Phylogenetic Diversity Research Articles

Oral microbiome diversity and oral human papillomavirus-associated differences in Black vs. White individuals.

e18065 Background: Recent evidence suggests an association between oral microbiome diversity with oral HPV infection, the precursor of HPV-associated oropharyngeal cancer. There is significantly higher prevalence of HPV-associated oropharyngeal cancer in White (70.2%) than Black individuals (46.3%). Black individuals are significantly less likely to develop HPV-associated oropharyngeal cancer, which has better prognosis than HPV-negative disease. We examine racial differences in oral microbiome diversity to explore potential biological underpinnings for the racial differences seen in HPV-associated head and neck cancer. Methods: We analyzed differences in oral microbiome diversity in 3775 Black & White participants from the National Health and Nutrition Examination Study (NHANES) cycles 2009-2012. Oral rinse samples were 16S rRNA amplicon-sequenced (V4 region) and diversity metrics were calculated using QIIME1. Four alpha diversity measures, reflecting the richness and/or evenness of a single participant’s sample, were calculated: observed number of ASVs, Faith’s Phylogenetic Diversity, Shannon-Wiener index, and Inverse Simpson index. Three beta diversity measures, reflecting the dissimilarity between pairwise samples, were calculated: unweighted UniFrac, weighted UniFrac, and Bray-Curtis. A survey-weighted generalized linear model was fitted to assess associations between alpha diversity and combined self-reported race and oral HPV status. Principal coordinate analysis and permutational multivariate analysis of variance tested for differences in microbial community composition by combined race/HPV status. Results: Weighted medians of alpha diversity were significantly different by race and HPV status [Kruskal-Wallis: Observed ASVs (p<0.001); Faith’s Phylogenetic Diversity (p<0.001); Shannon-Wiener (p<0.001); Inverse Simpson (p=0.005)]. Black/HPV-positive participants exhibited significantly greater alpha diversity, for all four alpha diversity measures, compared to White HPV-negative participants (p < 0.01). Black/HPV-negative participants also showed significantly greater alpha diversity compared to White/HPV-negative participants (p < 0.01), but not for Inverse Simpson index. Significant differences in microbial community were identified by race and HPV status for Bray-Curtis (BC: R 2 =0.32%, SE R 2 =0.020%, p<0.001) and Unweighted UniFrac (R 2 =0.55%, SE R 2 =0.029%, p<0.001) distances, but not Weighted UniFrac (R 2 =0.26%, SE R 2 =0.017%, p=0.8). Conclusions: Microbial diversity differences by race and HPV status may contribute to racial differences in HPV-associated head and neck cancer. While the mechanism of these differences is unclear, microbial diversity represents a modifiable risk factor that could inform interventions to supplement or disrupt the microbiome.

Association between oral microbiome and depression: A population-based study.

Association between oral microbiome and depression: A population-based study.

Gut microbiome diversity is associated with muscle mass, strength and quality in post-stroke patients.

Gut microbiome diversity is associated with muscle mass, strength and quality in post-stroke patients.

Mycotoxin and microbiome profiling for aflatoxin control in the Korean traditional fermented soybean paste Doenjang.

Mycotoxin and microbiome profiling for aflatoxin control in the Korean traditional fermented soybean paste Doenjang.

Phylogenetic diversity and structure above the tree line in the central Chilean Andes in the light of competing macroecological hypotheses

Phylogenetic diversity and structure above the tree line in the central Chilean Andes in the light of competing macroecological hypotheses

The effects of perfluoroalkyl substance pollution on microbial community and key metabolic pathways in the Pearl River Estuary.

The effects of perfluoroalkyl substance pollution on microbial community and key metabolic pathways in the Pearl River Estuary.

Gut microbiome changes in pediatric AML and association with event free survival.

