Genetic Capacities Research Articles

The North Pacific Eukaryotic Gene Catalog of metatranscriptome assemblies and annotations

Marine microbial eukaryotes (protists) perform essential metabolic functions in oceanic ecosystems. The diversity of protist functions remains poorly understood as few species have been isolated in laboratory settings. Metatranscriptomes provide an invaluable tool for exploring protist diversity and genetic capacities within their natural habitats. Here, we introduce the North Pacific Eukaryotic Gene Catalog, a compilation of metatranscriptome data derived from a total of 261 metatranscriptomes: 169 metatranscriptomes were derived from samples collected on three meridional surface transects along 158°W, each spanning ~20 degrees of latitude from the North Pacific Subtropical Gyre (NPSG) to the North Pacific Transition Zone (NPTZ); 92 metatranscriptomes were derived from two diel-resolved field studies, one in the NPSG at 157°W, 23°N, one in the NPTZ at 158°W, 41°N. The metatranscriptome sequences were de novo assembled into 175 assemblies and pooled into five datasets each containing between 22 M and 49 M contigs clustered at 99% protein identity. Assemblies were annotated by taxonomy and function, and enumerated by short read alignment. All data are available in the Zenodo repository, with underlying code available on github.

Is it time for a precision health approach to the management of newborn hyperbilirubinemia?

Newborn hyperbilirubinemia during the first two weeks of lifeis one of most common problems requiring management decisions by a pediatrician. However, high bilirubin levels in the circulation have been associated with neurologic injury under a variety of conditions encountered in the newborn infant, such as hemolysis. The risk for developing dangerous hyperbilirubinemia is multifactorial and is determined by a complex set of factors related to a newborn infant's genetic capacities as well as intra- and extrauterine exposures. To this end, a precision health approach based on the integration of prenatal genetic and postnatal diagnostic measures might improve the management of neonatal hyperbilirubinemia.

From Depths to Discoveries: Unraveling the Potential of Marine Biotechnology

With the oceans covering over 70% of our world, there is a lot of unrealized potential there. There is a wealth of marine life in these depths that presents a variety of opportunities for biotechnology. The most recent developments in marine biotechnology are helping us discover the mysteries of nature and are revolutionizing the fields of industry, sustainability, and healthcare to meet the challenges of the 21st century. Deep sea exploration has revealed a secret world full of many life forms, each of which may contain one or more special bioactive chemicals. Microalgae such as Chlorella and Spirulina offer a rich repository of bioactive compounds, from anti-inflammatory agents to proteins, enriching pharmaceuticals, cosmetics, and nutritional supplements. Actinobacteria, notably Streptomyces, contribute significantly to antibiotic compounds critical in combating infections [1]. Marine-based food products are enhanced by fatty acids from marine sources, especially omega-3 and omega-6 fatty acids, which are found in fish and algae and provide special health benefits not available in land-based sources. Furthermore, because of their extraordinary qualities and capacity to withstand harsh environments, enzymes derived from marine creatures are indispensable in the food processing industry. While corals, sponges, and invertebrates boast bioactive substances, their practical use in industry and health care faces challenges due to sustainability concerns [2]. Although accessing deep waters can be challenging, innovative technology such as remotely operated vehicles, facilitates the collecting of samples. The complexity of analyzing and categorizing marine bacteria affects the development of new drugs. Weekly, thousands of possible bioactive compounds are tested using high-throughput approaches to overcome the limitations of traditional screening. Novel strategies that combine bioinformatics and enhanced screening work well to identify bioactive compounds obtained from marine sources. Drug development appears to be promising as genomics and metagenomics reveal genetic capacities and find bioactive components from previously uncultivable microbes [3]. The fusion of biology, technology, and the boundless oceans sparks unparalleled opportunities. It urges collaboration among researchers, policymakers, and industries to explore the sea's potential responsibly. Exploring the ocean's depths reveals scientific marvels but also provides the answer to a healthier and more sustainable future for coming generations.

