Microbiology Resource Announcements
● American Society for Microbiology
Preprints posted in the last 90 days, ranked by how well they match Microbiology Resource Announcements's content profile, based on 22 papers previously published here. The average preprint has a 0.03% match score for this journal, so anything above that is already an above-average fit.
ELUFISAN, T. O.; Rodriguez-Luna, I. C.; Sanchez-Varela, A.; Bustos, P.; Lozano-Aguirre Beltran, L. F.; Gonzalez, E. D.; Oyedara, O. O.; Correa-Basurto, J.; Estrada-Perez, A. R.; Cortes-Espinosa, D. V.; Villolobos-Lopez, M. A.; Guo, X.
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ASS1 was isolated as a motile Stenotrophomonas strain from crude oil-contaminated soils in Tabasco, Mexico. We characterized this strain using physiological and biochemical traits. ASS1 grew at temperature 25-37 (optimally at 37 {degrees} C) and at pH 6 to 8 (optimally at pH 7 to 8). The assembled genome has a total length of 4.56MB with a G + C content of 66.6%. The 16S rRNA gene sequence analysis confirmed that this strain belongs to the genus Stenotrophomonas. Based on the 16S rRNA analysis, Stenotrophomonas geniculata ATCC 19374 is the closest species, and it shares 99.86% similarity with ASS1. Similarly, a phylogenomic tree based on core genome sequence revealed that the closest species to ASS1 is Stenotrophomonas geniculata ATCC 19374. The major fatty acids in ASS1 are C16:0, antesio C15:0, iso C12:0, iso C15:0, iso C17:0 and C18:0. The genome of ASS1 consists of 4,373,402 bp. The Average Nucleotide Identity (ANI) values for ASS1 which it shared with its closest phylogenetic neighbors, are Stenotrophomonas geniculata ATCC 19374 = JCM 13324 [T] 92.66 %, Stenotrophomonas maltophilia 13637[T] 92.15%, Stenotrophomonas maltophilia K279a 92.13% Stenotrophomonas maltophilia R551-3 92.15% Stenotrophomonas maltophilia MTCC 434 [T] 92.08% and Pseudomonas hibisicicola ATCC [T] 91.66%. ASS1 possesses genes that are essential for the degradation of Polycyclic Aromatic hydrocarbon. Genes such as 1, 2 dihydroxyl 1, 2 dihydronaphthalene dehydrogenase; MG068 17425, homologous to 2 hydroxyl chromene 2 carboxylate isomerases; MG 18055, homologous to salicylaldehyde dehydrogenase and MG068 20095, homologous to naphthalene 1, 2 dioxygenases were identified in ASS1. The dDDH value between ASS1 and its closest neighbor Stenotrophomonas geniculata ATCC 19374 = JCM 13324 [T] is 50%, which is the highest for all the typed species and as such we proposed that ASS1 is a novel species with the name Stenotrophomonas oleivorans sp. nov. sp. nov. and ASS1T as the typed strain
Timm, L. E.; Hsieh, Y.; Lopez, J. A.; Almgren, S. A.; Glass, J. R.
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Pacific herring (Clupea pallasii) serve as a critical trophic link between plankton and many marine species targeted by fisheries. With a broad distribution throughout the North Pacific Ocean, from the Arctic to temperate latitudes, herring hold ecological, economic, and cultural importance. Despite this importance, genomic resources for this species, such as reference genome sequences, have only recently become available. To date, only one scaffold-level reference genome, representing a specimen from the Gulf of Alaska (Vancouver; 1,379 scaffolds), has been published to NCBI. Addressing this data gap, we produced a high quality 795Mb genome sequence organized into 26 chromosomes combining long read sequencing with short read sequencing of proximity ligation libraries. Our assembly is highly complete (BUSCO score of 97.7%) and contiguous (922 contigs, N50 = 7,338,470, L50 = 38; 26 scaffolds, N50 = 31,494,017; L50 = 12). Pacific herring south of the Aleutian Islands and the Alaska Peninsula are genetically differentiated from those in the Bering Sea, making a reference genome from the eastern Bering Sea an important addition to the Pacific herrings genomic toolbox.
