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Altimiras, F., Garcia, J. A., Palacios-Garcia, I., Hurley, M. J., Deacon, R., Gonzalez, B., et al. (2021). Altered Gut Microbiota in a Fragile X Syndrome Mouse Model. Front. Neurosci., 15, 653120.
Abstract: The human gut microbiome is the ecosystem of microorganisms that live in the human digestive system. Several studies have related gut microbiome variants to metabolic, immune and nervous system disorders. Fragile X syndrome (FXS) is a neurodevelopmental disorder considered the most common cause of inherited intellectual disability and the leading monogenetic cause of autism. The role of the gut microbiome in FXS remains largely unexplored. Here, we report the results of a gut microbiome analysis using a FXS mouse model and 16S ribosomal RNA gene sequencing. We identified alterations in the fmr1 KO2 gut microbiome associated with different bacterial species, including those in the genera Akkermansia, Sutterella, Allobaculum, Bifidobacterium, Odoribacter, Turicibacter, Flexispira, Bacteroides, and Oscillospira. Several gut bacterial metabolic pathways were significantly altered in fmr1 KO2 mice, including menaquinone degradation, catechol degradation, vitamin B6 biosynthesis, fatty acid biosynthesis, and nucleotide metabolism. Several of these metabolic pathways, including catechol degradation, nucleotide metabolism and fatty acid biosynthesis, were previously reported to be altered in children and adults with autism. The present study reports a potential association of the gut microbiome with FXS, thereby opening new possibilities for exploring reliable treatments and non-invasive biomarkers.
Keywords: AKKERMANSIA-MUCINIPHILA; BRAIN; AUTISM; METABOLISM; ECOLOGY; HEALTH; BOWEL
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Narum, S. R., Di Genova, A., Micheletti, S. J., & Maass, A. (2018). Genomic variation underlying complex life-history traits revealed by genome sequencing in Chinook salmon. Proc. R. Soc. B-Biol. Sci., 285(1883), 9 pp.
Abstract: A broad portfolio of phenotypic diversity in natural organisms can buffer against exploitation and increase species persistence in disturbed ecosystems. The study of genomic variation that accounts for ecological and evolutionary adaptation can represent a powerful approach to extend understanding of phenotypic variation in nature. Here we present a chromosome-level reference genome assembly for Chinook salmon (Oncorhynchus tshawytscha; 2.36 Gb) that enabled association mapping of life-history variation and phenotypic traits for this species. Whole-genome re-sequencing of populations with distinct life-history traits provided evidence that divergent selection was extensive throughout the genome within and among phylogenetic lineages, indicating that a broad portfolio of phenotypic diversity exists in this species that is related to local adaptation and life-history variation. Association mapping with millions of genome-wide SNPs revealed that a genomic region of major effect on chromosome 28 was associated with phenotypes for premature and mature arrival to spawning grounds and was consistent across three distinct phylogenetic lineages. Our results demonstrate how genomic resources can enlighten the genetic basis of known phenotypes in exploited species and assist in clarifying phenotypic variation that may be difficult to observe in naturally occurring organisms.
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Orostica, M. H., Hawkins, S. J., Broitman, B. R., & Jenkins, S. R. (2021). Performance of a warm-water limpet species towards its poleward range edge compared to a colder-water congener. Mar. Ecol.-Prog. Ser., 656, 207–225.
Abstract: The demography and individual performance of species at their range edges provide important insight into how climate warming is impacting species distributions. The boreal limpet Patella vulgata and the Lusitanian limpet P. depressa have overlapping geographic ranges and local distributions in Britain. We measured individual performance at the 2 leading edges of P. depressa distribution (North Wales and South/South-east England) and in non-range edge populations in South-west England. Individuals of P. depressa towards both leading edges were expected to have reduced growth rates and higher mortality rates when compared with non-range edge populations. Conversely, P. vulgata was expected to have equivalent performance across regions, coinciding with the centre of its range. Tagged individuals did not show betweenspecies differences in growth and mortality over a 12 mo period. Nonetheless, individual growth rates and population mortality rates of both Patella species were higher towards the range edge of P. depressa in South/South-east England, when compared with populations at its poleward edge and those in South-west England. Further analysis showed that growth and mortality rates were higher in denser populations for both P. depressa and P. vulgata, with equivalent site-specific performance patterns for both species in all regions. Thus, performance patterns of P. depressa reflected local factors in the same way as P. vulgata, overriding patterns of declining performance expected towards species borders. Comparisons between key congeneric species and their unexpected patterns of performance across their ranges provide insights into processes setting species boundaries and thereby their responses to climate change.