Readiness for Parkinson’s disease genetic testing and counseling in patients and their relatives in urban settings in the Dominican Republic

Genetic testing for Parkinson’s disease (PD) is increasing globally, and genetic counseling is an important service that provides information and promotes understanding about PD genetics and genetic testing. PD research studies have initiated outreach to underrepresented regions in North America, including regions in Latin America, such as the Dominican Republic (DR); some studies may include return of genetic test results. Thus, understanding what individuals know about PD, genetic testing for PD, and their interest in speaking with a genetic counselor, is crucial when assessing readiness. In this cross-sectional study, a survey was distributed to people with Parkinson’s disease (PwP) and their unaffected biological relatives in the DR. Questions assessed genetics knowledge, attitude toward genetic testing, and interest in genetic testing and counseling. Of 45 participants, 69% scored the maximum on the attitude scale, indicating an overall positive attitude toward genetic testing; 95% indicated interest in genetic testing for PD, and 98% were at least somewhat interested in meeting with a genetic counselor. The mean PD genetics knowledge score was similar to previously published data. Through free text responses, participants expressed a desire to know more about PD treatment and management, prevention, cause, and their personal risk for PD. These results provide further evidence of readiness for genetic testing in this country but also underscore some gaps in knowledge that should be addressed with targeted educational efforts, as part of building genetic testing and counseling capacities.

Metagenomic insights into genetic factors driving bacterial niche differentiation between bulk and rhizosphere soils

Cellular motility is crucial for effective colonization of the rhizosphere, but it is not yet clear whether bacterial motility is particularly linked to other genetic traits. Here, we applied genome-resolved metagenomics and phylogenomics to investigate the ecological significance of cellular motility for niche differentiation and the links between the genetic makeup of motile bacteria and rhizosphere colonization within a four-decade maize field experiment. Indeed, highly diverse sets of genes encoding cellular motility, including chemotaxis, flagellar assembly and motility proteins, and utilization of polymeric carbon were the important predictors of bacterial niche differentiation between bulk and rhizosphere soils. This is well exemplified by metagenome-assembled genomes encoding high motility capacity (hmc_MAGs). Their collective abundance was, on average, sixfold higher in rhizosphere soil than in bulk soil. All bulk-soil-derived MAGs showed low motility capacities (lmc). The hmc_MAGs were highly enriched in beneficial traits involved in carbohydrate utilization, assimilatory (nasA) and dissimilatory (nirBD) nitrate reduction, inorganic phosphate solubilization (gcd), and organic phosphate mineralization (phoD). Belonging to the families Sphingomonadaceae, Burkholderiaceae and Steroidobacteraceae, the hmc_MAGs showed a ninefold greater enrichment in these traits than proteobacterial lmc_MAGs and a twofold greater enrichment than 264 genomes publicly available for the above three families, thereby substantiating that a specific rhizosphere effect acted on the microbes represented by the hmc_MAGs. The particular link between the genetic capacities for high cellular motility and increased carbohydrate depolymerization as the key determinant for plant-selected rhizosphere colonization was further substantiated by the analysis of public bulk-rhizosphere soil metagenomes retrieved from wheat and cucumber field sites.

Gene Editing Technologies, Utopianism, and Disability Politics

Scholars have long speculated about what a future affected by gene editing technologies might hold. This article enters current debates over the future of gene editing and the place of disability within it. Specifically, I evaluate contemporary utopian thinking about gene editing found in two different schools of thought: transhumanism and critical disability studies, ultimately judging the latter to be richer and more politically promising than the former. If we take it as our goal to protect and promote future people’s autonomy interests, I argue that current political efforts should be directed toward modifying ableist environments rather than employing genetic technologies to avoid disability or enhance capacity. The article concludes by drawing from disability justice scholarship to make the case that the “right to an open future” should be understood as the “right to an accessible future,” one wherein society is “open” to people with diverse genetic traits and capacities.