Peralta, C.; Sauka, D. H.; Felipe, V.; Del Valle, E. E.; Palma, L.
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The Bacillus genus comprises physiologically versatile, endospore-forming bacteria widely distributed in natural environments. In this study, we report the isolation and genomic characterization of strain Bva_UNVM-123, recovered from agricultural soil in Pergamino, Argentina. Whole-genome sequencing using Illumina technology yielded a 5.1 Mbp draft genome assembled in 67 contigs with a GC content of 36%. Comparative genomic analyses using the TYGS server and digital DNADNA hybridization (dDDH) values supported its classification as a potentially novel species within the Bacillus sensu lato (s.l.) group. Genome annotation revealed 4,866 protein-coding genes, including multiple determinants conferring resistance to antibiotics (e.g., fosfomycin, tetracycline, beta-lactams) and toxic heavy metals (e.g., arsenic, cadmium, mercury), supporting its potential application in bioremediation. Additionally, PathogenFinder predicted a low probability of human pathogenicity (0.207), reinforcing its safety for environmental use. Functional classification based on Swiss-Prot further supported a metabolically versatile profile and revealed the presence of resistance-related categories associated with environmental adaptation. This study adds to the growing knowledge of environmental Bacillus species and their biotechnological potential
Dittami, S. M.; Hudson, J.; Brillet-Gueguen, L.; Ficko-Blean, E.; Tanguy, G.; Rousvoal, S.; Legeay, E.; Markov, G. V.; Delage, L.; Godfroy, O.; Corre, E.; Collen, J.; Leblanc, C.; Egan, S.
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BackgroundRed macroalgae (Rhodophyta) are ecologically and economically important marine primary producers, yet genomic resources for most species remain scarce. Delisea pulchra, a temperate red alga known for its halogenated furanone-based chemical defenses, serves as a model for studying algal-microbe interactions, antifouling mechanisms, and disease dynamics. ResultsHere we present a high-quality genome assembly of this species. The nuclear genome comprises 134 Mbp across 271 contigs with an N50 of 1.47 Mbp and encodes 13,387 predicted protein-coding genes. Comparative genomics with other red algae revealed expansions in gene families involved in DNA methylation, and oxidative stress responses, including glutathione S-transferases and superoxide dismutases. Analysis of glycosyltransferases, sulfatases, and sulfurylases implicated in galactan biosynthesis suggests D. pulchra possesses a complex and potentially novel extracellular matrix. We also identified several vanadium haloperoxidases (vHPOs), heme-dependent haloperoxidases (hHPOs), and two type III polyketide synthase (PKS) genes unique to the D. pulchra, which together represent promising candidate genes for bromofuranone production. ConclusionThe D. pulchra genome provides a foundation for molecular investigations into defense, signaling, and host-microbe interactions. It has been deposited at the European Nucleotide Archive under accession number PRJEB101077. All datasets, annotations, and interactive tools for exploring the genome are also available through the Rhodoexplorer portal at https://rhodoexplorer.sb-roscoff.fr.
Sharma, A.; Patil, P. B.
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Non-pathogenic Xanthomonas (NPX) from a diverse plant hosts are being reported on an increasing basis. There are also reports of multiple species forming communities on a single host plant, such as rice, and, given their role as core endophytes in protecting plants from pathogens, it is essential to isolate and characterization of more NPX species from diverse host plants. Using phylogenomic analysis of publicly available Xanthomonas genome sequences, we identified a novel clade comprising NPX strains from diverse hosts. One of the strains previously reported from our lab is from healthy rice seeds and was reported to be non-pathogenic, with bio-protection function against the bacterial leaf blight pathogen. Genomic investigation confirmed the lack of type III secretion system and its effectors, consistent with their non-pathogenic nature. These strains also harbour core and unique biosynthetic loci identified in other non-pathogenic Xanthomonas (NPX) strains. Further investigation using multiple genomic-based taxonomic indices indicates that these strains represent a potential new species. Hence, we propose Xanthomonas imtechensis sp. nov. as a new species of the genus Xanthomonas, with the type strain being PPL568 = MTCC 13186 = CFBP 9040 = ICMP 24395.