10026 Background: Pediatric acute myeloid leukemia (AML) is characterized by months of hospitalization with a high risk for infections and a higher rate of relapse than many pediatric leukemias. Recent studies have highlighted the relationship between gut microbiome changes, long term cancer outcomes, and development of comorbidities. However, no study to date has examined the longitudinal changes in the gut microbiome in pediatric AML patients. Methods: In this retrospective study, longitudinal stool samples were taken from 14 pediatric patients with AML treated at Children’s Hospital Colorado. Sample collection started after initial diagnosis for 11 patients and after first relapse for 3 patients. These samples were analyzed using 16S ribosomal RNA (rRNA) gene sequencing along with clinical data extracted via manual chart review. Results: We found that the relative abundance of genus Fusobacterium was associated with relapses. Analysis indicated that Fusobacterium was significantly elevated in the stool of 3 of 6 newly diagnosed patients who relapsed within 5 years (using a linear model that also accounted for risk stratification based on genetics and treatment response (p = 0.03)). These patients had elevated Fusobacterium at multiple timepoints during treatment. Samples from the 5 newly diagnosed patients who did not relapse showed minimal Fusobacterium . Fusobacterium has previously been associated with other cancers, oncogenesis and immune evasion. Of the 14 patients, 5 experienced 1-4 cases of Streptococcus mitis bacteremia (SMB) during the sample collection period. Genus Streptococcus abundance in stool samples collected immediately prior to SMB did not correlate with positive blood cultures, although this genus was highly prevalent in the gut microbiome of patients with repeated episodes. Using mixed effects random forest model (MERFM) to broadly survey whether changes in any other gut bacteria predicted a positive SM blood culture, we found evidence for a negative relationship between SMB and change in relative abundance of genus Blautia , and a positive relationship with the genera Marvinbryantia, Anaerococcus, Parabacteroides and Dielma . This suggests that other aspects of microbiome composition may influence whether Streptococcus can translocate into the bloodstream. Of the 14 patients, 4 developed Clostridioides difficile infections (CDI) during the collection period. Increases in genus Clostridioides relative abundance occurred prior to clinical CDI. Using MERFM, Faith Phylogenetic Diversity was negatively related to development of CDI and presence of the genera Anarofustis, Bilophila, Alistipes and was positively related to CDI. Conclusions: These results show that the gut microbiome may be implicated or serve as a prognostic indicator for relapse in pediatric AML. Additionally, longitudinal gut microbiome changes in patients may be associated with various clinical complications.

Exploring metrics of biological diversity to better predict and respond to emerging diseases.

The emergence of infectious diseases is largely driven by spillover events from animal communities into human populations, with zoonotic pathogens accounting for 75% of novel infectious agents. In recent years, incidence and prevalence of these pathogens is on the rise and efforts to understand the underlying ecological principles responsible for the reported increase have highlighted the role of biodiversity loss as a major contributing factor. Despite its role in pathogen emergence, how biodiversity is measured can differ drastically and may underlie variability in study results, making the impacts of biodiversity on pathogen behavior difficult to untangle. Here, we first examine how landscape parameters affect disease transmission and then evaluate metrics used in various disease systems to discuss the ways that different aspects of biodiversity, such as functional, phylogenetic, and trophic diversity, can provide novel insight into the relationship between host communities and disease emergence and transmission. We focus on the tick-borne pathogen that causes Lyme disease in this review and discuss how functional, trophic, and phylogenetic diversity can improve our understanding of the relationship between host community structure and disease transmission. The growing public health burden of tick-borne diseases necessitates holistic thinking to inform actions to decrease the risk of disease to humans and protect natural communities.

A curated benchmark dataset for molecular identification based on genome skimming

Genome skimming is a promising sequencing strategy for DNA-based taxonomic identification. However, the lack of standardized datasets for benchmarking genome skimming tools presents a challenge in comparing new methods to existing ones. As part of the development of varKoder, a new tool for DNA-based identification, we curated four datasets designed for comparing molecular identification tools using low-coverage genomes. These datasets comprise vast phylogenetic and taxonomic diversity from closely related species to all taxa currently represented on NCBI SRA. One of them consists of novel sequences from taxonomically verified samples in the plant clade Malpighiales, while the other three datasets compile publicly available data. All include raw genome skim sequences to enable comprehensive testing and validation of a variety molecular species identification methods. We also provide the two-dimensional graphical representations of genomic data used in varKoder. These datasets represent a reliable resource for researchers to assess the accuracy, efficiency, and robustness of new tools to varKoder and other methods in a consistent and reproducible manner.