Detecting Natural Wolbachia Infection and Supergroup Identification of Metochus uniguttatus in North India

Introduction: Insect endosymbionts have a crucial evolutionary and ecological role. Insects, particularly arthropods, have evolved to tolerate a wide range of endosymbionts that provide them with external biochemical, genetic, and reproductive capacities that improve their fitness. Wolbachia is a widely prevalent bacterial endosymbiont that is gaining popularity in insect research due to its utility in pest and vector management. Although India has a diverse insect population, little research has been undertaken on insect-microbe interactions. Therefore, This study aimed to ascertain the spread of Wolbachia in a randomly sampled set of insects, identify any novel Wolbachia infections, and determine the Wolbachia infection’s supergroup. Materials and methods: Field capture of insects was carried out manually with netting and gloves, and the insects were immediately stored in absolute ethanol to immobilize them. Phenol-chloroform-isoamyl alcohol was the method used to extract the insect DNA. Insect species identification was carried out via the CO1 mitochondrial gene using PCR amplification. PCR was utilized to identify the presence of Wolbachia, and 16S Wspec DNA was amplified to confirm its presence. The Sanger method was used to sequence the amplified CO1 and the positive samples for Wspec. Using NCBI blast, the sequences of the infected insects were compared with the database sequences. The obtained FASTAs were then aligned using Sequencher 5.4.6, and the chromatograms were examined to ensure contig quality and similarity. Results: Among the 21 insects screened, one was found weakly positive (Playpleura octoguttata) and two were strongly positive (Metochus uniguttatus and Velarifictorus micado) with Wolbachia, which represented an infection rate of 14.29%. Although the individual infection rate in this limited sample size falls at the lower end compared to extensive surveys reporting rates between 20% and 76%. This study indicated the dissemination of Wolbachia in randomly screened insects. Moreover, this is one of the first records of Metochus uniguttatus being infected with Wolbachia in North India. Conclusion: This study represents an initial exploration of insects not previously considered hosts of the Wolbachia endosymbiont. The results could be useful for future studies on insect biocontrol and pest management.

A case for genomic medicine in South African paediatric patients with neuromuscular disease.

Paediatric neuromuscular diseases are under-recognised and under-diagnosed in Africa, especially those of genetic origin. This may be attributable to various factors, inclusive of socioeconomic barriers, high burden of communicable and non-communicable diseases, resource constraints, lack of expertise in specialised fields and paucity of genetic testing facilities and biobanks in the African population, making access to and interpretation of results more challenging. As new treatments become available that are effective for specific sub-phenotypes, it is even more important to confirm a genetic diagnosis for affected children to be eligible for drug trials and potential treatments. This perspective article aims to create awareness of the major neuromuscular diseases clinically diagnosed in the South African paediatric populations, as well as the current challenges and possible solutions. With this in mind, we introduce a multi-centred research platform (ICGNMD), which aims to address the limited knowledge on NMD aetiology and to improve genetic diagnostic capacities in South African and other African populations.

The 3P Framework: A Comprehensive Approach to Coping with the Emerging Infectious Disease Crisis

The COVID-19 pandemic is the latest example of the profound socioeconomic impact of the emerging infectious disease (EID) crisis. Current health security measures are based on a failed evolutionary paradigm that presumes EID is rare and cannot be predicted because emergence requires the prior evolution of novel genetic capacities for colonizing a new host. Consequently, crisis response through preparation for previously emerged diseases and palliation following outbreaks have been the only health security options, which have become unsustainably expensive and unsuccessful. The Stockholm paradigm (SP) is an alternative evolutionary framework that suggests host changes are the result of changing conditions that bring pathogens into contact with susceptible hosts, with novel genetic variants arising in the new host after infection. Host changes leading to EID can be predicted because preexisting capacities for colonizing new hosts are highly specific and phylogenetically conservative. This makes EID prevention through limiting exposure to susceptible hosts possible. The DAMA (Document, Assess, Monitor, Act) protocol is a policy extension of the SP that can both prevent and mitigate EID by enhancing traditional efforts through adding early warning signs and predicting transmission dynamics. Prevention, preparation, and palliation compose the 3P framework, a comprehensive plan for reducing the socioeconomic impact of EID.

