Compare_Genomes: A Comparative Genomics Workflow to Streamline the Analysis of Evolutionary Divergence Across Eukaryotic Genomes.

The dawn of cost-effective genome assembly is enabling deep comparative genomics to address fundamental evolutionary questions by comparing the genomes of multiple species. However, comparative genomics analyses frequently deploy multiple, often purpose-built frameworks, limiting their transferability and replicability. Here, we present compare_genomes, a transferable and extensible comparative genomics workflow package we developed that streamlines the identification of orthologous families within and across eukaryotic genomes and tests for the presence of several mechanisms of evolution (gene family expansion or contraction and substitution rates within protein-coding sequences). The workflow is available for Linux, written as a Nextflow workflow that calls established genomics and phylogenetics tools to streamline the analysis and visualization of eukaryotic genome divergence. This workflow is freely available at https://github.com/jeffersonfparil/compare_genomes, distributed under the GNU General Public License version 3 (GPLv3). © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: Comparative genomics with Nextflow and Conda.

Lost world of complex life and the late rise of the eukaryotic crown.

Eukaryotic life appears to have flourished surprisingly late in the history of our planet. This view is based on the low diversity of diagnostic eukaryotic fossils in marine sediments of mid-Proterozoic age (around 1,600 to 800 million years ago) and an absence of steranes, the molecular fossils of eukaryotic membrane sterols1,2. This scarcity of eukaryotic remains is difficult to reconcile with molecular clocks that suggest that the last eukaryotic common ancestor (LECA) had already emerged between around 1,200 and more than 1,800 million years ago. LECA, in turn, must have been preceded by stem-group eukaryotic forms by several hundred million years3. Here we report the discovery of abundant protosteroids in sedimentary rocks of mid-Proterozoic age. These primordial compounds had previously remained unnoticed because their structures represent early intermediates of the modern sterol biosynthetic pathway, as predicted by Konrad Bloch4. The protosteroids reveal an ecologically prominent 'protosterol biota' that was widespread and abundant in aquatic environments from at least 1,640 to around 800 million years ago and that probably comprised ancient protosterol-producing bacteria and deep-branching stem-group eukaryotes. Modern eukaryotes started to appear in the Tonian period (1,000 to 720 million years ago), fuelled by the proliferation of red algae (rhodophytes) by around 800 million years ago. This 'Tonian transformation' emerges as one of the most profound ecological turning points in the Earth's history.

Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes.

In the ongoing debates about eukaryogenesis-the series of evolutionary events leading to the emergence of the eukaryotic cell from prokaryotic ancestors-members of the Asgard archaea play a key part as the closest archaeal relatives of eukaryotes1. However, the nature and phylogenetic identity of the last common ancestor of Asgard archaea and eukaryotes remain unresolved2-4. Here we analyse distinct phylogenetic marker datasets of an expanded genomic sampling of Asgard archaea and evaluate competing evolutionary scenarios using state-of-the-art phylogenomic approaches. We find that eukaryotes are placed, with high confidence, as a well-nested clade within Asgard archaea and as a sister lineage to Hodarchaeales, a newly proposed order within Heimdallarchaeia. Using sophisticated gene tree and species tree reconciliation approaches, we show that analogous to the evolution of eukaryotic genomes, genome evolution in Asgard archaea involved significantly more gene duplication and fewer gene loss events compared with other archaea. Finally, we infer that the last common ancestor of Asgard archaea was probably a thermophilic chemolithotroph and that the lineage from which eukaryotes evolved adapted to mesophilic conditions and acquired the genetic potential to support a heterotrophic lifestyle. Our work provides key insights into the prokaryote-to-eukaryote transition and a platform for better understanding the emergence of cellular complexity in eukaryotic cells.

Exploration of aminoacyl-tRNA synthetases from eukaryotic parasites for drug development.

