@article {pmid38972908,
year = {2024},
author = {Ma, C and Xu, C and Zhang, T and Mu, Q and Lv, J and Xing, Q and Yang, Z and Xu, Z and Guan, Y and Chen, C and Ni, K and Dai, X and Ding, W and Hu, J and Bao, Z and Wang, S and Liu, P},
title = {Tracking the hologenome dynamics in aquatic invertebrates by the holo-2bRAD approach.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {827},
pmid = {38972908},
issn = {2399-3642},
support = {32130107//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; *Aquatic Organisms/genetics ; Invertebrates/genetics/physiology ; Microbiota ; Polymorphism, Single Nucleotide ; },
abstract = {The "hologenome" concept is an increasingly popular way of thinking about microbiome-host for marine organisms. However, it is challenging to track hologenome dynamics because of the large amount of material, with tracking itself usually resulting in damage or death of the research object. Here we show the simple and efficient holo-2bRAD approach for the tracking of hologenome dynamics in marine invertebrates (i.e., scallop and shrimp) from one holo-2bRAD library. The stable performance of our approach was shown with high genotyping accuracy of 99.91% and a high correlation of r > 0.99 for the species-level profiling of microorganisms. To explore the host-microbe association underlying mass mortality events of bivalve larvae, core microbial species changed with the stages were found, and two potentially associated host SNPs were identified. Overall, our research provides a powerful tool with various advantages (e.g., cost-effective, simple, and applicable for challenging samples) in genetic, ecological, and evolutionary studies.},
}

Animals
*Aquatic Organisms/genetics
Invertebrates/genetics/physiology
Microbiota
Polymorphism, Single Nucleotide

@article {pmid38196068,
year = {2024},
author = {Szeőcs, D and Vida, B and Petővári, G and Póliska, S and Janka, E and Sipos, A and Uray, K and Sebestyén, A and Krasznai, Z and Bai, P},
title = {Cell-free ascites from ovarian cancer patients induces Warburg metabolism and cell proliferation through TGFβ-ERK signaling.},
journal = {GeroScience},
volume = {46},
number = {4},
pages = {3581-3597},
pmid = {38196068},
issn = {2509-2723},
support = {K142141//NKFIH/ ; FK128387//NKFIH/ ; TKP2021-EGA-19//NKFIH/ ; TKP2021-EGA-20//NKFIH/ ; Bolyai Fellowship//Magyar Tudományos Akadémia/ ; NKM2022-30//Magyar Tudományos Akadémia/ ; POST-COVID2021-33//Magyar Tudományos Akadémia/ ; FK146852//Nemzeti Kutatási Fejlesztési és Innovációs Hivatal/ ; },
mesh = {Humans ; Female ; *Ovarian Neoplasms/metabolism/pathology ; *Cell Proliferation ; *Ascites/metabolism ; *Transforming Growth Factor beta/metabolism ; Cell Line, Tumor ; MAP Kinase Signaling System/physiology ; Warburg Effect, Oncologic ; Middle Aged ; },
abstract = {Ascites plays a key role in supporting the metastatic potential of ovarian cancer cells. Shear stress and carry-over of cancer cells by ascites flow support carcinogenesis and metastasis formation. In addition, soluble factors may participate in the procarcinogenic effects of ascites in ovarian cancer. This study aimed to determine the biological effects of cell-free ascites on carcinogenesis in ovarian cancer cells. Cell-free ascites from ovarian cancer patients (ASC) non-selectively induced cell proliferation in multiple models of ovarian cancer and untransformed primary human dermal fibroblasts. Furthermore, ASC induced a Warburg-type rearrangement of cellular metabolism in A2780 ovarian cancer cells characterized by increases in cellular oxygen consumption and glycolytic flux; increases in glycolytic flux were dominant. ASC induced mitochondrial uncoupling and fundamentally reduced fatty acid oxidation. Ascites-elicited effects were uniform among ascites specimens. ASC-elicited transcriptomic changes in A2780 ovarian cancer cells included induction of the TGFβ-ERK/MEK pathway, which plays a key role in inducing cell proliferation and oncometabolism. ASC-induced gene expression changes, as well as the overexpression of members of the TGFβ signaling system, were associated with poor survival in ovarian cancer patients. We provided evidence that the activation of the autocrine/paracrine of TGFβ signaling system may be present in bladder urothelial carcinoma and stomach adenocarcinoma. Database analysis suggests that the TGFβ system may feed forward bladder urothelial carcinoma and stomach adenocarcinoma. Soluble components of ASC support the progression of ovarian cancer. These results suggest that reducing ascites production may play an essential role in the treatment of ovarian cancer by inhibiting the progression and reducing the severity of the disease.},
}

Humans
Female
*Ovarian Neoplasms/metabolism/pathology
*Cell Proliferation
*Ascites/metabolism
*Transforming Growth Factor beta/metabolism
Cell Line, Tumor
MAP Kinase Signaling System/physiology
Warburg Effect, Oncologic
Middle Aged

@article {pmid38965478,
year = {2024},
author = {Yang, J and Woo, JJ and Sesal, C and Gökalsın, B and Eldem, V and Açıkgöz, B and Başaran, TI and Kurtuluş, G and Hur, JS},
title = {Continental scale comparison of mycobiomes in Parmelia and Peltigera lichens from Turkey and South Korea.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {243},
pmid = {38965478},
issn = {1471-2180},
support = {NRF-2021K2A9A1A06086000//National Research Foundation of Korea/ ; 2023R1A6C101B022//Korea Basic Science Institute/ ; 221N004//Turkish Technological Research Council/ ; },
mesh = {*Mycobiome ; Republic of Korea ; Turkey ; *Lichens/microbiology/classification ; *DNA, Fungal/genetics ; Ascomycota/classification/isolation & purification/genetics ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Fungi/classification/isolation & purification/genetics ; Parmeliaceae/genetics ; },
abstract = {BACKGROUND: Lichens, traditionally considered as a simple partnership primarily between mycobiont and photobiont, are, in reality, complex holobionts comprised of a multitude of microorganisms. Lichen mycobiome represents fungal community residing within lichen thalli. While it is acknowledged that factors like the host lichen species and environmental conditions influence the structure of the lichen mycobiome, the existing research remains insufficient. To investigate which factor, host genus or location, has a greater impact on the lichen mycobiome, we conducted a comparative analysis of mycobiomes within Parmelia and Peltigera collected from both Turkey and South Korea, using high-throughput sequencing based on internal transcribed spacer region amplification.

RESULTS: Overall, the lichen mycobiome was dominated by Capnodiales (Dothideomycetes), regardless of host or location. At the order level, the taxonomic composition was not significantly different according to lichen genus host or geographical distance. Hierarchical clustering of the top 100 abundant ASVs did not clearly indicate whether the lichen mycobiome was more influenced by host genus or location. Analyses of community similarity and partitioning variables revealed that the structure of the lichen mycobiome is more significantly influenced by location than by host genus. When analyzing the core mycobiome by host genus, the Peltigera mycobiome contained more ASV members than the Parmelia mycobiome. These two core mycobiomes also share common fungal strains, including basidiomycete yeast. Additionally, we used chi-squared tests to identify host genus-specialists and location-specialists.