Landscape of germline cancer predisposition mutations testing and management in pediatrics: Implications for research and clinical care.

As germline genetic testing capacities have improved over the last two decades, increasingly more people are newly diagnosed with germline cancer susceptibility mutations. In the wake of this growth, there remain limitations in both testing strategies and translation of these results into morbidity- and mortality-reducing practices, with pediatric populations remaining especially vulnerable. To face the challenges evoked by an expanding diversity of germline cancer mutations, we can draw upon a model cancer-associated genetic condition for which we have developed a breadth of expertise in managing, Trisomy 21. We can additionally apply advances in other disciplines, such as oncofertility and pharmacogenomics, to enhance care delivery. Herein, we describe the history of germline mutation testing, epidemiology of known germline cancer mutations and their associations with childhood cancer, testing limitations, and future directions for research and clinical care.

Alterations of gut microbial pathways and virulence factors in hemodialysis patients.

Alterations in gut microbiota might contribute to uremic toxicity and immune dysregulation in patients with end-stage renal disease. Hemodialysis patients are prone to infection and higher mortality following sepsis. The virulence factors in the gut metagenome have not been well studied in hemodialysis patients, which could be employed by microorganisms to successfully thrive and flourish in their hosts. In this study, we performed shotgun metagenomics sequencing on fecal DNA collected from 16 control subjects and 24 hemodialysis patients. Our analysis shows that a number of microbial species, metabolic pathways, antibiotic resistance, and virulence factors were significantly altered in hemodialysis patients compared with controls. In particular, erythromycin resistance methylase, pyridoxamine 5-phosphate oxidase, and streptothricin-acetyl-transferase were significantly increased in hemodialysis patients. The findings in our study laid a valuable foundation to further elucidate the causative role of virulence factors in predisposing HD patients to infection and to develop treatment strategies to reduce the genetic capacities of antibiotic resistance and virulence factors in HD patients.

Prospects for the peat using as the basis of the soil-like substrate in mini-ecosystems modelling

Global urbanization is causing a constant decline in arable land as cities and associated industrial zones are “attacking” adjacent agricultural areas. One of the promising ways to solve the problem of increasing food production for the constantly growing population of the planet against the background of rapidly decreasing land resources is the development of fundamentally new alternative methods for the production of crop products, including in greenhouses. The fundamental basis for technological optimization of plant cultivation parameters and the output of the productive process of a particular crop to the maximum of its genetic capacities can be the development of artificial mini-ecosystems based on the reproduction of nature-like processes, implying the balance and combination in one volume of the processes of plant production and reduction of organic waste, initiated directly in the zone of the rhizosphere of plants due to the introduction of technological earthworms into the reduction zone. According to the results of model studies presented in this article, peat is an acceptable basis for the substrate of the root block of a mini-ecosystem, and the introduction of earthworms Eisenia fetida Sav. into the reduction zone does not have a negative effect on lettuce plants, provided that it is used as an energy substrate for cattle manure worms in quantities not exceeding 10 - 20% of the total volume of the substrate.

Functional and Genomic Analysis of Rouxiella badensis SER3 as a Novel Biocontrol Agent of Fungal Pathogens.