Parasitic diseases result in considerable human morbidity and mortality. The continuous emergence and spread of new drug-resistant parasite strains is an obstacle to controlling and eliminating many parasitic diseases. Aminoacyl-tRNA synthetases (aaRSs) are ubiquitous enzymes essential for protein synthesis. The design and development of diverse small molecule, drug-like inhibitors against parasite-encoded and expressed aaRSs have validated this enzyme family as druggable. In this work, we have compiled the progress to date towards establishing the druggability of aaRSs in terms of their biochemical characterization, validation as targets, inhibitor development, and structural interpretation from parasites responsible for malaria (Plasmodium), lymphatic filariasis (Brugia,Wuchereria bancrofti), giardiasis (Giardia), toxoplasmosis (Toxoplasma gondii), leishmaniasis (Leishmania), cryptosporidiosis (Cryptosporidium), and trypanosomiasis (Trypanosoma). This work thus provides a robust framework for the systematic dissection of aaRSs from these pathogens and will facilitate the cross-usage of potential inhibitors to jump-start anti-parasite drug development.

Actin cytoskeleton and complex cell architecture in an Asgard archaeon.

Asgard archaea are considered to be the closest known relatives of eukaryotes. Their genomes contain hundreds of eukaryotic signature proteins (ESPs), which inspired hypotheses on the evolution of the eukaryotic cell1-3. A role of ESPs in the formation of an elaborate cytoskeleton and complex cellular structures has been postulated4-6, but never visualized. Here we describe a highly enriched culture of 'Candidatus Lokiarchaeum ossiferum', a member of the Asgard phylum, which thrives anaerobically at 20 °C on organic carbon sources. It divides every 7-14 days, reaches cell densities of up to 5 × 107 cells per ml and has a significantly larger genome compared with the single previously cultivated Asgard strain7. ESPs represent 5% of its protein-coding genes, including four actin homologues. We imaged the enrichment culture using cryo-electron tomography, identifying 'Ca. L. ossiferum' cells on the basis of characteristic expansion segments of their ribosomes. Cells exhibited coccoid cell bodies and a network of branched protrusions with frequent constrictions. The cell envelope consists of a single membrane and complex surface structures. A long-range cytoskeleton extends throughout the cell bodies, protrusions and constrictions. The twisted double-stranded architecture of the filaments is consistent with F-actin. Immunostaining indicates that the filaments comprise Lokiactin-one of the most highly conserved ESPs in Asgard archaea. We propose that a complex actin-based cytoskeleton predated the emergence of the first eukaryotes and was a crucial feature in the evolution of the Asgard phylum by scaffolding elaborate cellular structures.

Microbial predators form a new supergroup of eukaryotes.

Molecular phylogenetics of microbial eukaryotes has reshaped the tree of life by establishing broad taxonomic divisions, termed supergroups, that supersede the traditional kingdoms of animals, fungi and plants, and encompass a much greater breadth of eukaryotic diversity1. The vast majority of newly discovered species fall into a small number of known supergroups. Recently, however, a handful of species with no clear relationship to other supergroups have been described2-4, raising questions about the nature and degree of undiscovered diversity, and exposing the limitations of strictly molecular-based exploration. Here we report ten previously undescribed strains of microbial predators isolated through culture that collectively form a diverse new supergroup of eukaryotes, termed Provora. The Provora supergroup is genetically, morphologically and behaviourally distinct from other eukaryotes, and comprises two divergent clades of predators-Nebulidia and Nibbleridia-that are superficially similar to each other, but differ fundamentally in ultrastructure, behaviour and gene content. These predators are globally distributed in marine and freshwater environments, but are numerically rare and have consequently been overlooked by molecular-diversity surveys. In the age of high-throughput analyses, investigation of eukaryotic diversity through culture remains indispensable for the discovery of rare but ecologically and evolutionarily important eukaryotes.

Embryonic origins of adult pluripotent stem cells.