CONCLUSIONS: By comparing lichen mycobiomes of the same genera across different countries, our study advances our comprehension of these microbial communities. Our study elucidates that, although host species play a contributory role, geographic distance exerts a more pronounced impact on the structure of lichen mycobiome. We have made foundational contributions to understanding the lichen mycobiome occupying ecologically crucial niches. We anticipate that broader global-scale investigations into the fungal community structures will provide more detailed insights into fungal residents within lichens.},
}

*Mycobiome
Republic of Korea
Turkey
*Lichens/microbiology/classification
*DNA, Fungal/genetics
Ascomycota/classification/isolation & purification/genetics
High-Throughput Nucleotide Sequencing
Phylogeny
Fungi/classification/isolation & purification/genetics
Parmeliaceae/genetics

@article {pmid38964709,
year = {2024},
author = {Williams, CE and Fontaine, SS},
title = {Commentary: The microbial dependence continuum: Towards a comparative physiology approach to understand host reliance on microbes.},
journal = {Comparative biochemistry and physiology. Part A, Molecular & integrative physiology},
volume = {},
number = {},
pages = {111690},
doi = {10.1016/j.cbpa.2024.111690},
pmid = {38964709},
issn = {1531-4332},
abstract = {Comparative physiologists often compare physiological traits across organisms to understand the selective pressures influencing their evolution in different environments. Traditionally focused on the organisms themselves, comparative physiology has more recently incorporated studies of the microbiome-the communities of microbes living in and on animals that influence host physiology. In this commentary, we describe the utility of applying a comparative framework to study the microbiome, particularly in understanding how hosts vary in their dependence on microbial communities for physiological function, a concept we term the "microbial dependence continuum". This hypothesis suggests that hosts exist on a spectrum ranging from high to low reliance on their microbiota. Certain physiological traits may be highly dependent on microbes for proper function in some species but microbially independent in others. Comparative physiology can elucidate the selective pressures driving species along this continuum. Here, we discuss the microbial dependence continuum in detail and how comparative physiology can be useful to study it. Then, we discuss two example traits, herbivory and flight, where comparative physiology has helped reveal the selective pressures influencing host dependence on microbial communities. Lastly, we discuss useful experimental approaches for studying the microbial dependence continuum in a comparative physiology context.},
}

@article {pmid38963125,
year = {2024},
author = {Kobel, CM and Merkesvik, J and Burgos, IMT and Lai, W and Øyås, O and Pope, PB and Hvidsten, TR and Aho, VTE},
title = {Integrating host and microbiome biology using holo-omics.},
journal = {Molecular omics},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4mo00017j},
pmid = {38963125},
issn = {2515-4184},
abstract = {Holo-omics is the use of omics data to study a host and its inherent microbiomes - a biological system known as a "holobiont". A microbiome that exists in such a space often encounters habitat stability and in return provides metabolic capacities that can benefit their host. Here we present an overview of beneficial host-microbiome systems and propose and discuss several methodological frameworks that can be used to investigate the intricacies of the many as yet undefined host-microbiome interactions that influence holobiont homeostasis. While this is an emerging field, we anticipate that ongoing methodological advancements will enhance the biological resolution that is necessary to improve our understanding of host-microbiome interplay to make meaningful interpretations and biotechnological applications.},
}

@article {pmid38960756,
year = {2024},
author = {Robinson, JM and Barnes, AD and Fickling, N and Costin, S and Sun, X and Breed, MF},
title = {Food webs in food webs: the micro-macro interplay of multilayered networks.},
journal = {Trends in ecology & evolution},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tree.2024.06.006},
pmid = {38960756},
issn = {1872-8383},
abstract = {Food webs are typically defined as being macro-organism-based (e.g., plants, mammals, birds) or microbial (e.g., bacteria, fungi, viruses). However, these characterizations have limits. We propose a multilayered food web conceptual model where microbial food webs are nested within food webs composed of macro-organisms. Nesting occurs through host-microbe interactions, which influence the health and behavior of host macro-organisms, such that host microbiomes likely alter population dynamics of interacting macro-organisms and vice versa. Here, we explore the theoretical underpinnings of multilayered food webs and the implications of this new conceptual model on food web ecology. Our framework opens avenues for new empirical investigations into complex ecological networks and provides a new lens through which to view a network's response to ecosystem changes.},
}

@article {pmid38943206,
year = {2024},
author = {Larzul, C and Estellé, J and Borey, M and Blanc, F and Lemonnier, G and Billon, Y and Thiam, MG and Quinquis, B and Galleron, N and Jardet, D and Lecardonnel, J and Plaza Oñate, F and Rogel-Gaillard, C},
title = {Driving gut microbiota enterotypes through host genetics.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {116},
pmid = {38943206},
issn = {2049-2618},
support = {Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; ANR-11-DPBS-0001//Agence Nationale de la Recherche/ ; ANR-11-DPBS-0001//Agence Nationale de la Recherche/ ; ANR-11-DPBS-0001//Agence Nationale de la Recherche/ ; ANR-11-DPBS-0001//Agence Nationale de la Recherche/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Swine/microbiology ; *Feces/microbiology ; Bacteria/classification/genetics ; Metagenomics/methods ; Prevotella/genetics/classification ; Ruminococcus/genetics ; Treponema/genetics ; },
abstract = {BACKGROUND: Population stratification based on interindividual variability in gut microbiota composition has revealed the existence of several ecotypes named enterotypes in humans and various animal species. Enterotypes are often associated with environmental factors including diet, but knowledge of the role of host genetics remains scarce. Moreover, enterotypes harbor functionalities likely associated with varying abilities and susceptibilities of their host. Previously, we showed that under controlled conditions, 60-day-old pig populations consistently split into two enterotypes with either Prevotella and Mitsuokella (PM enterotype) or Ruminococcus and Treponema (RT enterotype) as keystone taxa. Here, our aim was to rely on pig as a model to study the influence of host genetics to assemble enterotypes, and to provide clues on enterotype functional differences and their links with growth traits.

RESULTS: We established two pig lines contrasted for abundances of the genera pairs specifying each enterotype at 60 days of age and assessed them for fecal microbiota composition and growth throughout three consecutive generations. Response to selection across three generations revealed, per line, an increase in the prevalence of the selected enterotype and in the average relative abundances of directly and indirectly selected bacterial genera. The PM enterotype was found less diverse than the RT enterotype but more efficient for piglet growth during the post-weaning period. Shotgun metagenomics revealed differentially abundant bacterial species between the two enterotypes. By using the KEGG Orthology database, we show that functions related to starch degradation and polysaccharide metabolism are enriched in the PM enterotype, whereas functions related to general nucleoside transport and peptide/nickel transport are enriched in the RT enterotype. Our results also suggest that the PM and RT enterotypes might differ in the metabolism of valine, leucin, and isoleucine, favoring their biosynthesis and degradation, respectively.