Drivers of woody plant phylogenetic and taxonomic beta diversity across an urban density gradient

Urban plant diversity patterns are influenced by socioeconomic factors, yet our understanding of these relationships in Global South cities remains limited. We investigated how taxonomic and phylogenetic beta diversity of woody plants vary across Harare's socioeconomic gradient, examining patterns for indigenous and exotic species. We surveyed 300 household yards across 15 suburbs representing low-, medium-, and high-density areas, characterized by differences in property values, population density, and yard size. For combined species, both taxonomic and phylogenetic beta diversity showed significant positive relationships with property value and yard area, supporting the 'luxury effect' hypothesis. However, patterns differed when analysing species groups separately. Exotic species demonstrated strong socioeconomic filtering, with greater taxonomic diversity in wealthy areas but consistently low phylogenetic turnover across suburbs, suggesting selection of evolutionarily related species. Indigenous species showed unexpected resilience in high-density areas, maintaining greater phylogenetic diversity than affluent suburbs. While species turnover dominated overall beta-diversity patterns, phylogenetic nestedness contributed substantially more than taxonomic nestedness, particularly for exotic species. These findings challenge conventional urban ecology paradigms and highlight the importance of considering both taxonomic and phylogenetic dimensions when assessing urban biodiversity. The retention of phylogenetically diverse indigenous communities in high-density areas presents opportunities for biodiversity conservation in African cities.

The diversity of prokaryotes and fungi hosted in crude oils.

The diversity of prokaryotes and fungi in crude oils has not been understood clearly, though unique microbial communities may be hosted in crude oil. This study investigated the chemical compositions and microbial communities of crude oils from Henan, Bamianhe, and Jianghan oilfields of China. Statistical analysis revealed significant variations of both prokaryotic and fungal communities (P < 0.05) within different oilfields and oils with different biodegradation levels. Diversity analysis showed little difference in prokaryotic, but a significant difference in fungal (P < 0.05). Prokaryotic diversity was higher in heavily biodegraded oils than those in unaltered and slightly biodegraded oils; the opposite was true for fungal diversity (P < 0.05). Moreover, thermophilic prokaryotes were detected mainly in biodegraded heavy oils produced by the practice of thermal recovery from Henan and Bamianhe oilfields, and halophilic prokaryotes were detected mainly in oils from sandstone reservoirs containing hypersaline formation water from Jianghan Oilfield. Accordingly, microbial communities in oils are affected by oil biodegradation, extraction practices, and natural environments of native inhabitants in subsurface petroleum reservoirs.IMPORTANCEThe biological activities of endogenous microorganisms in crude oil play an important role in the production and development of crude oil. Although there have been many microbiological investigations of crude oil-contaminated sites, our understanding of the phylogenetic diversity, metabolic capabilities, and community dynamics of microbial communities within crude oil is far from complete. In this paper, the prokaryotic and fungal communities of three oil fields in different regions of China were analyzed, and several factors affecting microbial degradation were further identified. This study provides a new direction for the subsequent investigation of microbial activities inside crude oil.

The Origins of the Latitudinal Diversity Gradient: Revisiting the Tropical Conservatism Hypothesis

ABSTRACTAimUnderstanding the origins of species richness patterns (especially high tropical richness) is a long‐standing challenge at the intersection of biogeography, ecology, and evolutionary biology. One hypothesis that can potentially explain the latitudinal richness gradient is the tropical conservatism hypothesis (TCH). The TCH proposes that there are presently more species in tropical regions because many clades originated in the tropics and have only colonised the temperate zones more recently, leaving less time for speciation to build up temperate richness, and with niche conservatism limiting temperate colonisation by tropical clades. Here, we review the empirical evidence for the TCH. We first define this hypothesis, outline its major predictions, and describe its relationship to similar hypotheses. We then perform a systematic review to quantitatively evaluate the support for (and against) its major predictions. Finally, we describe several areas for future research.LocationGlobal.Time PeriodPresent to ~750 million years ago.Major Taxa StudiedAll (especially plants and animals).MethodsWe perform a systematic review of the evidence for the TCH over the last ~20 years.ResultsMost predictions of the TCH were supported in a significant majority of the studies that examined them. Further, a significant majority of relevant studies rejected the role of higher tropical diversification rates in driving the latitudinal diversity gradient (contrary to the diversification‐rate and out‐of‐the‐tropics hypotheses). Surprisingly, the importance of diversification rates did not depend on the ages of the clades studied.Main ConclusionsOur results generally support the TCH, but also highlight several important issues moving forward. Most studies tested very few predictions of the TCH, and the pivotal role of colonisation time was often untested. Many studies analysed phylogenetic diversity measures, but their relevance for explaining richness patterns remains disturbingly unclear. Finally, we discuss several unresolved questions about the TCH and the origins of richness patterns.

