Biology subjects

Sicheritz-Ponten, T.

Publications and source records attributed to Sicheritz-Ponten, T..

18 recordsLinked to original sources

bioRxiv2026

Antimicrobial-resistance plasmids encode Evangelion, a widespread DUF4062 anti-phage defence family

Mobile genetic elements have profoundly shaped the evolution of bacterial anti-phage immunity, yet much of this defence repertoire remains undiscovered. Antimicrobial-resistance plasmids are well known for disseminating antibiotic-resistance genes, but whether they also serve as reservoirs of previously unrecognised antiviral immunity remains poorly understood. Here, we identify Evangelion, a widespread family of single-gene anti-phage defence systems, through phenotype-guided interrogation of a naturally occurring methicillin-resistant Staphylococcus aureus plasmid. Eva01, the founding member of the family, protects against lytic Silviavirus phages and is built around a conserved DUF4062 core coupled to a highly diversified auxiliary region that is essential for defence activity. Evangelion systems are enriched on antimicrobial-resistance plasmids but are distributed across diverse bacterial hosts and mobile genetic elements, revealing an evolutionarily conserved defence framework that has diversified through horizontal gene transfer and adaptation to distinct phage environments. Genetic, structural and functional analyses support a model in which Eva01 senses intracellular phage replication-associated processes and couples activation of a DUF4062 effector to NAD depletion and abortive infection. Together, our findings define a previously unrecognised family of mobile anti-phage defence systems, establish DUF4062 proteins as a new component of the bacterial anti-phage repertoire, and demonstrate that phenotype-guided interrogation of mobile genetic elements provides a powerful strategy for discovering defence systems beyond the reach of current computational approaches.

molecular biology↗

bioRxiv2026

Bacteriophage genomics: What has five years of INPHARED taught us?

Bacteriophages are key drivers of microbial ecology and evolution, and the rapid expansion of phage sequencing has created sustained demand for curated reference genome databases. We released the INfrastructure for a PHAge REference Database (INPHARED) in January 2021 to provide quality-controlled metadata for complete phage genomes from cultured isolates. Here, we compare the 2021 and 2026 snapshots, spanning a five-year period that included a substantial overhaul of bacterial virus taxonomy by the ICTV. The database has approximately doubled, from 14,244 to 28,777 genomes, yet the proportion representing novel species-level diversity has declined, indicating that redundant sequencing is outpacing new discovery. Host bias persists despite the addition of 97 new host genera. We have incorporated genome quality assessments, lifestyle predictions, and defence and anti-defence system annotations, providing an updated resource and a snapshot of the current state of phage genomics.

microbiology↗

bioRxiv2026

Large scale antibiotic-phage synergy studies reveal key combinations for urinary tract infection and urosepsis treatments

The growing problem of AMR infections in healthcare has prompted the search for alternative treatments, with increasing interest in bacteriophages. However, most bacteriophage-antibiotic interactions are incompletely understood, and the benefits of combining them remains context dependent. In this study, we screened thousands of phage-antibiotic combinations to assess interaction outcomes in clinical E. coli and K. pneumoniae isolates. By integrating bacteriophages into an existing, scalable clinical MIC determination platform, we identified shifts in antibiotic MIC and susceptibility, revealing patterns of additivity and antagonism. Overall, interactions showed a species-specific profile; additive interactions predominated, particularly for E. coli. Hierarchical clustering highlighted frequent positive interactions between {beta}-lactams and Tequatroviruses. Notably, closely related phages sometimes displayed divergent phenotypes, indicating that interaction outcomes cannot be inferred solely from taxonomic relatedness or genomic similarity. Taken together, these results establish a foundation for rational, evidence-based development of phage-antibiotic therapies to restore and broaden treatment options against multidrug-resistant infections.

microbiology↗

bioRxiv2025

Hidden in plain sight: Bacterial genomes reveal thousands of lytic phages with therapeutic potential

Phages are typically classified as temperate, integrating into host genomes, or lytic, replicating and killing bacteria. Lytic phages are not expected in bacterial genome sequences, yet our analysis of 3.6 million bacterial assemblies from 1,226 species revealed >100,000 complete lytic phage genomes, which we term Bacterial Assembly-associated Phage Sequences (BAPS). This represents a [~]five-fold increase in the number of phages with known hosts and fundamentally reshapes our understanding of phage biology. Identifying BAPS has enabled the discovery of entirely novel phage clusters, including clusters distantly related to Salmonella Goslarviruses in E. coli, and Shigella, while significantly expanding known genera such as Seoulvirus (from 16 to >300 members). Notably, close relatives of therapeutic lytic phages were also detected, suggesting clinical isolate sequencing unknowingly archives viable phage candidates. The discovery of complete, lytic phage genomes within bacterial assemblies challenges long-standing assumptions and reveals a vast, untapped reservoir of phages.