Ferrador, L. P.; Grosso, F.; Duarte, B.; Ribeiro, T. G.; Peixe, L.
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The genus Gardnerella comprises a group of fastidious bacteria associated with the female urogenital tract and has undergone extensive taxonomic revision in recent years. In this study, a bacterial strain, designated CCPDSM, was isolated from the female urinary microbiome and subjected to a comprehensive polyphasic taxonomic characterization. The 16S rRNA gene sequence confirmed that this strain is a member of the genus Gardnerella, and phylogenetic analyses based on cpn60 sequences, together with phylogenomic reconstruction placed strain CCPDSM within the genus Gardnerella as a distinct and well-supported lineage. Genome-based relatedness indices (ANIb, ANIm, TETRA and dDDH), demonstrated clear separation of CCPDSM from all validly published Gardnerella species. In contrast, comparisons with two publicly available closely related genomes yielded values above accepted species delineation thresholds, supporting their assignment to the same taxon. Phenotypic characterization, together with genome-based functional predictions, revealed a fastidious, fermentative metabolic profile that further differentiated CCPDSM from its closest relatives, while remaining consistent with traits characteristic of the genus. On the basis of combined phylogenetic, genomic and phenotypic evidence, strain CCPDSM is proposed as representing a novel species within the genus Gardnerella, for which the name Gardnerella fastidiominuta sp. nov. is proposed, with strain CCPDSM (=CECT 31324=CCP 588) designated as the type strain. This study expands the recognized diversity of Gardnerella and highlights the female urinary tract as a reservoir of previously uncharacterized species within this genus.
Justen, L. J.; Rushford, C.; Hershey, O. S.; Floyd-O'Sullivan, R.; Grimm, S. L.; Bradshaw, W. J.; Bhasin, H.; Rice, D. P.; Stansifer, K.; Faraguna, J. D.; McLaren, M. R.; Zulli, A.; Tovar-Mendez, A.; Copen, E.; Shelton, K. K.; Amirali, A.; Kannoly, S.; Pesantez, S.; Stanciu, A.; Quiroga, I. C.; Silvera, L.; Greenwood, N.; Bongiovi, B.; Walkins, A.; Love, R.; Lening, S.; Patterson, K.; Johnston, T.; Hernandez, S.; Benitez, A.; McCarley, B. J.; Engelage, S.; Pillay, S.; Calender, C.; Herring, B.; Robinson, C.; Monett Wastewater Treatment Plant, ; Columbia Missouri Wastewater Treatment Plant, ;
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Wastewater monitoring enables non-invasive, population-scale tracking of community infections independent of healthcare-seeking behavior and clinical diagnosis. Metagenomic sequencing extends this capability by enabling broad, pathogen-agnostic detection, genomic characterization, and identification of novel or unexpected threats. Here, we present data from CASPER (the Coalition for Agnostic Sequencing of Pathogens from Environmental Reservoirs), a U.S.-based wastewater metagenomic sequencing network designed for deep, untargeted pathogen monitoring at national scale. This release includes 1,206 samples collected between December 2023 and December 2025 from 27 sites across nine states, covering 13 million people. Deep sequencing ([~]1 billion read pairs per sample) generated 1.2 trillion read pairs (357 terabases), enabling detection of even rare taxa, with CASPER representing 67% of all untargeted wastewater sequencing data currently available on the NCBI Sequence Read Archive. Virus abundance trends correlate with nationwide wastewater PCR and clinical data for SARS-CoV-2, influenza A, and respiratory syncytial virus, while the pathogen-agnostic approach captures emerging threats, including avian influenza H5N1 during initial dairy cattle outbreaks, West Nile virus, and measles, among hundreds of viral taxa. As the largest publicly available untargeted wastewater sequencing dataset to date, CASPER provides a shared and growing resource for pathogen surveillance and microbial ecology.