Although adult pluripotent stem cells (aPSCs) are found in many animal lineages, mechanisms for their formation during embryogenesis are unknown. Here, we leveraged Hofstenia miamia, a regenerative worm that possesses collectively pluripotent aPSCs called neoblasts and produces manipulable embryos. Lineage tracing and functional experiments revealed that one pair of blastomeres gives rise to cells that resemble neoblasts in distribution, behavior, and gene expression. In Hofstenia, aPSCs include transcriptionally distinct subpopulations that express markers associated with differentiated tissues; our data suggest that despite their heterogeneity, aPSCs are derived from one lineage, not from multiple tissue-specific lineages during development. Next, we combined single-cell transcriptome profiling across development with neoblast cell-lineage tracing and identified a molecular trajectory for neoblast formation that includes transcription factors Hes, FoxO, and Tbx. This identification of a cellular mechanism and molecular trajectory for aPSC formation opens the door for in vivo studies of aPSC regulation and evolution.

Phylogenetic diversity and spatiotemporal dynamics of bacterial and microeukaryotic plankton communities in Gwangyang Bay of the Korean Peninsula.

Nutrient dynamics function globally, flowing from rivers to the ocean (estuarine-coastal zone), and are vulnerable to climate change. Microbial habitats can be affected by marine nutrient dynamics and may provide a clue to predict microbial responses to environmental heterogeneity in estuarine-coastal zones. We surveyed surface seawater in Gwangyang Bay, a semi-enclosed estuary in Korea, from 2016 to 2018 using a metabarcoding approach with prokaryotic 16S and eukaryotic 18S rRNA genes. Bacterial and microeukaryotic communities in these waters showed distinct local communities in response to environmental heterogeneity and community transition at spatiotemporal scales in the estuarine-coastal zone. The relative abundance of prokaryotic and eukaryotic operational taxonomic units suggested a microbial trophic interaction in the Gwangyang Bay waters. We found that the community assembly process in prokaryotic communities was primarily influenced by biological interaction (immigration-emigration), whereas that in eukaryotic communities was more affected by environmental stress (habitat specificity) rather than by biotic factors. Our findings in the Gwangyang Bay waters may provide information on underlying (biotic or abiotic) factors of the assembly process in microbial communities in the estuarine-coastal zone.

Contrasting Community Assembly Mechanisms Underlie Similar Biogeographic Patterns of Surface Microbiota in the Tropical North Pacific Ocean.

Marine microbiota are critical components of global biogeochemical cycles. However, the biogeographic patterns and ecological processes that structure them remain poorly understood, especially in the oligotrophic ocean. In this study, we used high-throughput sequencing of 16S and 18S rRNA genes to investigate the distribution patterns of bacterial and microeukaryotic communities and their assembly mechanisms in the surface waters of the tropical North Pacific Ocean. The fact that both the bacterial and the microeukaryotic communities showed similar distribution patterns (i.e., similar distance-decay patterns) and were clustered according to their geographic origin (i.e., the western tropical North Pacific and central tropical North Pacific) suggested that there was a significant biogeographic pattern of microbiota in the North Pacific Ocean. Indices of alpha diversity such as species richness, phylogenetic diversity, and the Shannon diversity index also differed significantly between regions. The correlations were generally similar between spatial and environmental variables and the alpha and beta diversities of bacteria and microeukaryotes across the entire region. The relative importance of ecological processes differed between bacteria and microeukaryotes: ecological drift was the principal mechanism that accounted for the structure of bacterial communities; heterogeneous selection, dispersal limitation, and ecological drift collectively explained much of the turnover of the microeukaryote communities. IMPORTANCE Bacteria and microeukaryotes are extremely diverse groups in the ocean, where they regulate elemental cycling and energy flow. Studies of marine microbial ecology have benefited greatly from the rapid progress that has been made in genomic sequencing and theoretical microbial ecology. However, the spatial distribution of marine bacteria and microeukaryotes and the nature of the assembly mechanisms that determine their distribution patterns in oligotrophic marine waters are poorly understood. In this study, we used high-throughput sequencing methods to identify the distribution patterns and ecological processes of bacteria and microeukaryotes in an oligotrophic, tropical ocean. Our study showed that contrasting community assembly mechanisms underlaid similar biogeographic patterns of surface bacterial and microeukaryotic communities in the tropical North Pacific Ocean.