CONCLUSION: We experimentally demonstrated that enterotypes are functional ecosystems that can be selected as a whole by exerting pressure on the host genetics. We also highlight that holobionts should be considered as units of selection in breeding programs. These results pave the way for a holistic use of host genetics, microbiota diversity, and enterotype functionalities to understand holobiont shaping and adaptation. Video Abstract.},
}

Animals
*Gastrointestinal Microbiome/genetics
Swine/microbiology
*Feces/microbiology
Bacteria/classification/genetics
Metagenomics/methods
Prevotella/genetics/classification
Ruminococcus/genetics
Treponema/genetics

@article {pmid38942016,
year = {2024},
author = {Dehasque, M and Morales, HE and Díez-Del-Molino, D and Pečnerová, P and Chacón-Duque, JC and Kanellidou, F and Muller, H and Plotnikov, V and Protopopov, A and Tikhonov, A and Nikolskiy, P and Danilov, GK and Giannì, M and van der Sluis, L and Higham, T and Heintzman, PD and Oskolkov, N and Gilbert, MTP and Götherström, A and van der Valk, T and Vartanyan, S and Dalén, L},
title = {Temporal dynamics of woolly mammoth genome erosion prior to extinction.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2024.05.033},
pmid = {38942016},
issn = {1097-4172},
abstract = {A number of species have recently recovered from near-extinction. Although these species have avoided the immediate extinction threat, their long-term viability remains precarious due to the potential genetic consequences of population declines, which are poorly understood on a timescale beyond a few generations. Woolly mammoths (Mammuthus primigenius) became isolated on Wrangel Island around 10,000 years ago and persisted for over 200 generations before becoming extinct around 4,000 years ago. To study the evolutionary processes leading up to the mammoths' extinction, we analyzed 21 Siberian woolly mammoth genomes. Our results show that the population recovered quickly from a severe bottleneck and remained demographically stable during the ensuing six millennia. We find that mildly deleterious mutations gradually accumulated, whereas highly deleterious mutations were purged, suggesting ongoing inbreeding depression that lasted for hundreds of generations. The time-lag between demographic and genetic recovery has wide-ranging implications for conservation management of recently bottlenecked populations.},
}

@article {pmid38930599,
year = {2024},
author = {Liu, Y and Wu, H and Shu, Y and Hua, Y and Fu, P},
title = {Symbiodiniaceae and Ruegeria sp. Co-Cultivation to Enhance Nutrient Exchanges in Coral Holobiont.},
journal = {Microorganisms},
volume = {12},
number = {6},
pages = {},
doi = {10.3390/microorganisms12061217},
pmid = {38930599},
issn = {2076-2607},
abstract = {The symbiotic relationship between corals and their associated microorganisms is crucial for the health of coral reef eco-environmental systems. Recently, there has been a growing interest in unraveling how the manipulation of symbiont nutrient cycling affects the stress tolerance in the holobiont of coral reefs. However, most studies have primarily focused on coral-Symbiodiniaceae-bacterial interactions as a whole, neglecting the interactions between Symbiodiniaceae and bacteria, which remain largely unexplored. In this study, we proposed a hypothesis that there exists an inner symbiotic loop of Symbiodiniaceae and bacteria within the coral symbiotic loop. We conducted experiments to demonstrate how metabolic exchanges between Symbiodiniaceae and bacteria facilitate the nutritional supply necessary for cellular growth. It was seen that the beneficial bacterium, Ruegeria sp., supplied a nitrogen source to the Symbiodiniaceae strain Durusdinium sp., allowing this dinoflagellate to thrive in a nitrogen-free medium. The Ruegeria sp.-Durusdinium sp. interaction was confirmed through [15]N-stable isotope probing-single cell Raman spectroscopy, in which [15]N infiltrated into the bacterial cells for intracellular metabolism, and eventually the labeled nitrogen source was traced within the macromolecules of Symbiodiniaceae cells. The investigation into Symbiodiniaceae loop interactions validates our hypothesis and contributes to a comprehensive understanding of the intricate coral holobiont. These findings have the potential to enhance the health of coral reefs in the face of global climate change.},
}

@article {pmid38930577,
year = {2024},
author = {Hernández-Zulueta, J and Rubio-Bueno, S and Zamora-Tavares, MDP and Vargas-Ponce, O and Rodríguez-Troncoso, AP and Rodríguez-Zaragoza, FA},
title = {Metabarcoding the Bacterial Assemblages Associated with Toxopneustes roseus in the Mexican Central Pacific.},
journal = {Microorganisms},
volume = {12},
number = {6},
pages = {},
doi = {10.3390/microorganisms12061195},
pmid = {38930577},
issn = {2076-2607},
abstract = {The Mexican Central Pacific (MCP) region has discontinuous coral ecosystems with different protection and anthropogenic disturbance. Characterizing the bacterial assemblage associated with the sea urchin Toxopneustes roseus and its relationship with environmental variables will contribute to understanding the species' physiology and ecology. We collected sea urchins from coral ecosystems at six sites in the MCP during the summer and winter for two consecutive years. The spatial scale represented the most important variation in the T. roseus bacteriome, particularly because of Isla Isabel National Park (PNII). Likewise, spatial differences correlated with habitat structure variables, mainly the sponge and live coral cover. The PNII exhibited highly diverse bacterial assemblages compared to other sites, characterized by families associated with diseases and environmental stress (Saprospiraceae, Flammeovirgaceae, and Xanthobacteraceae). The remaining five sites presented a constant spatiotemporal pattern, where the predominance of the Campylobacteraceae and Helicobacteraceae families was key to T. roseus' holobiont. However, the dominance of certain bacterial families, such as Enterobacteriaceae, in the second analyzed year suggests that Punto B and Islas e islotes de Bahía Chamela Sanctuary were exposed to sewage contamination. Overall, our results improve the understanding of host-associated bacterial assemblages in specific time and space and their relationship with the environmental condition.},
}

@article {pmid38923181,
year = {2024},
author = {Bogale, AT and Braun, M and Bernhardt, J and Zühlke, D and Schiefelbein, U and Bog, M and Scheidegger, C and Zengerer, V and Becher, D and Grube, M and Riedel, K and Bengtsson, MM},
title = {The microbiome of the lichen Lobaria pulmonaria varies according to climate on a subcontinental scale.},
journal = {Environmental microbiology reports},
volume = {16},
number = {3},
pages = {e13289},
doi = {10.1111/1758-2229.13289},
pmid = {38923181},
issn = {1758-2229},
support = {//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Lichens/microbiology/physiology ; *Microbiota ; *Climate ; Bacteria/classification/genetics/isolation & purification ; Symbiosis ; Fungi/classification/genetics/isolation & purification/physiology ; Seasons ; Genotype ; },
abstract = {The Lobaria pulmonaria holobiont comprises algal, fungal, cyanobacterial and bacterial components. We investigated L. pulmonaria's bacterial microbiome in the adaptation of this ecologically sensitive lichen species to diverse climatic conditions. Our central hypothesis posited that microbiome composition and functionality aligns with subcontinental-scale (a stretch of ~1100 km) climatic parameters related to temperature and precipitation. We also tested the impact of short-term weather dynamics, sampling season and algal/fungal genotypes on microbiome variation. Metaproteomics provided insights into compositional and functional changes within the microbiome. Climatic variables explained 41.64% of microbiome variation, surpassing the combined influence of local weather and sampling season at 31.63%. Notably, annual mean temperature and temperature seasonality emerged as significant climatic drivers. Microbiome composition correlated with algal, not fungal genotype, suggesting similar environmental recruitment for the algal partner and microbiome. Differential abundance analyses revealed distinct protein compositions in Sub-Atlantic Lowland and Alpine regions, indicating differential microbiome responses to contrasting environmental/climatic conditions. Proteins involved in oxidative and cellular stress were notably different. Our findings highlight microbiome plasticity in adapting to stable climates, with limited responsiveness to short-term fluctuations, offering new insights into climate adaptation in lichen symbiosis.},
}

*Lichens/microbiology/physiology
*Microbiota
*Climate
Bacteria/classification/genetics/isolation & purification
Symbiosis
Fungi/classification/genetics/isolation & purification/physiology
Seasons
Genotype