Keywords: Climate change; Range edges; Leading edge; Intertidal ecology; Patella spp.
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Plominsky, A. M., Henriquez-Castillo, C., Delherbe, N., Podell, S., Ramirez-Flandes, S., Ugalde, J. A., et al. (2018). Distinctive Archaeal Composition of an Artisanal Crystallizer Pond and Functional Insights Into Salt-Saturated Hypersaline Environment Adaptation. Front. Microbiol., 9, 13 pp.
Abstract: Hypersaline environments represent some of the most challenging settings for life on Earth. Extremely halophilic microorganisms have been selected to colonize and thrive in these extreme environments by virtue of a broad spectrum of adaptations to counter high salinity and osmotic stress. Although there is substantial data on microbial taxonomic diversity in these challenging ecosystems and their primary osmoadaptation mechanisms, less is known about how hypersaline environments shape the genomes of microbial inhabitants at the functional level. In this study, we analyzed the microbial communities in five ponds along the discontinuous salinity gradient from brackish to salt-saturated environments and sequenced the metagenome of the salt (halite) precipitation pond in the artisanal Cahuil Solar Saltern system. We combined field measurements with spectrophotometric pigment analysis and flow cytometry to characterize the microbial ecology of the pond ecosystems, including primary producers and applied metagenomic sequencing for analysis of archaeal and bacterial taxonomic diversity of the salt crystallizer harvest pond. Comparative metagenomic analysis of the Cahuil salt crystallizer pond against microbial communities from other salt-saturated aquatic environments revealed a dominance of the archaeal genus Halorubrum and showed an unexpectedly low abundance of Haloquadratum in the Cahuil system. Functional comparison of 26 hypersaline microbial metagenomes revealed a high proportion of sequences associated with nucleotide excision repair, helicases, replication and restriction-methylation systems in all of them. Moreover, we found distinctive functional signatures between the microbial communities from salt-saturated (>30% [w/v] total salinity) compared to sub-saturated hypersaline environments mainly due to a higher representation of sequences related to replication, recombination and DNA repair in the former. The current study expands our understanding of the diversity and distribution of halophilic microbial populations inhabiting salt-saturated habitats and the functional attributes that sustain them.
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Ramirez-Flandes, S., Gonzalez, B., & Ulloa, O. (2019). Redox traits characterize the organization of global microbial communities. Proc. Natl. Acad. Sci. U. S. A., 116(9), 3630–3635.
Abstract: The structure of biological communities is conventionally described as profiles of taxonomic units, whose ecological functions are assumed to be known or, at least, predictable. In environmental microbiology, however, the functions of a majority of microorganisms are unknown and expected to be highly dynamic and collectively redundant, obscuring the link between taxonomic structure and ecosystem functioning. Although genetic trait-based approaches at the community level might overcome this problem, no obvious choice of gene categories can be identified as appropriate descriptive units in a general ecological context. We used 247 microbial metagenomes from 18 biomes to determine which set of genes better characterizes the differences among biomes on the global scale. We show that profiles of oxidoreductase genes support the highest biome differentiation compared with profiles of other categories of enzymes, general protein-coding genes, transporter genes, and taxonomic gene markers. Based on oxidoreductases' description of microbial communities, the role of energetics in differentiation and particular ecosystem function of different biomes become readily apparent. We also show that taxonomic diversity is decoupled from functional diversity, e. g., grasslands and rhizospheres were the most diverse biomes in oxidoreductases but not in taxonomy. Considering that microbes underpin biogeochemical processes and nutrient recycling through oxidoreductases, this functional diversity should be relevant for a better understanding of the stability and conservation of biomes. Consequently, this approach might help to quantify the impact of environmental stressors on microbial ecosystems in the context of the global-scale biome crisis that our planet currently faces.
Keywords: microbial ecology; functional traits; oxidoreductases; biomes; metagenomics
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