Genomicus in 2022: comparative tools for thousands of genomes and reconstructed ancestors.

Genomicus is a database and web-server dedicated to comparative genomics in eukaryotes. Its main functionality is to graphically represent the conservation of genomic blocks between multiple genomes, locally around a specific gene of interest or genome-wide through karyotype comparisons. Since 2010 and its first release, Genomicus has synchronized with 60 Ensembl releases and seen the addition of functions that have expanded the type of analyses that users can perform. Today, five public instances of Genomicus are supporting a total number of 1029 extant genomes and 621 ancestral reconstructions from all eukaryotes kingdoms available in Ensembl and Ensembl Genomes databases complemented with four additional instances specific to taxonomic groups of interest. New visualization and query tools are described in this manuscript. Genomicus is freely available at http://www.genomicus.bio.ens.psl.eu/genomicus.

LIRBase: a comprehensive database of long inverted repeats in eukaryotic genomes.

Small RNAs (sRNAs) constitute a large portion of functional elements in eukaryotic genomes. Long inverted repeats (LIRs) can be transcribed into long hairpin RNAs (hpRNAs), which can further be processed into small interfering RNAs (siRNAs) with vital biological roles. In this study, we systematically identified a total of 6 619 473 LIRs in 424 eukaryotic genomes and developed LIRBase (https://venyao.xyz/lirbase/), a specialized database of LIRs across different eukaryotic genomes aiming to facilitate the annotation and identification of LIRs encoding long hpRNAs and siRNAs. LIRBase houses a comprehensive collection of LIRs identified in a wide range of eukaryotic genomes. In addition, LIRBase not only allows users to browse and search the identified LIRs in any eukaryotic genome(s) of interest available in GenBank, but also provides friendly web functionalities to facilitate users to identify LIRs in user-uploaded sequences, align sRNA sequencing data to LIRs, perform differential expression analysis of LIRs, predict mRNA targets for LIR-derived siRNAs, and visualize the secondary structure of candidate long hpRNAs encoded by LIRs. As demonstrated by two case studies, collectively, LIRBase bears the great utility for systematic investigation and characterization of LIRs and functional exploration of potential roles of LIRs and their derived siRNAs in diverse species.

Shotgun sequence-based metataxonomic and predictive functional profiles of Pe poke, a naturally fermented soybean food of Myanmar.

Pe poke is a naturally fermented sticky soybean food of Myanmar. The present study was aimed to profile the whole microbial community structure and their predictive gene functionality of pe poke samples prepared in different fermentation periods viz. 3 day (3ds), 4 days (4ds), 5 days (5ds) and sun-dried sample (Sds). The pH of samples was 7.6 to 8.7, microbial load was 2.1-3.9 x 108 cfu/g with dynamic viscosity of 4.0±1.0 to 8.0±1.0cP. Metataxonomic profile of pe poke samples showed different domains viz. bacteria (99.08%), viruses (0.65%), eukaryota (0.08%), archaea (0.03%) and unclassified sequences (0.16%). Firmicutes (63.78%) was the most abundant phylum followed by Proteobacteria (29.54%) and Bacteroidetes (5.44%). Bacillus thermoamylovorans was significantly abundant in 3ds and 4ds (p<0.05); Ignatzschineria larvae was significantly abundant in 5ds (p<0.05), whereas, Bacillus subtilis was significantly abundant in Sds (p <0.05). A total of 172 species of Bacillus was detected. In minor abundance, the existence of bacteriophages, archaea, and eukaryotes were also detected. Alpha diversity analysis showed the highest Simpson's diversity index in Sds comparable to other samples. Similarly, a non-parametric Shannon's diversity index was also highest in Sds. Good's coverage of 0.99 was observed in all samples. Beta diversity analysis using PCoA showed no significant clustering. Several species were shared between samples and many species were unique to each sample. In KEGG database, a total number of 33 super-pathways and 173 metabolic sub-pathways were annotated from the metagenomic Open Reading Frames. Predictive functional features of pe poke metagenome revealed the genes for the synthesis and metabolism of wide range of bioactive compounds including various essential amino acids, different vitamins, and enzymes. Spearman's correlation was inferred between the abundant species and functional features.