@article {pmid38903121,
year = {2024},
author = {Bougiouri, K and Charlton, S and Harris, A and Carmagnini, A and Piličiauskienė, G and Feuerborn, TR and Scarsbrook, L and Tabadda, K and Blaževičius, P and Parker, HG and Gopalakrishnan, S and Larson, G and Ostrander, EA and Irving-Pease, EK and Frantz, LAF and Racimo, F},
title = {Imputation of ancient canid genomes reveals inbreeding history over the past 10,000 years.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38903121},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {The multi-millenia long history between dogs and humans has justly placed them at the forefront of archeological and genomic research. Despite ongoing efforts including the analysis of ancient dog and wolf genomes, many questions remain regarding their geographic and temporal origins, and the microevolutionary processes that led to the huge diversity of breeds today. Although ancient genomes provide valuable information, their use is significantly hindered by low depth of coverage and post-mortem damage, which often inhibits confident genotype calling. In the present study, we assess how genotype imputation of ancient dog and wolf genomes, utilising a large reference panel, can improve the resolution afforded by ancient genomic datasets. Imputation accuracy was evaluated by down-sampling 10 high coverage ancient and modern dog and wolf genomes to 0.05-2x coverage and comparing concordance between imputed and high coverage genotypes. We also measured the impact of imputation on principal component analyses (PCA) and runs of homozygosity (ROH). Our findings show high (R[2] > 0.9) imputation accuracy for dogs with coverage as low as 0.5x and for wolves as low as 1.0x. We then imputed a worldwide dataset of 81 published ancient dog and wolf genomes, in addition to nine newly sequenced medieval and early modern period European dogs, to assess changes in inbreeding during the last 10,000 years of dog evolution. Ancient dog and wolf populations generally exhibited lower inbreeding levels than present-day individuals, though with some exceptions occurring in ancient Arctic and European dogs. Interestingly, regions with low ROH density maintained across ancient and present-day samples were significantly associated with genes related to olfaction and immune response. Our study indicates that imputing ancient canine genomes is a viable strategy that allows for the use of analytical methods previously limited to high-quality genetic data.},
}

@article {pmid38918405,
year = {2024},
author = {Paës, C and Beaumont, M and Gidenne, T and Bébin, K and Duperray, J and Gohier, C and Guené-Grand, E and Rebours, G and Castinel, A and Barilly, C and Gabinaud, B and Bannelier, C and Gress, L and Laperruque, F and Aymard, P and Debrusse, AM and Cauquil, L and Pascal, G and Combes, S},
title = {A multi-omics dataset of the response to early plant polysaccharide ingestion in rabbits.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {684},
pmid = {38918405},
issn = {2052-4463},
mesh = {Animals ; Rabbits ; *Polysaccharides ; *Gastrointestinal Microbiome ; Transcriptome ; Cecum ; Weaning ; Metabolome ; Multiomics ; },
abstract = {The transition from a milk-based diet to exclusive solid feeding deeply modifies microbiota-host crosstalk. Specifically, early ingestion of plant polysaccharides would be one of the main nutritional components to drive host-microbiota-interaction. To capture the effects of polysaccharides early-life nutrition (starch vs rapidly fermentable fiber) on the holobiont development, we investigated on the one hand the gut bacteriome and metabolome and on the other hand the transcriptome of two host gut tissues. Rabbit model was used to study post-natal co-development of the gut microbiota and its host around weaning transition. The assessment of the microbial composition of the gut appendix together with the caecum was provided for the first time. Gene expression signatures were analyzed along the gut (ileum and caecum) through high-throughput qPCR. The data collected were completed by the analysis of animal growth changes and time-series assessment of blood biomarkers. Those accessible and reusable data could help highlight the gut development dynamics as well as biological adaptation processes at the onset of solid feeding.},
}

Animals
Rabbits
*Polysaccharides
*Gastrointestinal Microbiome
Transcriptome
Cecum
Weaning
Metabolome
Multiomics

@article {pmid38905343,
year = {2024},
author = {Buschi, E and Dell'Anno, A and Tangherlini, M and Candela, M and Rampelli, S and Turroni, S and Palladino, G and Esposito, E and Martire, ML and Musco, L and Stefanni, S and Munari, C and Fiori, J and Danovaro, R and Corinaldesi, C},
title = {Resistance to freezing conditions of endemic Antarctic polychaetes is enhanced by cryoprotective proteins produced by their microbiome.},
journal = {Science advances},
volume = {10},
number = {25},
pages = {eadk9117},
doi = {10.1126/sciadv.adk9117},
pmid = {38905343},
issn = {2375-2548},
mesh = {*Polychaeta/microbiology ; Animals ; Antarctic Regions ; *Microbiota ; *Freezing ; Phylogeny ; Bacterial Proteins/metabolism/genetics ; },
abstract = {The microbiome plays a key role in the health of all metazoans. Whether and how the microbiome favors the adaptation processes of organisms to extreme conditions, such as those of Antarctica, which are incompatible with most metazoans, is still unknown. We investigated the microbiome of three endemic and widespread species of Antarctic polychaetes: Leitoscoloplos geminus, Aphelochaeta palmeri, and Aglaophamus trissophyllus. We report here that these invertebrates contain a stable bacterial core dominated by Meiothermus and Anoxybacillus, equipped with a versatile genetic makeup and a unique portfolio of proteins useful for coping with extremely cold conditions as revealed by pangenomic and metaproteomic analyses. The close phylosymbiosis between Meiothermus and Anoxybacillus and these Antarctic polychaetes indicates a connection with their hosts that started in the past to support holobiont adaptation to the Antarctic Ocean. The wide suite of bacterial cryoprotective proteins found in Antarctic polychaetes may be useful for the development of nature-based biotechnological applications.},
}

*Polychaeta/microbiology
Animals
Antarctic Regions
*Microbiota
*Freezing
Phylogeny
Bacterial Proteins/metabolism/genetics

@article {pmid38892721,
year = {2024},
author = {Mafra, D and Borges, NA and Baptista, BG and Martins, LF and Borland, G and Shiels, PG and Stenvinkel, P},
title = {What Can the Gut Microbiota of Animals Teach Us about the Relationship between Nutrition and Burden of Lifestyle Diseases?.},
journal = {Nutrients},
volume = {16},
number = {11},
pages = {},
pmid = {38892721},
issn = {2072-6643},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Humans ; Life Style ; Nutritional Status ; Chronic Disease ; },
abstract = {The gut microbiota performs several crucial roles in a holobiont with its host, including immune regulation, nutrient absorption, synthesis, and defense against external pathogens, significantly influencing host physiology. Disruption of the gut microbiota has been linked to various chronic conditions, including cardiovascular, kidney, liver, respiratory, and intestinal diseases. Studying how animals adapt their gut microbiota across their life course at different life stages and under the dynamics of extreme environmental conditions can provide valuable insights from the natural world into how the microbiota modulates host biology, with a view to translating these into treatments or preventative measures for human diseases. By modulating the gut microbiota, opportunities to address many complications associated with chronic diseases appear. Such a biomimetic approach holds promise for exploring new strategies in healthcare and disease management.},
}

Animals
*Gastrointestinal Microbiome/physiology
Humans
Life Style
Nutritional Status
Chronic Disease