In recent decades, various bacterial species have been characterized as biocontrol agents for plant crop diseases; however, only a few genera have been predominantly reported in the literature. Therefore, the identification of new antagonists against phytopathogens is essential for boosting sustainable food production systems. In this study, we evaluated the role of strain SER3 from the recently discovered Rouxiella badensis as a biocontrol agent. SER3 was isolated from the phyllosphere of decaying strawberry fruit (Fragaria × ananassa) and showed different grades of antagonism against 20 fungal pathogens of berries, based on confrontation assays, due to the action of its diffusible and volatile compounds. These fungal pathogens were isolated from decayed strawberry, blackberry, and blueberry fruit and were characterized through internal transcribed spacer (ITS) sequencing and homology searches, exhibiting similarity with well-known postharvest pathogens such as Botrytis, Fusarium, Geotrichum, Mucor, Penicillium, Alternaria, and Botryosphaeria. Koch’s postulates were confirmed for most pathogens by reinfecting berry fruit. SER3 showed good capacity to inhibit the growth of Botrytis cinerea and Fusarium brachygibbosum in strawberry fruit, affecting mycelial development. To gain better understanding of the genetic and metabolic capacities of the SER3 strain, its draft genome was determined and was found to comprise a single chromosome of 5.08 Mb, 52.8% G + C content, and 4,545 protein-coding genes. Phylogenetic analysis indicated that the SER3 strain is affiliated with the R. badensis species, with an average nucleotide identity >96% and a genome-to-genome distance >70%. A comparison of the genomic properties of R. badensis SER3 and other close bacterial relatives showed several genes with potential functions in biocontrol activities, such as those encoding siderophores, non-ribosomal peptide synthetases, and polyketide synthases. This is the first study to demonstrate a novel role of the recently discovered R. badensis species (and any other species of the genus Rouxiella) as a biocontrol agent against postharvest fungal pathogens.

Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale

BackgroundBiogeochemical exports from watersheds are modulated by the activity of microorganisms that function over micron scales. Here, we tested the hypothesis that meander-bound regions share a core microbiome and exhibit patterns of metabolic potential that broadly predict biogeochemical processes in floodplain soils along a river corridor.ResultsWe intensively sampled the microbiomes of floodplain soils located in the upper, middle, and lower reaches of the East River, Colorado. Despite the very high microbial diversity and complexity of the soils, we reconstructed 248 quality draft genomes representative of subspecies. Approximately one third of these bacterial subspecies was detected across all three locations at similar abundance levels, and ~ 15% of species were detected in two consecutive years. Within the meander-bound floodplains, we did not detect systematic patterns of gene abundance based on sampling position relative to the river. However, across meanders, we identified a core floodplain microbiome that is enriched in capacities for aerobic respiration, aerobic CO oxidation, and thiosulfate oxidation with the formation of elemental sulfur. Given this, we conducted a transcriptomic analysis of the middle floodplain. In contrast to predictions made based on the prominence of gene inventories, the most highly transcribed genes were relatively rare amoCAB and nxrAB (for nitrification) genes, followed by genes involved in methanol and formate oxidation, and nitrogen and CO2 fixation. Within all three meanders, low soil organic carbon correlated with high activity of genes involved in methanol, formate, sulfide, hydrogen, and ammonia oxidation, nitrite oxidoreduction, and nitrate and nitrite reduction. Overall, the results emphasize the importance of sulfur, one-carbon and nitrogen compound metabolism in soils of the riparian corridor.ConclusionsThe disparity between the scale of a microbial cell and the scale of a watershed currently limits the development of genomically informed predictive models describing watershed biogeochemical function. Meander-bound floodplains appear to serve as scaling motifs that predict aggregate capacities for biogeochemical transformations, providing a foundation for incorporating riparian soil microbiomes in watershed models. Widely represented genetic capacities did not predict in situ activity at one time point, but rather they define a reservoir of biogeochemical potential available as conditions change.AU1kaDmL5ojSw8dBEKS2i-Video abstract

Tipping the Scales With Zebrafish to Understand Adaptive Tumor Immunity.