microbiology↗

bioRxiv2024

taxmyPHAGE: Automated taxonomy of dsDNA phage genomes at the genus and species

BackgroundBacteriophages are now classified into genera and species based on genomic similarity. To identify new species and genera requires comparison against all phage genomes currently defined by the International Committee on the Taxonomy of Viruses. With increasing amounts of phage genomic data there is a clear need to fully automate the classification of phages into existing and new genera and species. Materials and MethodsWe created a MASH database for rapid searching of closely related phages, to then be compared with BLASTn to compute intergenomic similarity between bacteriophages (https://github.com/amillard/tax_myPHAGE/tree/main). ResultsTaxmyphage is provided as a conda repository and via a user-friendly website, that allows rapid classification of phages into existing taxa at the genus and species level. ConclusionsTaxmyphage allows the rapid and accurate classification of phage genomes into existing genera and species, at a scale that is compatible with existing sequencing output.

microbiology↗

bioRxiv2024

The low abundance of antimicrobial resistance genes (ARGs) in bacteriophages and their transfer bottlenecks limit the ability of phages to contribute to the spread of ARGs

The role of bacteriophages in the spread of antimicrobial resistance genes (ARGs) has been debated over the past decade. Several questions regarding the ARG dissemination potential of bacteriophages remain unanswered. For example, what is the frequency of acquisition of ARGs in phages? Are phages selective in acquiring the ARGs compared to other host genes? What is the predominant mechanism of transferring ARGs to phages? To address these questions, we thoroughly analyzed the available phage genomes, viromes, temperate phage, and prophage sequences for the presence of all known ARGs. Out of the 38,861 phage genome sequences we analyzed, only 182 phages contained a total of 314 ARGs. Interestingly, a few of the Streptococcus and Acinetobacter phages were found to carry an ARG cluster with four or more genes. One of the uncharacterized Myoviridae phages was found to carry the entire vancomycin operon. Furthermore, based on the presence of lysogenic marker sequences, the terminal location of ARGs on phage genomes, and complete ARG clusters transferred to phages, we suggest that ARGs are predominantly acquired from hosts by temperate phages via specialized transduction. The close association of most phage ARGs with lysogenic markers and mobile genetic elements (MGEs) also points towards specialized transduction as a potent mechanism of acquisition of ARGs by phages. Our study further suggests that the acquisition of ARGs by phages occurs by chance rather than through a selective process. Taken together, the limited presence of ARGs in phages, alongside various transfer bottlenecks, significantly restricts the role of phages in the dissemination of ARGs.

microbiology↗

bioRxiv2023

Genomic plasticity is a blueprint of diversity in Salmonella lineages

The flexible genome, organised in regions of genomic plasticity (RGP), serves as a potent facilitator of the dynamic evolution of bacterial genomes through gene acquisition and loss. Here we explored the genomic plasticity across Salmonella lineages, revealing a purposeful, non-random integration pattern of pathogenicity-related gene clusters into specific RGP. Noteworthy examples include the correlation between the type I-E CRISPR-Cas system, gold tolerance, and specific RGP. The scattered prevalence of RGP across Salmonella lineages profoundly shapes the pathogenicity makeup of Salmonella strains. The preferences of RGP seem guided by conserved flanking genes that likely share regulatory and functional coordination. For example, metal resistance genes are predominant in RGP positioned near stress resistance genes, indicating a regulatory network to efficiently counter stressors. Additionally, we observed that different plasmid incompatibility types and prophage genera carry distinct pathogenicity genes. Similar to RGP, their distribution across Salmonella lineages plays a critical role in defining pathogenicity. By uncovering these intricate connections among gene clusters, RGP, mobile genetic elements, and pathogenic attributes, our study offers novel insights into the evolutionary trajectory of Salmonella and holds promise for predicting future adaptations and developing targeted interventions against infections.