Spatial Variability in Streambed Microbial Community Structure across Two Watersheds.

Both spatial and temporal variability are key attributes of sedimentary microbial communities, and while spatial effects on beta-diversity appear to dominate at larger distances, the character of spatial variability at finer scales remains poorly understood, especially for headwater stream communities. We investigated patterns of microbial community structure (MCS) in biofilms attached to streambed sediments from two watersheds across spatial scales spanning <1 m within a single stream to several hundred kilometers between watersheds. Analyses of phospholipid fatty acid (PLFA) profiles indicated that the variations in MCS were driven by increases in the relative abundance of microeukaryotic photoautotrophs and their contribution to total microbial biomass. Furthermore, streams within watersheds had similar MCS, underscoring watershed-level controls of microbial communities. Moreover, bacterial community structure assayed as either PCR-denaturing gradient gel electrophoresis (PCR-DGGE) fingerprints or PLFA profiles edited to remove microeukaryotes indicated a distinct watershed-level biogeography. No distinct stream order-level distributions were identified, although DGGE analyses clearly indicated that there was greater variability in community structure among 1st-order streams than among 2nd- and 3rd-order streams. Longitudinal gradients in microbial biomass and structure showed that the greatest variations were associated with 1st-order streams within a watershed, and 68% of the variation in total microbial biomass was explained by sediment atomic carbon-to-nitrogen ratio (C:N ratio), percent carbon, sediment surface area, and percent water content. This study confirms a distinct microbial biogeography for headwater stream communities driven by environmental heterogeneity across distant watersheds and suggests that eukaryotic photoautotrophs play a key role in structuring bacterial communities on streambed sediments. IMPORTANCE Microorganisms in streams drive many biogeochemical reactions of global significance, including nutrient cycling and energy flow; yet, the mechanisms responsible for the distribution and composition of streambed microbial communities are not well known. We sampled sediments from multiple streams in two watersheds (Neversink River [New York] and White Clay Creek [WCC; Pennsylvania] watersheds) and measured microbial biomass and total microbial and bacterial community structures using phospholipid and molecular methods. Microbial and bacterial community structures displayed a distinct watershed-level biogeography. The smallest headwater streams within a watershed showed the greatest variation in microbial biomass, and 68% of that variation was explained by the atomic carbon-to-nitrogen ratio (C:N ratio), percent carbon, sediment surface area, and percent water content. Our study revealed a nonrandom distribution of microbial communities in streambeds, and showed that microeukaryotic photoautotrophs, environmental heterogeneity, and geographical distance influence microbial composition and spatial distribution.

House fly larval grazing alters dairy cattle manure microbial communities.