Markov, S. A.; Childs, S.; Averitt, J. K.; Johansen, R. A.
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This paper evaluated and compared the relative microalgal biomass accumulation of rocking, floating, and stationary bag photobioreactors. Microalga Neochloris oleoabundans was grown in these photobioreactors in batch mode for 24 days under illumination. The 50 L plastic bags (cell suspension volume 25 L) were placed on the surface of a rocking platform, an artificial pond or a stationary platform. In the pond, waves were generated by electrical fans which shake and mix microalgal cells within the plastic bags. The bags were supplied with 5% CO2 in air under elevated pressure inside of the bags. The rocking bag method significantly increased biomass yields to approximately 3-4 g * L-1, as compared to 0.16 g * L-1 in the floating photobioreactor and only 0.03 g * L-1 in the stationary type photobioreactor.
Shtengel, D.; Shtengel, G.; Xu, C. S.; Hess, H. F.
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Electron Microscopy (EM) is widely used in many scientific fields, particularly in life sciences, offering high-resolution information on the ultrastructure of biological organisms. Accurate characterization of EM image quality is important for assessing the EM tool performance, in addition to sample preparation protocol, imaging conditions, etc. This paper provides an overview of tools we developed as plugins for the popular image processing package Fiji (ImageJ) (1). These tools include signal-to-noise ratio analysis, contrast evaluation, and resolution analysis, as well as the capability to import images acquired on custom FIB-SEM instruments (2). We have also made these tools available in Python, with both versions available on GitHub.
Fiesinger, A.; Sharaf, A.; Alderdice, R.; Perna, G.; Manns, H.; Burt, J. A.; Voolstra, C. R.
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We present a genome assembly from the coral species Porites harrisoni from the southern Persian/Arabian Gulf, the hottest ocean basin where corals live. The assembly is 626.7 Mb in size, spanning 1,883 contigs with a contig N50 of 807.4 kb, including a single-contig mitochondrial genome. The assembly has a BUSCO completeness of 86.3% (single = 72.5%, duplicated = 13.7%, fragmented = 1.2%, missing = 12.5%) using the eukaryota_odb10 reference set (n = 255). A total of 59.23% of the nuclear genome consists of repeats, comprising 15.89% retroelements, 10.00% DNA transposons, and 31.71% unclassified repeats. Gene annotation of this nuclear genome assembly identified 27,823 protein-coding genes. The mitogenome has an assembly size of 18,639 bp with 13 protein-coding genes as well as 2 tRNAs and 2 rRNAs. The genome of P. harrisoni provides a valuable genomic resource of a coral from an extreme environment, which will enable comparative analyses, enhancing our understanding of the genomic architecture underlying thermal resilience. Such comparisons will contribute to elucidating the evolutionary basis of heat tolerance and adaptive capacity of corals in the context of rapid climate change.
Miranda-Riveros, J.; Tichy-Navarro, D.; Navarrete, M. J.; Reyes-Jara, A.; Toro, M.; Ugalde, J. A.; Moreno-Switt, A. I.; Pina-Iturbe, A.
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The spread of extended-spectrum {beta}-lactamase (ESBL)-producing and fluoroquinolone-resistant Salmonella pose a global public health challenge in addition to the high burden of infections associated with this foodborne pathogen. In this study we aimed to characterize a multidrug-resistant strain of Salmonella serovar Amager isolated from a Chilean river in October 2023. Antimicrobial susceptibility testing revealed a resistance phenotype against multiple antibiotic families, including fluoroquinolones and {beta}-lactams, showing ESBL production. Hybrid genome sequencing allowed the identification of a 311,303 bp plasmid carrying the aadA1, aph(4)-Ia, aac(3)-IVa, floR, sul1, tet(A), and blaCTX-M-65 genes, sharing 99.98% sequence identity with the Salmonella Infantis pESI-like megaplasmid. In addition, the qnrB19 gene was found in a {approx}2.7 kbp plasmid of widespread distribution. Population structure and temporal phylogenetic analysis at the global scale revealed the emergence of a Salmonella Amager lineage from the HC20_35565 cluster, carrying the Salmonella Infantis blaCTX-M-65-positive pESI-like megaplasmid and causing human infections in the United States and the United Kingdom. Our work describes the emergence of a Salmonella lineage with resistance against first-line antibiotics used for treating severe infections, underscoring the relevance of environmental surveillance as a means for detecting emergent pathogens and anticipating human infections.