Determinants of global variation in taxonomic and phylogenetic diversity of invasive plants

Abstract Information on the determinants of taxonomic and phylogenetic diversity of invasive plant species is crucial for managing invasive plants. With globalization, most countries have experienced substantial economic losses and environmental damage due to biological invasions. We analysed the determinants of variation in the diversity and phylogenetic structure of invasive plants among countries worldwide. To do so, we used a comprehensive checklist of invasive plants in 152 countries worldwide to calculate taxonomic and phylogenetic diversity (i.e. Faith’s PD metric) and phylogenetic structure, using mean phylogenetic distance (MPD) and mean nearest taxon distance (MNTD). We then combined these data in minimum adequate models with data on geographic, climatic, socio‐economic and international trade variables. We also conducted randomization tests to determine whether the phylogenetic diversity of invasive plants in these countries was clustered or overdispersed. Taxonomic and phylogenetic diversity of invasive plants exhibited spatial congruence. Taxonomic and phylogenetic diversity were positively correlated with insularity, mean annual precipitation (MAP) and HS‐12 (seeds, grains and medicinal plants) import values per capita, but negatively associated with mean annual temperature (MAT) and HS‐07 (vegetables) import evenness. In addition, taxonomic diversity also increased with airport density, HS‐12 import evenness and lower HS‐08 (fruit and nuts) imports. MPD increased with greater land area and airport density and fewer HS‐12 exporting source countries. MNTD increased with MAT but declined with greater land area and insularity. Phylogenetic clustering occurred in 28.9%–49.3% of countries, whereas phylogenetic overdispersion was rare, observed only in 0.6%–5.3% of countries. Synthesis. Our study reveals that variation in taxonomic and phylogenetic diversity of invasive plant species among countries is shaped by geographic, socio‐economic, climatic and international trade factors. Nearly one‐third of the countries showed phylogenetic clustering of invasive plant species, indicating a relatively consistent global pattern. These findings underscore the importance of integrating both taxonomic and phylogenetic perspectives in invasion ecology, emphasizing the need for regionally tailored management strategies that effectively account for regional geographic, climatic, socio‐economic and trade‐related factors to mitigate future plant invasions.

Body-site specific associations between human skin microbiome composition and psychological wellbeing.

There is increasing scientific interest in understanding the interplay between psychological wellbeing and the human microbiome, with a particular focus on the gut microbiome's impact on psychological health. However, the role of the skin microbiome remains underexplored. The current study addresses this gap by investigating the relationship between the human skin microbiome at various body sites (face, scalp, forearm, axilla) and psychological wellbeing. This unique multi body site investigation aims to provide an understanding of the skin microbiome's role in psychological health. Fifty-three participants underwent microbiome sampling via skin swabbing from four body regions (forearm, face, scalp, and axilla) and completed psychological measures of global/general wellbeing (Affect Grid, Sleep Quality, Stress NRS-11, PSS-10) and body site-related wellbeing (Hair & ScalpCARE, SkinCARE, UnderarmCARE). All bacterial DNA extracts were analysed using quantitative polymerase chain reaction (qPCR) and Illumina sequencing of the V1 - V2 region of the 16S gene. Microbial diversity was computed as Shannon diversity and Faith's Phylogenetic diversity. Correlations were determined between psychological measures, microbial diversity, and genera for each body site. The current study uncovered that specific bacterial genera were associated with aspects of wellbeing. Specifically, Cutibacterium showed consistent associations with psychological wellbeing across multiple body locations. Key findings showed increased Cutibacterium on the face and axilla was associated with reduced stress, increased Cutibacterium in the axilla was associated with increased mood pleasantness. These findings highlight, for the first time, the nuanced relationship between skin microbiome and psychological wellbeing. Increased Cutibacterium across multiple body-sites was consistently associated with positive wellbeing outcomes. This underscores the need for further investigation into specific bacterial taxa that may be involved in a skin-brain axis, as well as the importance of specific microbial communities on the body and their potential influence on this connection.