BACKGROUND: House fly larvae (Musca domestica L.) require a live microbial community to successfully develop. Cattle manure is rich in organic matter and microorganisms, comprising a suitable substrate for larvae who feed on both the decomposing manure and the prokaryotic and eukaryotic microbes therein. Microbial communities change as manure ages, and when fly larvae are present changes attributable to larval grazing also occur. Here, we used high throughput sequencing of 16S and 18S rRNA genes to characterize microbial communities in dairy cattle manure and evaluated the changes in those communities over time by comparing the communities in fresh manure to aged manure with or without house fly larvae. RESULTS: Bacteria, archaea and protist community compositions significantly differed across manure types (e.g. fresh, aged, larval-grazed). Irrespective of manure type, microbial communities were dominated by the following phyla: Euryarchaeota (Archaea); Proteobacteria, Firmicutes and Bacteroidetes (Bacteria); Ciliophora, Metamonanda, Ochrophyta, Apicomplexa, Discoba, Lobosa and Cercozoa (Protists). Larval grazing significantly reduced the abundances of Bacteroidetes, Ciliophora, Cercozoa and increased the abundances of Apicomplexa and Discoba. Manure aging alone significantly altered the abundance bacteria (Acinetobacter, Clostridium, Petrimonas, Succinovibro), protists (Buxtonella, Enteromonas) and archaea (Methanosphaera and Methanomassiliicoccus). Larval grazing also altered the abundance of several bacterial genera (Pseudomonas, Bacteroides, Flavobacterium, Taibaiella, Sphingopyxis, Sphingobacterium), protists (Oxytricha, Cercomonas, Colpodella, Parabodo) and archaea (Methanobrevibacter and Methanocorpusculum). Overall, larval grazing significantly reduced bacterial and archaeal diversities but increased protist diversity. Moreover, total carbon (TC) and nitrogen (TN) decreased in larval grazed manure, and both TC and TN were highly correlated with several of bacterial, archaeal and protist communities. CONCLUSIONS: House fly larval grazing altered the abundance and diversity of bacterial, archaeal and protist communities differently than manure aging alone. Fly larvae likely alter community composition by directly feeding on and eliminating microbes and by competing with predatory microbes for available nutrients and microbial prey. Our results lend insight into the role house fly larvae play in shaping manure microbial communities and help identify microbes that house fly larvae utilize as food sources in manure. Information extrapolated from this study can be used to develop manure management strategies to interfere with house fly development and reduce house fly populations.

Phytoplankton settling quality has a subtle but significant effect on sediment microeukaryotic and bacterial communities.

In coastal aphotic sediments, organic matter (OM) input from phytoplankton is the primary food resource for benthic organisms. Current observations from temperate ecosystems like the Baltic Sea report a decline in spring bloom diatoms, while summer cyanobacteria blooms are becoming more frequent and intense. These climate-driven changes in phytoplankton communities may in turn have important consequences for benthic biodiversity and ecosystem functions, but such questions are not yet sufficiently explored experimentally. Here, in a 4-week experiment, we investigated the response of microeukaryotic and bacterial communities to different types of OM inputs comprising five ratios of two common phytoplankton species in the Baltic Sea, the diatom Skeletonema marinoi and filamentous cyanobacterium Nodularia spumigena. Metabarcoding analyses on 16S and 18S ribosomal RNA (rRNA) at the experiment termination revealed subtle but significant changes in diversity and community composition of microeukaryotes in response to settling OM quality. Sediment bacteria were less affected, although we observed a clear effect on denitrification gene expression (nirS and nosZ), which was positively correlated with increasing proportions of cyanobacteria. Altogether, these results suggest that future changes in OM input to the seafloor may have important effects on both the composition and function of microbenthic communities.

Single cell genomics reveals plastid-lacking Picozoa are close relatives of red algae.

The endosymbiotic origin of plastids from cyanobacteria gave eukaryotes photosynthetic capabilities and launched the diversification of countless forms of algae. These primary plastids are found in members of the eukaryotic supergroup Archaeplastida. All known archaeplastids still retain some form of primary plastids, which are widely assumed to have a single origin. Here, we use single-cell genomics from natural samples combined with phylogenomics to infer the evolutionary origin of the phylum Picozoa, a globally distributed but seemingly rare group of marine microbial heterotrophic eukaryotes. Strikingly, the analysis of 43 single-cell genomes shows that Picozoa belong to Archaeplastida, specifically related to red algae and the phagotrophic rhodelphids. These picozoan genomes support the hypothesis that Picozoa lack a plastid, and further reveal no evidence of an early cryptic endosymbiosis with cyanobacteria. These findings change our understanding of plastid evolution as they either represent the first complete plastid loss in a free-living taxon, or indicate that red algae and rhodelphids obtained their plastids independently of other archaeplastids.