microbiology↗

bioRxiv2021

The pangenome of the fungal pathogen Neonectria neomacrospora

The fungal plant pathogen Neonectria neomacrospora (C. Booth & Samuels) Mantiri & Samuels (Ascomycota, Hypocreales) is a bark parasite causing twig blight, canker, and in severe cases, dieback in fir (Abies spp.). Although often described as a mild pathogen, foresty and phytosanitary agencies have expressed their concern for potential economic impact. Two epidemics caused by this species are known: one from eastern Canada and one current within Northern Europe. We present key genome features of N. neomacrospora, to facilitate the research into the biology of this pathogen. We present the first genome assembly of N. neomacrospora as well as the first pangenome within this genus. The reference genome for N. neomacrospora is a long-read sequenced Danish isolate, while the pangenome is pieced together using additional 60 short-read sequenced strains covering the known geographical distribution of the species, including Europe, North America, and China. The gapless reference genome consist of twelve chromosomes sequenced telomere to telomere to a total length of 37.1 Mb. The mitochondrial genome was assembled and circularised with a length of 22 Kb. The gapless nuclear genome contains a total of 11,291 annotated genes, where 642 only have a hypothetical function, and a 4.3 % repeat content. Two minor chromosomes are enriched in transposable elements, AT content, and effector candidates. Chromosome 12 segregates within the population, indicating an accessory nature. The pangenome compile 15,101 genes, 34% more genes than present in the single isolate reference genome of N. neomacrospora. These genes organise into 13,069 homologous clusters, of which 8,316 clusters are present in all analysed strains, 985 are private to single strains. The British Columbian population branched out before the other populations and are characterized by comparatively larger genomes. The increased genome size can be explained by an expansion of repetitive elements. The comparative analysis finds a higher number of genes with a signal peptide within N. neomacrospora and species within the genus compared to the closely related genera. A species-specific pattern is observed in the carbohydrate-active enzyme repertoire, with a reduced number of polysaccharide lyases, compared to other species within the genus. The CAZymes battery responsible for plant cell wall degradation is similar to that observed in necrotrophic and hemibiotrophic plant pathogenic fungi. The genome size of N. neomacrospora is close to the median size for Ascomycota but is the smallest genome within the Neonectria genus. Comparative analysis revealed significant intraspecies genome size differences between populations explained by a difference in repeat content. Isolates with the smallest genomes formed a monophyletic group consisting of all strains from Europe and Quebec. Based on the field observations, we assume that N. neomacrospora is a hemibiotroph. Our analysis revealed a secretome consistent with a hemibiotrophic lifestyle.

genomics↗

bioRxiv2021

Genomic analyses of the extinct Sardinian dhole (Cynotherium sardous) reaveal its evolutionary history

The Sardinian dhole (Cynotherium sardous)1 was an iconic and unique canid species of canid that was endemic of Sardinia and Corsica until it became extinct at the end of the Late Pleistocene2-5. Given its peculiar dental morphology, small body size and high level of endemism, several canids have been proposed as possible ancestors of the Sardinian dhole, including the Asian dhole and African hunting dog ancestor 3,6-9. Morphometric analyses3,6,8-12 have failed to clarify the evolutionary relationship with other canids. We sequenced the genome of a ca 21,100 year old Sardinian dhole in order to understand its genomic history and clarify its phylogenetic position. We found it represents a separate taxon from all other living canids from Eurasia, Africa and North America, and that the Sardinian and Asian dhole lineages diverged ca 885 ka. We additionally detected historical gene flow between the Sardinian and Asian dhole lineages, that ended approximately 500-300 ka, when the landbridge between Sardinia and mainland Italy was broken, severing their population connectivity. Our sample showed low genome-wide diversity compared to other extant canids - probably a result of the long-term isolation - that could have contributed to the subsequent extinction of the Sardinian dhole.

genomics↗

bioRxiv2021

Different autotrophic enrichments yield efficient inocula for biocathodic applications