The future of improved immunotherapy against cancer depends on an in-depth understanding of the dynamic interactions between the immune system and tumors. Over the past two decades, the zebrafish has served as a valuable model system to provide fresh insights into both the development of the immune system and the etiologies of many different cancers. This well-established foundation of knowledge combined with the imaging and genetic capacities of the zebrafish provides a new frontier in cancer immunology research. In this review, we provide an overview of the development of the zebrafish immune system along with a side-by-side comparison of its human counterpart. We then introduce components of the adaptive immune system with a focus on their roles in the tumor microenvironment (TME) of teleosts. In addition, we summarize zebrafish models developed for the study of cancer and adaptive immunity along with other available tools and technology afforded by this experimental system. Finally, we discuss some recent research conducted using the zebrafish to investigate adaptive immune cell-tumor interactions. Without a doubt, the zebrafish will arise as one of the driving forces to help expand the knowledge of tumor immunity and facilitate the development of improved anti-cancer immunotherapy in the foreseeable future.

The adaptive potential of newborn calves under conditions of technogenic anthropobiocenosis

The article analyzes the organismal status that determines the adaptive potential of newborn calves to the conditions of technogenic anthropobiocenosis. A complex of zootechnical, clinical, hematological, morphological and statistical methods of research was used. Structural and functional changes in the fetal parts of the placentas of cows arise as a result of the aggressive impact on the mother's body of modern ecosystem conditions and determine the peculiarities of the body status of newborn calves. Determining the adaptive capabilities of one-day-old calves, including the morphology of their fetal part of the placenta, is of great importance not only for correcting the technology of growing and feeding, but also for carrying out preventive measures against infectious diseases. To create a healthy dairy herd of cows with a high degree of realization of the genetic capacities of productivity, we recommend using the developed criteria for assessing the body status of newborn calves. Keywords. Аdaptive potential, newborn calves, anthropobiocenosis, organismic status, fetal parts of the placenta.

Large-Scale Comparative Analyses of Tick Genomes Elucidate Their Genetic Diversity and Vector Capacities

Among arthropod vectors, ticks transmit the most diverse human and animal pathogens, leading to an increasing number of new challenges worldwide. Here we sequenced and assembled high-quality genomes of six ixodid tick species and further resequenced 678 tick specimens to understand three key aspects of ticks: genetic diversity, population structure, and pathogen distribution. We explored the genetic basis common to ticks, including heme and hemoglobin digestion, iron metabolism, and reactive oxygen species, and unveiled for the first time that genetic structure and pathogen composition in different tick species are mainly shaped by ecological and geographic factors. We further identified species-specific determinants associated with different host ranges, life cycles, and distributions. The findings of this study are an invaluable resource for research and control of ticks and tick-borne diseases.

Identification of Microbial Genetic Capacities and Potential Mechanisms Within the Rumen Microbiome Explaining Differences in Beef Cattle Feed Efficiency.

In this study, Bos Taurus cattle offered one high concentrate diet (92% concentrate-8% straw) during two independent trials allowed us to classify 72 animals comprising of two cattle breeds as “Low” or “High” feed efficiency groups. Digesta samples were taken from individual beef cattle at the abattoir. After metagenomic sequencing, the rumen microbiome composition and genes were determined. Applying a targeted approach based on current biological evidence, 27 genes associated with host-microbiome interaction activities were selected. Partial least square analysis enabled the identification of the most significant genes and genera of feed efficiency (VIP > 0.8) across years of the trial and breeds when comparing all potential genes or genera together. As a result, limited number of genes explained about 40% of the variability in both feed efficiency indicators. Combining information from rumen metagenome-assembled genomes and partial least square analysis results, microbial genera carrying these genes were determined and indicated that a limited number of important genera impacting on feed efficiency. In addition, potential mechanisms explaining significant difference between Low and High feed efficiency animals were analyzed considering, based on the literature, their gastrointestinal location of action. High feed efficiency animals were associated with microbial species including several Eubacterium having the genetic capacity to form biofilm or releasing metabolites like butyrate or propionate known to provide a greater contribution to cattle energy requirements compared to acetate. Populations associated with fucose sensing or hemolysin production, both mechanisms specifically described in the lower gut by activating the immune system to compete with pathogenic colonizers, were also identified to affect feed efficiency using rumen microbiome information. Microbial mechanisms associated with low feed efficiency animals involved potential pathogens within Proteobacteria and Spirochaetales, releasing less energetic substrates (e.g., acetate) or producing sialic acid to avoid the host immune system. Therefore, this study focusing on genes known to be involved in host-microbiome interaction improved the identification of rumen microbial genetic capacities and potential mechanisms significantly impacting on feed efficiency in beef cattle fed high concentrate diet.