Heremia, L.; Langsbury, H.; Treece, J.; Miller, A.; Waller, S.; Ussher, J.; Manning, L.; Cleave, C.; Barford, Z.; Findlay, L.; Cameron, K.; Micheal, D.; Aliguna, A.; Mason, T.; O'Connor, B.; Badman, S.; Gemmell, N.; Geoghegan, J.; Stanton, J.-A.
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The global expansion of highly pathogenic avian influenza (HPAI) virus A(H5N1) underscores the need for rapid surveillance at high-risk wildlife interfaces. Taiaroa Head (45.7828{degrees} S, 170.7333{degrees} E) in the South Island of Aotearoa New Zealand hosts a plethora of aquatic wildlife including a large red-billed gull (Chroicocephalus novaehollandiae scopulinus) colony as well as the only mainland breeding colony of northern royal albatross (Diomedea sanfordi). The Royal Albatross Centre is also a major nature tourism destination, attracting tens of thousands of visitors annually, thereby creating a dense ecological and human-wildlife interface vulnerable to viral incursion. We evaluated the GeneXpert II platform using the Xpert(R) Xpress Flu/RSV cartridge as a field-deployable tool for avian influenza virus detection in environmental and wildlife-associated samples. The assay detected synthetic influenza A viral RNA and multiple endemic low pathogenic avian influenza virus subtypes (A(H3N8), A(H1N9), A(H5N2) and A(H7N7)) circulating in New Zealand birds. Influenza A virus was reliably identified in spiked environmental water samples with no consistent PCR inhibition as well as naturally occurring avian influenza virus in duck pond water. Field deployment demonstrated that the system could be operated by non-laboratory personnel with minimal training in a non-clinical setting. This study establishes the feasibility of near-real-time environmental monitoring. Repurposing clinical cartridge-based point-of-care diagnostics offers a practical early warning approach for avian influenza virus surveillance at ecologically and economically significant locations.
Wisecaver, J.; Jeje, T.; Watervoort, N. F.
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Jian et al. (2024) describe de novo genome assemblies for two strains of Prymnesium parvum (sensu lato, s.l.), a cryptic species complex of toxic, unicellular algae responsible for harmful algal blooms around the world. Here, we present evidence that the labels for UTEX 2797 and CCMP 3037 were inadvertently swapped by Jian et al. (2024). This resulted in sequence data labeled "UTEX 2797" but derived from strain CCMP 3037, and vice versa. Strain misidentification is a major risk with cryptic species like P. parvum s.l., and our reanalysis of the data in Jian et al. (2024) underscores the urgent need for clade-specific markers to ensure accurate and efficient strain identification.
Lautert-Dutra, W.; Pasinato Napp, A.; Back Sivinsk, E. A.; Staats, C. C.; dos Santos, F. M.; Lovato Melo, C.