@article {pmid38892420,
year = {2024},
author = {Qadri, QR and Lai, X and Zhao, W and Zhang, Z and Zhao, Q and Ma, P and Pan, Y and Wang, Q},
title = {Exploring the Interplay between the Hologenome and Complex Traits in Bovine and Porcine Animals Using Genome-Wide Association Analysis.},
journal = {International journal of molecular sciences},
volume = {25},
number = {11},
pages = {},
pmid = {38892420},
issn = {1422-0067},
support = {2021C02068-1//Zhejiang Science and Technology Major Program on Agricultural New Variety Breeding/ ; 2021YFD1200802//National Key Research and Development Program of China/ ; U21A20249//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Genome-Wide Association Study ; *Polymorphism, Single Nucleotide ; Cattle/genetics ; Swine/genetics ; *Quantitative Trait Loci ; Gastrointestinal Microbiome/genetics ; Rumen/microbiology/metabolism ; Phenotype ; Methane/metabolism ; Milk/metabolism ; Genome ; },
abstract = {Genome-wide association studies (GWAS) significantly enhance our ability to identify trait-associated genomic variants by considering the host genome. Moreover, the hologenome refers to the host organism's collective genetic material and its associated microbiome. In this study, we utilized the hologenome framework, called Hologenome-wide association studies (HWAS), to dissect the architecture of complex traits, including milk yield, methane emissions, rumen physiology in cattle, and gut microbial composition in pigs. We employed four statistical models: (1) GWAS, (2) Microbial GWAS (M-GWAS), (3) HWAS-CG (hologenome interaction estimated using COvariance between Random Effects Genome-based restricted maximum likelihood (CORE-GREML)), and (4) HWAS-H (hologenome interaction estimated using the Hadamard product method). We applied Bonferroni correction to interpret the significant associations in the complex traits. The GWAS and M-GWAS detected one and sixteen significant SNPs for milk yield traits, respectively, whereas the HWAS-CG and HWAS-H each identified eight SNPs. Moreover, HWAS-CG revealed four, and the remaining models identified three SNPs each for methane emissions traits. The GWAS and HWAS-CG detected one and three SNPs for rumen physiology traits, respectively. For the pigs' gut microbial composition traits, the GWAS, M-GWAS, HWAS-CG, and HWAS-H identified 14, 16, 13, and 12 SNPs, respectively. We further explored these associations through SNP annotation and by analyzing biological processes and functional pathways. Additionally, we integrated our GWA results with expression quantitative trait locus (eQTL) data using transcriptome-wide association studies (TWAS) and summary-based Mendelian randomization (SMR) methods for a more comprehensive understanding of SNP-trait associations. Our study revealed hologenomic variability in agriculturally important traits, enhancing our understanding of host-microbiome interactions.},
}

Animals
*Genome-Wide Association Study
*Polymorphism, Single Nucleotide
Cattle/genetics
Swine/genetics
*Quantitative Trait Loci
Gastrointestinal Microbiome/genetics
Rumen/microbiology/metabolism
Phenotype
Methane/metabolism
Milk/metabolism
Genome

@article {pmid38891668,
year = {2024},
author = {Recchia, M and Ghidini, S and Romeo, C and Scali, F and Maisano, AM and Guadagno, F and De Luca, S and Ianieri, A and Alborali, GL},
title = {An Integrated Analysis of Abattoir Lung Lesion Scores and Antimicrobial Use in Italian Heavy Pig Finishing Farms.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {11},
pages = {},
pmid = {38891668},
issn = {2076-2615},
support = {CLASSYFARM project (CUP: E55F21002890001)//Italian Ministry of Health/ ; },
abstract = {Respiratory diseases significantly affect intensive pig finishing farms, causing production losses and increased antimicrobial use (AMU). Lesion scoring at slaughter has been recognized as a beneficial practice to evaluate herd management. The integrated analysis of abattoir lesion scores and AMU data could improve decision-making by providing feedback to veterinarians and farmers on the effectiveness of antimicrobial treatments, thus rationalizing their use. This study compared lung and pleural lesion scores collected at Italian pig slaughterhouses with on-farm AMU, estimated through a treatment index per 100 days (TI100). Overall, 24,752 pig carcasses, belonging to 236 batches from 113 finishing farms, were inspected. Bronchopneumonia and chronic pleuritis were detected in 55% and 48% of the examined pigs, respectively. Antimicrobials were administered in 97% of the farms during the six months prior to slaughter (median TI100 = 5.2), notwithstanding compliance with the mandatory withdrawal period. EMA category B (critical) antimicrobials were administered in 15.2% of cases (median TI100 = 0.06). The lung score was not associated with the total AMU, but significant, positive associations were found with the past use of critical antimicrobials (p = 0.041) and macrolides (p = 0.044). This result highlights the potential of abattoir lung lesion monitoring to rationalize antimicrobial stewardship efforts, contributing to AMU reduction.},
}

@article {pmid38886248,
year = {2024},
author = {Bartels, N and Matthews, JL and Lawson, CA and Possell, M and Hughes, DJ and Raina, JB and Suggett, DJ},
title = {Paired metabolomics and volatilomics provides insight into transient high light stress response mechanisms of the coral Montipora mollis.},
journal = {Metabolomics : Official journal of the Metabolomic Society},
volume = {20},
number = {4},
pages = {66},
pmid = {38886248},
issn = {1573-3890},
mesh = {Animals ; *Anthozoa/metabolism ; *Metabolomics/methods ; *Light ; *Stress, Physiological ; Volatile Organic Compounds/metabolism/analysis ; Photosystem II Protein Complex/metabolism ; },
abstract = {The coral holobiont is underpinned by complex metabolic exchanges between different symbiotic partners, which are impacted by environmental stressors. The chemical diversity of the compounds produced by the holobiont is high and includes primary and secondary metabolites, as well as volatiles. However, metabolites and volatiles have only been characterised in isolation so far. Here, we applied a paired metabolomic-volatilomic approach to characterise holistically the chemical response of the holobiont under stress. Montipora mollis fragments were subjected to high-light stress (8-fold higher than the controls) for 30 min. Photosystem II (PSII) photochemical efficiency values were 7-fold higher in control versus treatment corals immediately following high-light exposure, but returned to pre-stress levels after 30 min of recovery. Under high-light stress, we identified an increase in carbohydrates (> 5-fold increase in arabinose and fructose) and saturated fatty acids (7-fold increase in myristic and oleic acid), together with a decrease in fatty acid derivatives in both metabolites and volatiles (e.g., 80% decrease in oleamide and nonanal), and other antioxidants (~ 85% decrease in sorbitol and galactitol). These changes suggest short-term light stress induces oxidative stress. Correlation analysis between volatiles and metabolites identified positive links between sorbitol, galactitol, six other metabolites and 11 volatiles, with four of these compounds previously identified as antioxidants. This suggests that these 19 compounds may be related and share similar functions. Taken together, our findings demonstrate how paired metabolomics-volatilomics may illuminate broader metabolic shifts occurring under stress and identify linkages between uncharacterised compounds to putatively determine their functions.},
}

Animals
*Anthozoa/metabolism
*Metabolomics/methods
*Light
*Stress, Physiological
Volatile Organic Compounds/metabolism/analysis
Photosystem II Protein Complex/metabolism