The uptake of extracellular electrons from cathodes by microbes is a recently discovered phenomenon. However, current knowledge on the diversity of microbes accepting extracellular electrons and populating biocathodes is scarce. Research is required to explore the distribution of extracellular electron uptake metabolism in the tree of life across microbial guilds. Here we characterize the electron uptake ability of microbial guilds enriched on H2, S2O32-, or CH4 and NH4+ from the same inoculum taken from a groundwater treatment sand-filter. We hypothesized that functional microbes having dense outer membrane cytochromes in their native pathway, such as pathways of NH4+, CH4, S2O32- and H2, can perform extracellular electron uptake. We aimed of addressing the following questions: (1) Are there any known microbial member of anticipated function performing extracellular electron transfer? (2) How does electron uptake efficiency vary between the different functional guilds? (3) How is the dissipated electron energy distributed across metabolisms? We developed and applied a novel pipeline to identify taxa utilizing direct electron energy and utilizing secondary microbial products. We report the putative direct electron uptake metabolism of types belonging to Methylomonas, UBA6140, and Nitrosomonas. Furthermore, members of Streptococcaceae, Rhizobiaceae, Streptococcus, Brevundimonas, Chryseobacterium, and Pseudomonas are detected as electroactive taxa. Our results reveal novel insights into the diversity, electrochemical activity, and metabolism of taxa performing direct electron uptake.

ecology↗

bioRxiv2020

Population genomics of the emerging forest pathogen Neonectria neomacrospora

The fungal pathogen Neonectria neomacrospora is of increasing concern in Europe where, within the last decade, it has caused substantial damage to forest stands and ornamental trees of the genus Abies (Mill.). Using whole-genome sequencing of a comprehensive collection of isolates, we show the extent of three major clades within N. neomacrospora, which most likely diverged around the end of the last Ice Age. We find it likely that the current European epidemic of N. neomacrospora was founded from a population belonging to the east North American clade. All European isolates (1957-2019) had a common evolutionary history, but substantial and asymmetrical gene flow from the larger American source population could be detected. The European population shows multiple signs of having gone through a bottleneck and subsequent population expansion.

genomics↗

bioRxiv2020

Analysis of selection methods to develop novel phage therapy cocktails against antimicrobial resistant clinical isolates of bacteria

Antimicrobial resistance (AMR) is a major problem globally. The main bacterial organisms associated with urinary tract infection (UTI) associated sepsis are E. coli and Klebsiella along with Enterobacter species. These all have AMR strains known as ESBL (Extended Spectrum Beta-Lactamase), which are featured on the WHO priority pathogens list as critical for research. Bacteriophages (phages) as viruses that can infect and kill bacteria, could provide an effective tool to tackle these AMR strains. There is currently no gold standard for developing a phage cocktail. Here we describe a novel approach to develop an effective phage cocktail against a set of ESBL-producing E. coli and Klebsiella largely isolated from patients in UK hospitals. By comparing different measures of phage efficacy, we show which are the most robust, and suggest an efficient screening cascade that could be used to develop phage cocktails to target other AMR bacterial species. A target panel of 38 ESBL-producing clinical strains isolated from urine samples was collated and used to test phage efficacy. After an initial screening of 68 phages, six were identified and tested against these 38 strains to determine their clinical coverage and killing efficiency. To achieve this, we assessed four different methods to assess phage virulence across these bacterial isolates. These were the Direct Spot Test (DST), the Efficiency of Plating (EOP) assay, the planktonic killing assay and the biofilm assay. The final ESBL cocktail of six phages could effectively kill 23/38 strains (61%) for Klebsiella 13/19 (68%) and for E. coli 10/19 (53%) based on the planktonic killing assay data. The ESBL E. coli collection had six isolates from the prevalent UTI-associated ST131 sequence type, five of which were targeted effectively by the final cocktail. Of the four methods used to assess phage virulence, the data suggests that planktonic killing assays are as effective as the much more time-consuming EOPs and data for the two assays correlates well. This suggests that planktonic killing is a good proxy to determine which phages should be used in a cocktail. This assay when combined with the virulence index also allows phage synergy to inform cocktail design.

microbiology↗

bioRxiv2020

Rapid discovery of novel prophages using biological feature engineering and machine learning

Prophages are phages that are integrated into bacterial genomes and which are key to understanding many aspects of bacterial biology. Their extreme diversity means they are challenging to detect using sequence similarity, yet this remains the paradigm and thus many phages remain unidentified. We present a novel, fast and generalizing machine learning method based on feature space to facilitate novel prophage discovery. To validate the approach, we reanalyzed publicly available marine viromes and single-cell genomes using our feature-based approaches and found consistently more phages than were detected using current state-of-the-art tools while being notably faster. This demonstrates that our approach significantly enhances bacteriophage discovery and thus provides a new starting point for exploring new biologies.

bioinformatics↗

bioRxiv2020

Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum)