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The urgent need for sustainable solutions to mitigate climate change has intensified research into carbon capture, utilization, and storage (CCUS) strategies. Biological approaches, particularly involving extremophilic microorganisms, offer promising alternatives to conventional methods due to their adaptability and potential for bioproduct synthesis. In this study, we report the complete genome sequencing and functional characterization of isolate BS253, derived from a hypersaline alkaline lake in Brazils Pantanal region. Using a hybrid sequencing strategy combining Oxford Nanopore long reads and Illumina short reads, we assembled a circular chromosome of 3.76 Mb and identified two plasmids. Phylogenetic and comparative genomic analyses identified the isolate as Vreelandella zhaodongensis. Digital DNA-DNA hybridization (dDDH % = 71.4%) and ANI (96,83%) values supported the designation of BS253 as a distinct subspecies of V. zhaodongensis. The genome reveals genes associated with salt and alkali tolerance, hydrocarbon and plastic degradation, and the biosynthesis of secondary metabolites. Phenotypically, BS253 is a moderately halophilic, facultatively anaerobic, Gram-negative rod exhibiting biosurfactant activity, with an emulsification index of 51.7% under defined culture conditions. These findings highlight BS253 as a metabolically versatile extremophile with potential applications in different types of industries and biotechnological CCUS systems. ImportanceMicroorganisms adapted to extreme environments represent an untapped source of biotechnologically valuable traits. Vreelandella zhaodongensis BS253, isolated from a hypersaline alkaline lake in the Brazilian Pantanal, expands the known diversity of extremophiles and offers metabolic features with relevance to sustainable bioprocesses. Its complete genome reveals genes involved in salt and alkali tolerance, plastic and hydrocarbon degradation, and the biosynthesis of biosurfactant-like compounds, positioning this strain as a promising chassis for applications in emerging carbon capture, utilization, and storage (CCUS) strategies. The ability of BS253 to produce bioemulsifying molecules under defined nutritional conditions, combined with pathways for degrading recalcitrant pollutants, reinforces its potential for environmentally friendly industrial processes. By characterizing BS253 at the genomic and physiological levels, this work provides foundational information for future exploitation of extremophiles in biotechnological innovations aimed at reducing carbon emissions and supporting circular bioeconomy initiatives.
Saw, J. H.; Shlafstein, M. D.; Pavloudi, C.; Monsalve, N.; Prescott, R. D.; Chain, P. S. G.; Decho, A. W.; Donachie, S. P.
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The Hawaiian islands are among the most geologically and volcanically active places on Earth. While the Hawaiian Archipelago is known for its animal and plant diversity, much less is known about microbial diversity in the areas diverse habitats. In this study, we focused on steam vent associated biofilms found on the most volcanically active island of Hawai{square}i, also known as the Big Island. From 46 samples from various biofilms and associated features around fumaroles emitting water steam, we generated amplicon and metagenomic sequences. Amplicon data showed that Chloroflexota and Cyanobacteriota are the numerically dominant phyla in these biofilm communities. We constructed 363 non-redundant medium to high-quality metagenome-assembled genomes (MAGs) that are at least 70% complete and with less than 5% contamination. Ten MAGs belong in the domain Archaea, and 353 belong in the domain Bacteria. This dataset could provide valuable insights into microbial diversity and ecology around volcanic features in Hawai i and elsewhere.
Lu, A. C.; Zhang, L.; Wu, R.; Lan, R.
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Aeromonas taxonomy has long been complicated by overlapping phenotypic, biochemical, and protein profiles. Here, we establish a robust genome-based framework for Aeromonas species delineation. We analyzed genome-wide average nucleotide identity (ANI) across 3,782 genomes representing the 33 currently recognized Aeromonas species and identified 95.2% ANI as the species boundary. This threshold defined 34 ANI-based species, comprising 30 corresponding to existing Aeromonas species and four potential novel species, while three existing species were merged into closely related species. A genus-level core genome of 673 loci was defined using 392 representative genomes, and core-genome phylogenetic analysis of 1,505 genomes showed consistency with ANI-based clustering. Digital DNA-DNA hybridization (dDDH) values between clusters were [≤] 55%, further supporting species separation. We also found that nine Aeromonas species had intraspecies dDDH values below 70%, cautioning the use of this cutoff for species delineation. We provide the tool Aeromonas ANI species typer (AeromonasANIStyper), an ANI-based species typing tool that assigns query genomes using ANI similarity to medoid genomes and achieved 100% accuracy. This framework supports standardized genome-based Aeromonas taxonomy and future surveillance. ImportanceAeromonas species have gained increased attention as emerging human enteric pathogens. Aeromonas taxonomy has long been complicated by overlapping phenotypic, biochemical, and protein profiles. Although an average nucleotide identity (ANI) threshold was proposed previously for the Aeromonas species delineation, the growing number and diversity of genomes requires a more rigorous reassessment of species boundaries. By analyzing 3,782 Aeromonas genomes, we identified 95.2 % ANI as an optimal cutoff for defining Aeromonas species. Using this threshold, we delineated 34 ANI-defined species, which were further validated by core genome phylogeny and digital DNA-DNA hybridization (dDDH). In addition, we clarified previously misidentified species. Importantly, we provide the Aeromonas ANI species typer (AeromonasANIStyper), a tool that accurately assigns Aeromonas genomes to ANI-defined species. These findings clarify Aeromonas species identification and support improved pathogen surveillance, evolutionary and epidemiological studies.