@article {pmid38884497,
year = {2024},
author = {Han, S and Akhtar, MR and Xia, X},
title = {Functions and regulations of insect gut bacteria.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.8261},
pmid = {38884497},
issn = {1526-4998},
support = {31871968//National Natural Science Foundation of China/ ; MIMCP-202302//Open Project of Fujian Key Laboratory of Crop Pest Monitoring and Control/ ; KFB23024A//Science and Technology Innovation Fund of Fujian Agriculture and Forestry University/ ; },
abstract = {The insect gut is a complicated ecosystem that inhabits a large number of symbiotic bacteria. As an important organ of the host insect, the symbiotic bacteria of the insect gut play very important roles in regulating physiological and metabolic processes. Recently, much progress has been made in the study of symbiotic bacteria in insect guts with the development of high-throughput sequencing technology and molecular biology. This review summarizes the primary functions of symbiotic bacteria in insect guts, such as enhancing insecticide resistance, facilitating food digestion, promoting detoxification, and regulating mating behavior and egg hatching. It also addresses some possible pathways of gut bacteria symbiont regulation governed by external habitats, physiological conditions and immunity of the host insect. This review provides solid foundations for further studies on novel theories, new technologies and practical applications of symbiotic bacteria in insect guts. © 2024 Society of Chemical Industry.},
}

@article {pmid38879040,
year = {2024},
author = {Zhang, L and Vaccari, F and Bandini, F and Puglisi, E and Trevisan, M and Lucini, L},
title = {The short-term effect of microplastics in lettuce involves size- and dose-dependent coordinate shaping of root metabolome, exudation profile and rhizomicrobiome.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {174001},
doi = {10.1016/j.scitotenv.2024.174001},
pmid = {38879040},
issn = {1879-1026},
abstract = {Micro- and nano-plastics (MNPs) in the soil can impact the microbial diversity within rhizospheres and induce modifications in plants' morphological, physiological, and biochemical parameters. However, a significant knowledge gap still needs to be addressed regarding the specific effects of varying particle sizes and concentrations on the comprehensive interplay among soil dynamics, root exudation, and the overall plant system. In this sense, different omics techniques were employed to clarify the mechanisms of the action exerted by four different particle sizes of polyethylene plastics considering four different concentrations on the soil-roots exudates-plant system was studied using lettuce (Lactuca sativa L. var. capitata) as a model plant. The impact of MNPs was investigated using a multi-omics integrated approach, focusing on the tripartite interaction between the root metabolic process, exudation pattern, and rhizosphere microbial modulation. Our results showed that particle size and their concentrations significantly modulated the soil-roots exudates-plant system. Untargeted metabolomics highlighted that fatty acids, amino acids, and hormone biosynthesis pathways were significantly affected by MNPs. Additionally, they were associated with the reduction of rhizosphere bacterial α-diversity, following a size-dependent trend for specific taxa. The omics data integration highlighted a correlation between Pseudomonadata and Actinomycetota phyla and Bacillaceae family (Peribacillus simplex) and the exudation of flavonoids, phenolic acids, and lignans in lettuce exposed to increasing sizes of MNPs. This study provides a novel insight into the potential effects of different particle sizes and concentrations of MNPs on the soil-plant continuum, providing evidence about size- and concentration-dependent effects, suggesting the need for further investigation focused on medium- to long-term exposure.},
}

@article {pmid38864655,
year = {2024},
author = {McCaw, BA and Leonard, AM and Stevenson, TJ and Lancaster, LT},
title = {A role of epigenetic mechanisms in regulating female reproductive responses to temperature in a pest beetle.},
journal = {Insect molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/imb.12933},
pmid = {38864655},
issn = {1365-2583},
support = {BB/M010996/1//UKRI Biotechnology and Biological Sciences Research Council (BBSRC)/ ; //University of Aberdeen/ ; },
abstract = {Many species are threatened by climate change and must rapidly respond to survive in changing environments. Epigenetic modifications, such as DNA methylation, can facilitate plastic responses by regulating gene expression in response to environmental cues. Understanding epigenetic responses is therefore essential for predicting species' ability to rapidly adapt in the context of global environmental change. Here, we investigated the functional significance of different methylation-associated cellular processes on temperature-dependent life history in seed beetles, Callosobruchus maculatus Fabricius 1775 (Coleoptera: Bruchidae). We assessed changes under thermal stress in (1) DNA methyltransferase (Dnmt1 and Dnmt2) expression levels, (2) genome-wide methylation and (3) reproductive performance, with (2) and (3) following treatment with 3-aminobenzamide (3AB) and zebularine (Zeb) over two generations. These drugs are well-documented to alter DNA methylation across the tree of life. We found that Dnmt1 and Dnmt2 were expressed throughout the body in males and females, but were highly expressed in females compared with males and exhibited temperature dependence. However, whole-genome methylation did not significantly vary with temperature, and only marginally or inconclusively with drug treatment. Both 3AB and Zeb led to profound temperature-dependent shifts in female reproductive life history trade-off allocation, often increasing fitness compared with control beetles. Mismatch between magnitude of treatment effects on DNA methylation versus life history effects suggest potential of 3AB and Zeb to alter reproductive trade-offs via changes in DNA repair and recycling processes, rather than or in addition to (subtle) changes in DNA methylation. Together, our results suggest that epigenetic mechanisms relating to Dnmt expression, DNA repair and recycling pathways, and possibly DNA methylation, are strongly implicated in modulating insect life history trade-offs in response to temperature change.},
}

@article {pmid38858806,
year = {2024},
author = {Brüssow, F and Bruessow, F and Brüssow, H},
title = {The role of the plant microbiome for forestry, agriculture and urban greenspace in times of environmental change.},
journal = {Microbial biotechnology},
volume = {17},
number = {6},
pages = {e14482},
doi = {10.1111/1751-7915.14482},
pmid = {38858806},
issn = {1751-7915},
abstract = {This Lilliput article provides a literature overview on ecological effects of the plant microbiome with a focus on practical application in forestry, agriculture and urban greenspace under the spectre of climate change. After an overview of the mostly bacterial microbiome of the model plant Arabidopsis thaliana, worldwide data from forests reveal ecological differentiation with respect to major guilds of predominantly fungal plant root symbionts. The plant-microbiome association forms a new holobiont, an integrated unit for ecological adaptation and evolutionary selection. Researchers explored the impact of the microbiome on the capacity of plants to adapt to changing climate conditions. They investigated the impact of the microbiome in reforestation programs, after wildfire, drought, salination and pollution events in forestry, grasslands and agriculture. With increasing temperatures plant populations migrate to higher latitudes and higher altitudes. Ecological studies compared the dispersal capacity of plant seeds with that of soil microbes and the response of soil and root microbes to experimental heating of soils. These studies described a succession of microbiome associations and the kinetics of a release of stored soil carbon into the atmosphere enhancing global warming. Scientists explored the impact of synthetic microbial communities (SynComs) on rice productivity or tea quality; of whole soil addition in grassland restoration; or single fungal inoculation in maize fields. Meta-analyses of fungal inoculation showed overall a positive effect, but also a wide variation in effect sizes. Climate change will be particularly prominent in urban areas ("urban heat islands") where more than half of the world population is living. Urban landscape architecture will thus have an important impact on human health and studies started to explore the contribution of the microbiome from urban greenspace to ecosystem services.},
}