General decline in the diversity of the airborne microbiota under future climatic scenarios.

Microorganisms attached to aerosols can travel intercontinental distances, survive, and further colonize remote environments. Airborne microbes are influenced by environmental and climatic patterns that are predicted to change in the near future, with unknown consequences. We developed a new predictive method that dynamically addressed the temporal evolution of biodiversity in response to environmental covariates, linked to future climatic scenarios of the IPCC (AR5). We fitted these models against a 7-year monitoring of airborne microbes, collected in wet depositions. We found that Bacteria were more influenced by climatic variables than by aerosols sources, while the opposite was detected for Eukarya. Also, model simulations showed a general decline in bacterial richness, idiosyncratic responses of Eukarya, and changes in seasonality, with higher intensity within the worst-case climatic scenario (RCP 8.5). Additionally, the model predicted lower richness for airborne potential eukaryotic (fungi) pathogens of plants and humans. Our work pioneers on the potential effects of environmental variability on the airborne microbiome under the uncertain context of climate change.

Diversification of Ferredoxins across Living Organisms.

Ferredoxins, iron-sulfur (Fe-S) cluster proteins, play a key role in oxidoreduction reactions. To date, evolutionary analysis of these proteins across the domains of life have been confined to observing the abundance of Fe-S cluster types (2Fe-2S, 3Fe-4S, 4Fe-4S, 7Fe-8S (3Fe-4s and 4Fe-4S) and 2[4Fe-4S]) and the diversity of ferredoxins within these cluster types was not studied. To address this research gap, here we propose a subtype classification and nomenclature for ferredoxins based on the characteristic spacing between the cysteine amino acids of the Fe-S binding motif as a subtype signature to assess the diversity of ferredoxins across the living organisms. To test this hypothesis, comparative analysis of ferredoxins between bacterial groups, Alphaproteobacteria and Firmicutes and ferredoxins collected from species of different domains of life that are reported in the literature has been carried out. Ferredoxins were found to be highly diverse within their types. Large numbers of alphaproteobacterial species ferredoxin subtypes were found in Firmicutes species and the same ferredoxin subtypes across the species of Bacteria, Archaea, and Eukarya, suggesting shared common ancestral origin of ferredoxins between Archaea and Bacteria and lateral gene transfer of ferredoxins from prokaryotes (Archaea/Bacteria) to eukaryotes. This study opened new vistas for further analysis of diversity of ferredoxins in living organisms.

Evolution of Multicellularity.

The emergence of multicellular organisms was, perhaps, the most spectacular of the major transitions during the evolutionary history of life on this planet [...].

Updating changes in human gut microbial communities associated with Clostridioides difficile infection.

Clostridioides difficile is the causative agent of antibiotic-associated diarrhea, a worldwide public health problem. Different factors can promote the progression of C. difficile infection (CDI), mainly altered intestinal microbiota composition. Microbial species belonging to different domains (i.e., bacteria, archaea, eukaryotes, and even viruses) are synergistically and antagonistically associated with CDI. This review was aimed at updating changes regarding CDI-related human microbiota composition using recent data and an integral approach that included the different microorganism domains. The three domains of life contribute to intestinal microbiota homeostasis at different levels in which relationships among microorganisms could explain the wide range of clinical manifestations. A holistic understanding of intestinal ecosystem functioning will facilitate identifying new predictive factors for infection and developing better treatment and new diagnostic tools, thereby reducing this disease's morbidity and mortality.