Drivers of taxonomic, phylogenetic and functional diversity of waterbirds in urban wetlands

Abstract Urban wetlands are considered as "habitat islands" within the urban matrix that contribute to species conservation. Waterbirds are sensitive pollution indicators in terrestrial and aquatic ecosystems and their diversity in urban wetlands reflects the response of wildlife to urbanization. However, very few studies have investigated seasonal differences in the multidimensional diversity of waterbirds in urbanized landscapes. In this study, we analyzed various wetland parameters that could potentially affect the seasonal variations in multidimensional diversity of waterbirds in Nanjing, China. We surveyed waterbirds in 29 urban wetlands using the point count method during breeding and non-breeding seasons from November 2022 to June 2023. We then employed multiple linear regressions and information-theoretic approaches to investigate the impact of wetland characteristics on waterbird diversity. We found that water body area and buffer zone connectivity consistently emerged as positive factors affecting waterbird taxonomic and phylogenetic diversity across seasons. Conversely, the urbanization synthetic index was negatively correlated with waterbird diversity only during the breeding season. Regarding functional diversity, we found that the positive correlation between buffer zone connectivity and waterbird diversity was specific to the breeding season. Therefore, for effective conservation of waterbird diversity in our system, wetland planning should prioritize expanding wetland water body areas, enhancing wetland connectivity, minimizing human disturbance during the breeding season, and implementing ecological restoration measures in urbanized wetlands to mitigate adverse effects of urbanization.

Integrating a phylogenetic framework for mapping biodiversity patterns to set conservation priorities for an oceanic island flora

AbstractEffective biodiversity conservation requires accurate assessments to inform management decisions, particularly in biodiversity‐rich regions. The Gran Canaria Biosphere Reserve (GCBR) is located in one of the Canary Islands, an oceanic archipelago that belongs to the Mediterranean biodiversity hotspot and lies &lt;100 km from NW Africa. We aim to help improve conservation in this territory by complementing traditional biodiversity metrics with phylogenetic analyses, using the two official plant DNA barcode sequences (matK and rbcL), and distribution data for 202 endemic angiosperm taxa within the GCBR, which encompasses about 42% of Gran Canaria's territory. We compare the geographical patterns of Phylogenetic Diversity (PD) and Phylogenetic Endemism (PE) with traditional diversity metrics such as Species Richness (SR) and Weighted Endemism (WE), and we use categorical analyses of neo‐and paleo‐endemism. Our results highlight significant centres of PD and PE that do not entirely overlap with those detected for SR and WE. Notably, the northern region of the GCBR includes important conservation areas, representing either accumulations of ancestral diversity or spots of incipient speciation. Moreover, evolutionarily significant areas displaying high values of neo‐ and paleo‐phylogenetic endemism were identified in the east and southeast of the GCBR beyond the current core zones and protected areas. These results highlight the enhanced resolution provided by PD and related metrics, and offer a more nuanced understanding of plant biodiversity compared to SR alone. This study underscores the need to establish a new core zone to preserve all key plant evolutionary sites within the GCBR and to ensure comprehensive protection of the endemic flora, which will require coordination among conservation biologists and decision‐makers. The methodology used showcases the value of integrating taxonomic and phylogenetic diversity metrics for guiding the design of protected areas and improving territorial management in the Canaries and other oceanic archipelagos.

Advances in polyhydroxyalkanoate (PHA) production by halophilic microorganisms: phylogeny, biosynthesis, and biotechnology for sustainable applications: A review

Polyhydroxyalkanoates (PHAs) are biodegradable polymers produced by various microorganisms as intracellular storage compounds. Among other PHA-producing microorganisms, halophiles are considered a promising PHA producer due to their unique metabolic capabilities and adaptability to extreme conditions. Halophiles are also a promising approach to sustainable and cost-effective PHA production, which uses low-cost substrates and simplified bioprocessing conditions. This review explores the phylogenetic diversity of halophiles, the biotechnological advancement in their cultivation, the factors that influence PHA production, and the methods used to detect, extract, and characterize PHAs from halophiles, highlighting opportunities in optimizing PHA production. By studying these aspects, this review focuses on providing a comprehensive understanding of the potential of halophiles in bio-plastic production and their role in reducing plastic waste pollution.