@article {pmid38857541,
year = {2024},
author = {Spooren, J and van Bentum, S and Thomashow, LS and Pieterse, CMJ and Weller, DM and Berendsen, RL},
title = {Plant-Driven Assembly of Disease-Suppressive Soil Microbiomes.},
journal = {Annual review of phytopathology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-phyto-021622-100127},
pmid = {38857541},
issn = {1545-2107},
abstract = {Plants have coevolved together with the microbes that surround them and this assemblage of host and microbes functions as a discrete ecological unit called a holobiont. This review outlines plant-driven assembly of disease-suppressive microbiomes. Plants are colonized by microbes from seed, soil, and air but selectively shape the microbiome with root exudates, creating microenvironment hot spots where microbes thrive. Using plant immunity for gatekeeping and surveillance, host-plant genetic properties govern microbiome assembly and can confer adaptive advantages to the holobiont. These advantages manifest in disease-suppressive soils, where buildup of specific microbes inhibits the causal agent of disease, that typically develop after an initial disease outbreak. Based on disease-suppressive soils such as take-all decline, we developed a conceptual model of how plants in response to pathogen attack cry for help and recruit plant-protective microbes that confer increased resistance. Thereby, plants create a soilborne legacy that protects subsequent generations and forms disease-suppressive soils.},
}

@article {pmid38851755,
year = {2024},
author = {Paix, B and van der Valk, E and de Voogd, NJ},
title = {Dynamics, diversity, and roles of bacterial transmission modes during the first asexual life stages of the freshwater sponge Spongilla lacustris.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {37},
pmid = {38851755},
issn = {2524-6372},
support = {16.161.301//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; },
abstract = {BACKGROUND: Sponge-associated bacteria play important roles in the physiology of their host, whose recruitment processes are crucial to maintain symbiotic associations. However, the acquisition of bacterial communities within freshwater sponges is still under explored. Spongilla lacustris is a model sponge widely distributed in European rivers and lakes, producing dormant cysts (named gemmules) for their asexual reproduction, before winter. Through an in vitro experiment, this study aims to describe the dynamics of bacterial communities and their transmission modes following the hatching of these gemmules.

RESULTS: An overall change of bacterial β-diversity was observed through the ontology of the juvenile sponges. These temporal differences were potentially linked, first to the osculum acquisition and the development of a canal system, and then, the increasing colonization of the Chlorella-like photosymbionts. Gemmules hatching with a sterilized surface were found to have a more dispersed and less diverse microbiome, revealing the importance of gemmule epibacteria for the whole holobiont stability. These epibacteria were suggested to be vertically transmitted from the maternal tissues to the gemmule surface. Vertical transmission through the incorporation of bacterial communities inside of the gemmule, was also found as a dominant transmission mode, especially with the nitrogen fixers Terasakiellaceae. Finally, we showed that almost no ASVs were shared between the free-living community and the juveniles, suggesting that horizontal recruitment is unlikely to happen during the first stages of development. However, the free-living bacteria filtered are probably used as a source of nutrients, allowing an enrichment of copiotrophic bacteria already present within its microbiome.

CONCLUSIONS: This study brings new insight for a better understanding of the microbiome acquisition during the first stages of freshwater sponge development. We showed the importance of epibacterial communities on gemmules for the whole holobiont stability, and demonstrated the near absence of recruitment of free-living bacteria during the first stages.},
}

@article {pmid38846022,
year = {2024},
author = {Yakovleva, E and Danilova, I and Maximova, I and Shabaev, A and Dmitrieva, A and Belov, A and Klyukina, A and Perfilieva, K and Bonch-Osmolovskaya, E and Markov, A},
title = {Salt concentration in substrate modulates the composition of bacterial and yeast microbiomes of Drosophila melanogaster.},
journal = {Microbiome research reports},
volume = {3},
number = {2},
pages = {19},
pmid = {38846022},
issn = {2771-5965},
abstract = {Aim: Microbiomes influence the physiology and behavior of multicellular organisms and contribute to their adaptation to changing environmental conditions. However, yeast and bacterial microbiota have usually been studied separately; therefore, the interaction between bacterial and yeast communities in the gut of Drosophila melanogaster (D. melanogaster) is often overlooked. In this study, we investigate the correlation between bacterial and yeast communities in the gut of D. melanogaster. Methods: We studied the shifts in the joint microbiome of Drosophila melanogaster, encompassing both yeasts and bacteria, during adaptation to substrate with varying salt concentrations (0%, 2%, 4%, and 7%) using plating for both yeasts and bacteria and NGS-sequencing of variable 16S rRNA gene regions for bacteria. Results: The microbiome of flies and their substrates was gradually altered at moderate NaCl concentrations (2% and 4% compared with the 0% control) and completely transformed at high salt concentrations (7%). The relative abundance of Acetobacter, potentially beneficial to D. melanogaster, decreased as NaCl concentration increased, whereas the relative abundance of the more halotolerant lactobacilli first increased, peaking at 4% NaCl, and then declined dramatically at 7%. At this salinity level, potentially pathogenic bacteria of the genera Leuconostoc and Providencia were dominant. The yeast microbiome of D. melanogaster also undergoes significant changes with an increase in salt concentration in the substrate. The total yeast abundance undergoes nonlinear changes: it is lowest at 0% salt concentration and highest at 2%-4%. At a 7% concentration, the yeast abundance in flies and their substrate is lower than at 2%-4% but significantly higher than at 0%. Conclusions: The abundance and diversity of bacteria that are potentially beneficial to the flies decreased, while the proportion of potential pathogens, Leuconostoc and Providencia, increased with an increase in salt concentration in the substrate. In samples with a relatively high abundance and/or diversity of yeasts, the corresponding indicators for bacteria were often lowered, and vice versa. This may be due to the greater halotolerance of yeasts compared to bacteria and may also indicate antagonism between these groups of microorganisms.},
}

@article {pmid38839511,
year = {2024},
author = {Pepke, ML and Hansen, SB and Limborg, MT},
title = {Unraveling host regulation of gut microbiota through the epigenome-microbiome axis.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2024.05.006},
pmid = {38839511},
issn = {1878-4380},
abstract = {Recent studies of dynamic interactions between epigenetic modifications of a host organism and the composition or activity of its associated gut microbiota suggest an opportunity for the host to shape its microbiome through epigenetic alterations that lead to changes in gene expression and noncoding RNA activity. We use insights from microbiota-induced epigenetic changes to review the potential of the host to epigenetically regulate its gut microbiome, from which a bidirectional 'epigenome-microbiome axis' emerges. This axis embeds environmentally induced variation, which may influence the adaptive evolution of host-microbe interactions. We furthermore present our perspective on how the epigenome-microbiome axis can be understood and investigated within a holo-omic framework with potential applications in the applied health and food sciences.},
}

@article {pmid38830414,
year = {2024},
author = {Koll, R and Theilen, J and Hauten, E and Woodhouse, JN and Thiel, R and Möllmann, C and Fabrizius, A},
title = {Network-based integration of omics, physiological and environmental data in real-world Elbe estuarine Zander.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {173656},
doi = {10.1016/j.scitotenv.2024.173656},
pmid = {38830414},
issn = {1879-1026},
abstract = {Coastal and estuarine environments are under endogenic and exogenic pressures jeopardizing survival and diversity of inhabiting biota. Information of possible synergistic effects of multiple (a)biotic stressors and holobiont interaction are largely missing in estuaries like the Elbe but are of importance to estimate unforeseen effects on animals' physiology. Here, we seek to leverage host-transcriptional RNA-seq and gill mucus microbial 16S rRNA metabarcoding data coupled with physiological and abiotic measurements in a network analysis approach to decipher the impact of multiple stressors on the health of juvenile Sander lucioperca along one of the largest European estuaries. We find mesohaline areas characterized by gill tissue specific transcriptional responses matching osmosensing and tissue remodeling. Liver transcriptomes instead emphasized that zander from highly turbid areas were undergoing starvation which was supported by compromised body condition. Potential pathogenic bacteria, including Shewanella, Acinetobacter, Aeromonas and Chryseobacterium, dominated the gill microbiome along the freshwater transition and oxygen minimum zone. Their occurrence coincided with a strong adaptive and innate transcriptional immune response in host gill and enhanced energy demand in liver tissue supporting their potential pathogenicity. Taken together, we show physiological responses of a fish species and its microbiome to abiotic factors whose impact is expected to increase with consequences of climate change. We further present a method for the close-meshed detection of the main stressors and bacterial species with disease potential in a highly productive ecosystem.},
}