Hadjeras, L.; Krauspe, V.; Gelhausen, R.; Heiniger, B.; Spaet, P.; Reimann, V.; Jaques, G.; Minges, P.; Bilger, R.; Gerstner, M.; Macek, B.; Ahrens, C. H.; Backofen, R.; Sharma, C. M.; Hess, W. R.
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Cyanobacteria are important primary producers and are used in biotechnology as microbial cell factories due to their ability to use solar light for oxygenic photosynthesis. Synechocystis sp. PCC 6803 is a popular model cyanobacterium, yet there are ambiguities in the precise coding regions of many genes, and numerous genes encoding small proteins have remained undetected. Here we present the results of a ribosome profiling (Ribo-seq) analysis involving inhibitors that stall ribosomes at translation initiation and termination sites (TIS- and TTS-Ribo-seq), combined with a proteogenomic reevaluation and reannotation of its entire genome. We report evidence for the translation of 3,050 annotated genes based on proteogenomics (83%), of 3,492 based on Ribo-seq (95.2%), and of 3,009 supported by both methods (82%). The data suggested both novel protein-coding genes and corrections for annotated ones. We validated 15 novel small proteins translated from antisense RNAs, from intergenic and intragenic regions and identified 69 novel, mostly small proteins based on proteogenomics. With slr0489, slr1079 and slr1082 we identified three genes with [~]300 nt long intragenic out-of-frame coding regions and show that both the internal and host reading frames are translated. The resulting proteins interact with each other, resembling certain defense or toxin-antitoxin systems. Our data illustrate the enormous value of consolidating genome annotations in the context of integrated experimental data and suggest that genome annotations in general need to be extended and revised. All of our data can be accessed via an intuitive and interactive genome browser platform at https://www.bioinf.uni-freiburg.de/~ribobase/.
Chang, E. S.; Connelly, M. T.; Travert, M.; Barreira, S. N.; Rivera, A. M.; Katzer, A. M.; Yu, R.; Cartwright, P.; Baxevanis, A. D.
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Cnidarians are important models for the studying the evolution of animal development, regeneration, cell type differentiation, and allorecognition. The marine hydrozoan Podocoryna americana is related to the well-established model species Hydractinia symbiolongicarpus. Although both species possess a sessile polyp stage, P. americana differs in that it also has a free-swimming medusa (jellyfish) stage in its life cycle. We used a combination of PacBio CLR long-read and Illumina Hi-C short-read genome sequencing to produce a chromosome-level genome assembly for P. americana. The final assembly is 327 Mbp in total length with 17 chromosome-scale scaffolds representing 98% of the assembly. Comprehensive functional annotation with BRAKER3 generated a total of 19,085 predicted protein-coding genes in this assembly, covering 91.2% of the metazoan BUCSO gene set. Comparison of the P. americana genome to other chromosome-level cnidarian genome assemblies revealed a high degree of macrosynteny conservation, and ortholog identification and gene family evolution analysis identified 522 expanded and 1,026 contracted gene families in P. americana. This high-quality, chromosome-level genome assembly of P. americana will be an invaluable resource for researchers studying the evolution of development, regeneration, and allorecognition in cnidarians and other metazoans.