Large vertebrates are extremely sensitive to anthropogenic pressure, and their populations are declining fast. The white rhinoceros (Ceratotherium simum) is a paradigmatic case: this African megaherbivore suffered a remarkable population reduction in the last 150 years due to human activities. The two white rhinoceros subspecies, the northern (NWR) and the southern white rhinoceros (SWR), however, underwent opposite fates: the NWR vanished quickly after the onset of the decline, while the SWR recovered after a severe bottleneck. Such demographic events are predicted to have an erosive effect at the genomic level, in connection with the extirpation of diversity, and increased genetic drift and inbreeding. However there is currently little empirical data available that allows us to directly reconstruct the subtleties of such processes in light of distinct demographic histories. Therefore to assess these effects, we generated a whole-genome, temporal dataset consisting of 52 re-sequenced white rhinoceros genomes, that represents both subspecies at two time windows: before and during/after the bottleneck. Our data not only reveals previously unknown population substructure within both subspecies, but allowed us to quantify the genomic erosion undergone by both, with post-bottleneck white rhinoceroses harbouring significantly fewer heterozygous sites, and showing higher inbreeding coefficients than pre-bottleneck individuals. Moreover, the effective population size suffered a decrease of two and three orders of magnitude in the NWR and SWR respectively, due to the recent bottleneck. Our data therefore provides much needed empirical support for theoretical predictions about the genomic consequences of shrinking populations, information that is relevant for understanding the process of population extinction. Furthermore, our findings have the potential to inform management approaches for the conservation of the remaining white rhinoceroses.

evolutionary biology↗

bioRxiv2019

Distinct life histories impact dikaryotic genome evolution in the rust fungus Puccinia striiformis causing stripe rust in wheat

Stripe rust of wheat, caused by the obligate biotrophic fungus Puccinia striiformis f. sp. tritici, is a major threat to wheat production world-wide with an estimated yearly loss of US $1 billion. The recent advances in long-read sequencing technologies and tailored-assembly algorithms enabled us to disentangle the two haploid genomes of Pst. This provides us with haplotype-specific information at a whole-genome level. Exploiting this novel information, we perform whole genome comparative genomics of two P. striiformis f. sp. tritici isolates with contrasting life histories. We compare one isolate of the old European lineage (PstS0), which has been asexual for over 50 years, and a Warrior isolate (PstS7 lineage) from a novel incursion into Europe in 2011 from a sexual population in the Himalayan region. This comparison provides evidence that long-term asexual evolution leads to genome expansion, accumulation of transposable elements, and increased heterozygosity at the single nucleotide, structural and allele levels. At the whole genome level, candidate effectors are not compartmentalized and do not exhibit reduced levels of synteny. Yet we were able to identify two subsets of candidate effector populations. About 70% of candidate effectors are invariant between the two isolates while 30% are hypervariable. The latter might be involved in host adaptation on wheat and explain the different phenotypes of the two isolates. Overall this detailed comparative analysis of two haplotype-aware assemblies of P. striiformis f. sp. tritici are the first steps in understanding the evolution of dikaryotic rust fungi at a whole genome level.

evolutionary biology↗

bioRxiv2017

Influence of Oenococcus oeni and Brettanomyces bruxellensis on Aged Wine Microbial Taxonomic and Functional Profiles

In the wine making process, the interactions between lactic acid bacteria (LAB), yeast and other wine microflora have an impact on the wine quality. In this study, we investigate the influence of the LAB Oenococcus oeni and the spoilage yeast Brettanomyces bruxellensis on the microbial community of a Cabernet Sauvignon wine. We generated metagenomic datasets from inoculations of three strains of B. bruxellensis, in combination with two O. oeni strains, one with and one without cinnamoyl esterase activity. This esterase activity releases hydroxycinnamic acids (HCAs) that can subsequently be processed by some B. bruxellensis strains able to generate off-flavor compounds. We evaluated the influence of the O. oeni and B. bruxellensis on the microbial taxonomic and functional potential profile, particularly regarding off-flavor formation due to HCAs. We found that the effect on the microbial profiles depends on i) the O. oeni and B. bruxellensis strains being combined and ii) the abundance they reach in the final wine, which depends on certain unidentified conditions. We confirmed that the potential of B. bruxellensis to produce off-flavor compounds from HCAs depends on the strain. Interestingly, the samples without microbial inoculants also had this potential, suggesting that native grape microbiota could also influence the levels of HCA. We also found that the presence of B. bruxellensis does not interfere with the malolactic fermentation of the evaluated O. oeni strains, which leads to a less acidic taste. We show that metagenomic approaches can help uncover the complex wine microbial community traits, such as flavor, impacted by the simultaneous presence of O. oeni and B. bruxellensis.