Archaea, specific genetic traits, and development of improved bacterial live biotherapeutic products: another face of next-generation probiotics.

Trimethylamine (TMA) and its oxide TMAO are important biomolecules involved in disease-associated processes in humans (e.g., trimethylaminuria and cardiovascular diseases). TMAO in plasma (pTMAO) stems from intestinal TMA, which is formed from various components of the diet in a complex interplay between diet, gut microbiota, and the human host. Most approaches to prevent the occurrence of such deleterious molecules focus on actions to interfere with gut microbiota metabolism to limit the synthesis of TMA. Some human gut archaea however use TMA as terminal electron acceptor for producing methane, thus indicating that intestinal TMA does not accumulate in some human subjects. Therefore, a rational alternative approach is to eliminate neo-synthesized intestinal TMA. This can be achieved through bioremediation of TMA by these peculiar methanogenic archaea, either by stimulating or providing them, leading to a novel kind of next-generation probiotics referred to as archaebiotics. Finally, specific components which are involved in this archaeal metabolism could also be used as intestinal TMA sequesters, facilitating TMA excretion along with stool. Referring to a standard pharmacological approach, these TMA traps could be synthesized ex vivo and then delivered into the human gut. Another approach is the engineering of known probiotic strain in order to metabolize TMA, i.e., live engineered biotherapeutic products. These alternatives would require, however, to take into account the necessity of synthesizing the 22nd amino acid pyrrolysine, i.e., some specificities of the genetics of TMA-consuming archaea. Here, we present an overview of these different strategies and recent advances in the field that will sustain such biotechnological developments. KEY POINTS: • Some autochthonous human archaea can use TMA for their essential metabolism, a methyl-dependent hydrogenotrophic methanogenesis. • They could therefore be used as next-generation probiotics for preventing some human diseases, especially cardiovascular diseases and trimethylaminuria. • Their genetic capacities can also be used to design live recombinant biotherapeutic products. • Encoding of the 22nd amino acid pyrrolysine is necessary for such alternative developments.

Genomic changes associated with adaptation to arid environments in cactophilic Drosophila species

BackgroundInsights into the genetic capacities of species to adapt to future climate change can be gained by using comparative genomic and transcriptomic data to reconstruct the genetic changes associated with such adaptations in the past. Here we investigate the genetic changes associated with adaptation to arid environments, specifically climatic extremes and new cactus hosts, through such an analysis of five repleta group Drosophila species.ResultsWe find disproportionately high rates of gene gains in internal branches in the species’ phylogeny where cactus use and subsequently cactus specialisation and high heat and desiccation tolerance evolved. The terminal branch leading to the most heat and desiccation resistant species, Drosophila aldrichi, also shows disproportionately high rates of both gene gains and positive selection. Several Gene Ontology terms related to metabolism were enriched in gene gain events in lineages where cactus use was evolving, while some regulatory and developmental genes were strongly selected in the Drosophila aldrichi branch. Transcriptomic analysis of flies subjected to sublethal heat shocks showed many more downregulation responses to the stress in a heat sensitive versus heat resistant species, confirming the existence of widespread regulatory as well as structural changes in the species’ differing adaptations. Gene Ontology terms related to metabolism were enriched in the differentially expressed genes in the resistant species while terms related to stress response were over-represented in the sensitive one.ConclusionAdaptations to new cactus hosts and hot desiccating environments were associated with periods of accelerated evolutionary change in diverse biochemistries. The hundreds of genes involved suggest adaptations of this sort would be difficult to achieve in the timeframes projected for anthropogenic climate change.