Abdul-Wahab, M. F.; Audu, J. O.; Ng, H. J.; Ibrahim, Z.; Ibrahim, N.; Dagang, W. R. Z. W.; Othman, M. H. D.
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Microbial fuel cell offers a promising approach to improve wastewater quality and generate bioenergy from dark fermented effluents. In this study, the use of dark-fermented palm oil mill effluent as an electron donor for bioelectricity generation was investigated using a double-chambered microbial fuel cell (MFC). The MFCs were operated at room temperature (29 {+/-} 2{degrees}C), anode electrolytes adjusted to pH 7, and a chemical catholyte as the oxidizing agent. The maximum power {+/-} 8.07 mW/m2 and 155.16 {+/-} 12.88 mA/m2, respectively, were generated from the MFCs inoculated with sludge, which was 5.9 times higher than control without inoculum. Microbial community analysis revealed the enrichment of fermentative and electrogenic representative taxa from the phyla Bacillota, Bacteroidota and Pseudomonadota on the anode electrodes. Optimizations of the running conditions were carried out, suggesting the optimum parameters of 0.5 k{Omega} external resistance, anolyte initial pH 9, and 75% DFPOME substrate concentration. Operation under the optimized conditions increased current production, wastewater treatment, and Coulombic efficiency compared to the non-optimized conditions. Multiple configurations were also evaluated, showing higher cumulative voltage, power, and current densities with the stacked MFC connections, compared to single MFC units. Parallel circuit connection produced higher power and current density than serial connection. This study demonstrated the feasibility of MFC as a promising downstream treatment for biohydrogen production processes, towards higher treatment efficiency and resource recovery.
Tenorio Rodas, C.; Hentschke, G. S.; Oliveira, F.; Lopes, G.; Duarte, A.; Morone, J.; Campos, A.; Vasconcelos, V.
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The strain LEGE 10371, isolated from the surface of a marine sponge at Praia da Memoria, Portugal, was characterized as a new Thalassoporum species (Pseudanabaenales) using a polyphasic approach that included 16S rRNA gene phylogenetic analysis (Maximum Likelihood and Bayesian Inference), 16S-23S ITS secondary structures, p-distance calculations, MALDI-TOF MS profiling, and morphological analysis by optical and scanning electron microscopy, as well as ecological and biochemical characterization. Phylogenetically, LEGE 10371 clustered within the Thalassoporum clade, however distant from the other existent species of the genus. The p-distance analysis revealed low sequence identity with other Thalassoporum species, with a maximum value of 97.2% to Th. komareki. The MALDI-TOF profile displayed high-intensity peaks at approximately 3,000, 4,000, 6,000 and 8,000 m/z, representing strong candidates for diagnostic markers of the new species. Morphologically, the new species differ from the other species of the genus by presenting trichomes with more than 10 cells and lack of aerotopes. Biocompatibility of the fractions was evaluated in HaCaT keratinocytes, showing no cytotoxic effects at most tested concentrations. PCR screening targeting mcyE, sxtG, anaC, and cyrA confirmed the absence of the genetic potential for the production of major cyanotoxins. Chemical characterization revealed a pigment-rich profile dominated by chlorophyll-a and carotenoids, including {beta}-carotene, zeaxanthin, lutein, and mixoxanthophyll. Bioactivity assays showed superoxide anion radical scavenging by the aqueous fraction (IC2 {approx} 0.042-0.045 mg mL-{superscript 1}), strong nitric oxide radical scavenging by the acetonic fraction (IC = 0.045 mg mL-{superscript 1}), and lipoxygenase inhibition ([~]41%, for a fraction concentration of 0.25 mg mL-), suggesting a potential contribution of these fractions to modulate inflammation-related pathways. Additionally to this results, the polyphasic analysis permitted to confirm previous data that Pseudanabaena and Limnothrix represent the same generic entity. Both genera clustered together, presented high 16S rRNA gene identity (up to 99.9%) and share the same morphological and ecological features. Consequently, we formally proposed the synonimization of Limnothrix into Pseudanabaena.