Phylospatial: An R package for spatial phylogenetic analysis with quantitative community data

Abstract Spatial phylogenetic approaches enhance biodiversity analyses by incorporating information about species' evolutionary similarity. However, existing software packages for analysing spatial phylogenetic diversity (PD) patterns only provide full support for binary (presence–absence) community data. A major gap exists in support for occurrence probabilities (such as from species distribution models), a common and valuable data type that captures spatial uncertainty and habitat suitability gradients. While abundance data are partially supported by existing PD tools, these lack features such as geospatial data integration and flexible null model analysis. These gaps limit PD research on quantitative features of species distributions and can introduce imprecision and bias if continuous biodiversity data are thresholded to work with existing tools. Here I present phylospatial, a new R package that fully supports probability, abundance, and binary community data across a range of spatial PD analyses. The package processes all three data types in a common framework, while handling them in distinct ways at key points in the analysis pipeline. It also integrates with raster and vector data formats, providing efficient workflows for geospatial data. phylospatial provides an integrated framework for performing various types of analyses, including calculating alpha PD and endemism, testing significance using community null models, identifying beta‐PD patterns including biogeographic regions, and conducting spatial conservation prioritization. I illustrate the package's functionality with worked examples using a dataset comprising a phylogeny and modelled occurrence probabilities for 5200 species of California plants. By facilitating spatial phylogenetic analysis of quantitative data types that more accurately represent the reality of species distributions, these methods and tools help broaden the range of questions and applications that can be addressed, and can help to increase the detail and statistical rigour of these studies.

Transition of D3c branch and novel recombination events contribute to the diversity of Coxsackievirus A6 in Beijing, China, from 2019 to 2023

Abstract Coxsackievirus A6 (CVA6) is a major pathogen responsible for numerous outbreaks of hand, foot, and mouth disease (HFMD) worldwide. This study investigates the molecular evolution and recombination of CVA6 in Beijing, China. Full-length sequences of 54 CVA6 from Beijing (2019–2023) were obtained through metagenomic next-generation sequencing (mNGS) and Sanger sequencing. These sequences were compared with representative sequences from GenBank to analyse their phylogenetic characteristics, recombination diversity, and evolutionary dynamics. The 54 CVA6 strains co-circulated with those from multiple provinces in China, as well as from South Korea and Japan. Phylogenetic analysis revealed a novel D3c branch, with the VP1 T283A amino acid mutation identified as a key change in its formation. One sequence belonged to the D3a branch, while 53 sequences belonged to the D3c branch. Recombination analysis identified RF-A (46, 85.1%) and three novel recombinant forms (RFs): RF-Z (1, 1.9%), RF-AA (1, 1.9%), and RF-AB (6, 11.1%). Bayesian phylogenetic analysis estimated that the most recent common ancestor (tMRCA) of D3c emerged in August 2013 (95% HPD: May 2012–September 2014), with recombination events occurring in RF-Z (2017–2019), RF-AA (2019–2023), and RF-AB (2021–2023). In conclusion, we revealed a globally circulating CVA6 D3c branch and identified three novel RFs, providing valuable insights for the intervention and control of HFMD.

Deep origin of eukaryotes outside Heimdallarchaeia within Asgardarchaeota.

Research on the morphology, physiology and genomics of Asgard archaea has provided valuable insights into the evolutionary history of eukaryotes1-3. A previous study suggested that eukaryotes are nested within Heimdallarchaeia4, but their exact phylogenetic placement within Asgard archaea remains controversial4,5. This debate complicates understanding of the metabolic features and timescales of early eukaryotic ancestors. Here we generated 223 metagenome-assembled nearly complete genomes of Asgard archaea that have not previously been documented. We identify 16 new lineages at the genus level or higher, which substantially expands the known phylogenetic diversity of Asgard archaea. Through sophisticated phylogenomic analysis of this expanded genomic dataset involving several marker sets we infer that eukaryotes evolved before the diversification of all sampled Heimdallarchaeia, rather than branching with Hodarchaeales within the Heimdallarchaeia. This difference in the placement of eukaryotes is probably caused by the previously underappreciated chimeric nature of Njordarchaeales genomes, which we find are composed of sequences of both Asgard and TACK archaea (Asgard's sister phylum). Using ancestral reconstruction and molecular dating, we infer that the last Asgard archaea and eukaryote common ancestor emerged before the Great Oxidation Event and was probably an anaerobic H2-dependent acetogen. Our findings support the hydrogen hypothesis of eukaryogenesis, which posits that eukaryotes arose from the fusion of a H2-consuming archaeal host and a H2-producing protomitochondrion.