microbiology↗

bioRxiv2017

Protective role of the vulture facial and gut microbiomes aid adaptation to scavenging

BackgroundVultures have adapted the remarkable ability to feed on carcasses that may contain microorganisms that would be pathogenic to most other animals. The holobiont concept suggests that the genetic basis of such adaptation may not only lie within their genomes, but additionally in their associated microbes. To explore this, we generated shotgun DNA sequencing datasets of the facial and gut microbiomes from the black and turkey vultures. We characterized i) the functional potential and taxonomic diversity of their microbiomes, ii) the potential pathogenic challenges they face, and iii) elements in the microbiome that could play a protective role to the vultures face and gut.\n\nResultsWe found elements involved in diseases, such as periodontitis and pneumonia (more abundant in the face), and gas gangrene and food poisoning (more abundant in the gut). Interestingly, we found taxa and functions with potential for playing health beneficial roles, such as antilisterial bacteria in the gut, and genes for the production of antiparasites and antiinsectisides in the face. Based on the identified phages, we suggest that phages aid in the control, and possibly elimination as in phage therapy, of microbes reported as pathogenic to a variety of species. Interestingly, we also identified Adineta vaga in the gut, an invertebrate that feeds on dead bacteria and protozoans, suggesting a defensive predatory mechanism. Finally, we suggest a colonization resistance role though biofilm formation played by Fusobacteria and Clostridia in the gut.\n\nConclusionsOur results highlight the importance of complementing genomic analyses with metagenomics in order to obtain a clearer understanding of the host-microbial alliance and show the importance of microbiome-mediated health protection for adaptation to extreme diets, such as scavenging.

bioinformatics↗

bioRxiv2017

Comparative Genomics Sheds Light On Niche Differentiation And The Evolutionary History Of Comammox Nitrospira

The description of comammox Nitrospira spp., performing complete ammonium-to-nitrate oxidation, and their co-occurrence with canonical betaproteobacterial ammonium oxidizing bacteria ({beta}-AOB) in the environment, call into question the metabolic potential of comammox Nitrospira and the evolutionary history of their ammonium oxidation pathway. We report four new comammox Nitrospira genomes, constituting two novel species, and the first comparative genomic analysis on comammox Nitrospira.\n\nComammox Nitrospira has lost the potential to use external nitrite as energy and nitrogen source: compared to strictly nitrite oxidizing Nitrospira; they lack genes for assimilative nitrite reduction and reverse electron transport from nitrite. By contrast, compared to other Nitrospira, their ammonium oxidizer physiology is exemplified by genes for ammonium and urea transporters and copper homeostasis and the lack of cyanate hydratase genes. Two comammox clades are different in their ammonium uptake systems. Contrary to {beta}-AOB, comammox Nitrospira genomes have single copies of the two central ammonium oxidation pathway genes, lack genes involved in nitric oxide reduction, and encode genes that would allow efficient growth at low oxygen concentrations. Hence, comammox Nitrospira seems attuned to oligotrophy and hypoxia compared to {beta}-AOB.\n\n{beta}-AOBs are the clear origin of the ammonium oxidation pathway in comammox Nitrospira: reconciliation analysis indicates two separate early amoA gene transfer events from {beta}-AOB to an ancestor of comammox Nitrospira, followed by clade specific losses. For haoA, one early transfer from {beta}-AOB to comammox Nitrospira is predicted - followed by intra-clade transfers. We postulate that the absence of comammox genes in most Nitrospira genomes is the result of subsequent loss.\n\nSignificanceThe recent discovery of comammox bacteria - members of the Nitrospira genus able to fully oxidize ammonia to nitrate - upset the long-held conviction that nitrification is a two-step process. It also opened key questions on the ecological and evolutionary relations of these bacteria with other nitrifying prokaryotes. Here, we report the first comparative genomic analysis of comammox Nitrospira and related nitrifiers. Ammonium oxidation genes in comammox Nitrospira had a surprisingly complex evolution, originating from ancient transfer from the phylogenetically distantly related ammonia-oxidizing betaproteobacteria, followed by within-lineage transfers and losses. The resulting comammox genomes are uniquely adapted to ammonia oxidation in nutrient-limited and low-oxygen environments and appear to have lost the genetic potential to grow by nitrite oxidation alone.

microbiology↗