@article {pmid38825980,
year = {2024},
author = {Hernández, M and Ancona, S and Hereira-Pacheco, S and Díaz de la Vega-Pérez, AH and Alberdi, A and Navarro-Noya, YE},
title = {Seasonal dietary changes relate to gut microbiota composition depending on the host species but do not correlate with gut microbiota diversity in arthropod-eating lizards.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17426},
doi = {10.1111/mec.17426},
pmid = {38825980},
issn = {1365-294X},
support = {205945//Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCYT)/ ; 883//Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCYT)/ ; 967648//Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCYT)/ ; CF-2019-137748//Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCYT)/ ; },
abstract = {The animal gut microbiota is strongly influenced by environmental factors that shape their temporal dynamics. Although diet is recognized as a major driver of gut microbiota variation, dietary patterns have seldom been linked to gut microbiota dynamics in wild animals. Here, we analysed the gut microbiota variation between dry and rainy seasons across four Sceloporus species (S. aeneus, S. bicanthalis, S. grammicus and S. spinosus) from central Mexico in light of temporal changes in diet composition. The lizard microbiota was dominated by Firmicutes (now Bacillota) and Bacteroidota, and the closely related species S. aeneus and S. bicanthalis shared a great number of core bacterial taxa. We report species-specific seasonal changes in gut microbiota diversity and composition: greater alpha diversity during the dry compared to the rainy season in S. bicanthalis, the opposite pattern in S. aeneus, and no seasonal differences in S. grammicus and S. spinosus. Our findings indicated a positive association between gut bacterial composition and dietary composition for S. bicanthalis and S. grammicus, but bacterial diversity did not increase linearly with dietary richness in any lizard species. In addition, seasonality affected bacterial composition, and microbial community similarity increased between S. aeneus and S. bicanthalis, as well as between S. grammicus and S. spinosus. Together, our results illustrate that seasonal variation and dietary composition play a role in shaping gut microbiota in lizard populations, but this is not a rule and other ecological factors influence microbiota variation.},
}

@article {pmid38825966,
year = {2024},
author = {Herlemann, DPR and Tammert, H and Kivistik, C and Käiro, K and Kisand, V},
title = {Distinct biogeographical patterns in snail gastrointestinal tract bacterial communities compared with sediment and water.},
journal = {MicrobiologyOpen},
volume = {13},
number = {3},
pages = {e13},
doi = {10.1002/mbo3.1413},
pmid = {38825966},
issn = {2045-8827},
support = {MOBTT24//Eesti Teadusagentuur/ ; PUT1389//Eesti Teadusagentuur/ ; Leibniz Institute for Baltic Sea Research Warnemü//Leibniz-Institut für Ostseeforschung Warnemünde/ ; Shallow Water Processes and Transitions//Leibniz-Institut für Ostseeforschung Warnemünde/ ; MOBTT24//European Regional Development Fund/ ; P190250PKKH//Eesti Maaülikool/ ; P200028PKKH//Eesti Maaülikool/ ; },
mesh = {*Geologic Sediments/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Tract/microbiology ; Animals ; *Snails/microbiology ; Germany ; Denmark ; Gastrointestinal Microbiome/genetics ; Water Microbiology ; Biodiversity ; Estonia ; Phylogeny ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; },
abstract = {The factors that influence the distribution of bacterial community composition are not well understood. The role of geographical patterns, which suggest limited dispersal, is still a topic of debate. Bacteria associated with hosts face unique dispersal challenges as they often rely on their hosts, which provide specific environments for their symbionts. In this study, we examined the effect of biogeographic distances on the bacterial diversity and composition of bacterial communities in the gastrointestinal tract of Ampullaceana balthica. We compared the effects on the host-associated bacterial community to those on bacterial communities in water and sediment. This comparison was made using 16S ribosomal RNA gene sequencing. We found that the bacterial communities we sampled in Estonia, Denmark, and Northern Germany varied between water, sediment, and the gastrointestinal tract. They also varied between countries within each substrate. This indicates that the type of substrate is a dominant factor in determining bacterial community composition. We separately analyzed the turnover rates of water, sediment, and gastrointestinal bacterial communities over increasing geographic distances. We observed that the turnover rate was lower for gastrointestinal bacterial communities compared to water bacterial communities. This implies that the composition of gastrointestinal bacteria remains relatively stable over distances, while water bacterial communities exhibit greater variability. However, the gastrointestinal tract had the lowest percentage of country-specific amplicon sequence variants, suggesting bacterial colonization from local bacterial communities. Since the overlap between the water and gastrointestinal tract was highest, it appears that the gastrointestinal bacterial community is colonized by the water bacterial community. Our study confirmed that biogeographical patterns in host-associated communities differ from those in water and sediment bacterial communities. These host-associated communities consist of numerous facultative symbionts derived from the water bacterial community.},
}

*Geologic Sediments/microbiology
*Bacteria/classification/genetics/isolation & purification
*RNA, Ribosomal, 16S/genetics
*Gastrointestinal Tract/microbiology
Animals
*Snails/microbiology
Germany
Denmark
Gastrointestinal Microbiome/genetics
Water Microbiology
Biodiversity
Estonia
Phylogeny
DNA, Bacterial/genetics
Sequence Analysis, DNA

@article {pmid38821056,
year = {2024},
author = {Swisa, A and Kieckhaefer, J and Daniel, SG and El-Mekkoussi, H and Kolev, HM and Tigue, M and Jin, C and Assenmacher, CA and Dohnalová, L and Thaiss, CA and Karlsson, NG and Bittinger, K and Kaestner, KH},
title = {The evolutionarily ancient FOXA transcription factors shape the murine gut microbiome via control of epithelial glycosylation.},
journal = {Developmental cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.devcel.2024.05.006},
pmid = {38821056},
issn = {1878-1551},
abstract = {Evolutionary adaptation of multicellular organisms to a closed gut created an internal microbiome differing from that of the environment. Although the composition of the gut microbiome is impacted by diet and disease state, we hypothesized that vertebrates promote colonization by commensal bacteria through shaping of the apical surface of the intestinal epithelium. Here, we determine that the evolutionarily ancient FOXA transcription factors control the composition of the gut microbiome by establishing favorable glycosylation on the colonic epithelial surface. FOXA proteins bind to regulatory elements of a network of glycosylation enzymes, which become deregulated when Foxa1 and Foxa2 are deleted from the intestinal epithelium. As a direct consequence, microbial composition shifts dramatically, and spontaneous inflammatory bowel disease ensues. Microbiome dysbiosis was quickly reversed upon fecal transplant into wild-type mice, establishing a dominant role for the host epithelium, in part mediated by FOXA factors, in controlling symbiosis in the vertebrate holobiont.},
}