Article
Ecology
Arthur Galleti-Lima, Chris A. Hamilton, Leandro M. Borges, Jose Paulo L. Guadanucci
Summary: This study proposes a new hypothesis for a group of genera in the subfamily Theraphosinae, using ultraconserved elements (UCEs) phylogenomics. It supports the transfer of species between different genera and describes a new species of Vitalius in Southern Brazil. As a result, there are now nine genera in the Lasiodoriform tarantula group and seven species in the genus Vitalius.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2023)
Article
Plant Sciences
Guangzhao Jin, Wenjun Li, Feng Song, Lei Yang, Zhibin Wen, Ying Feng
Summary: This study sequenced and compared the chloroplast genomes of 16 species within the subgenus Seriphidium, revealing genetic consistency and variation in the subgenus. It also identified repetitive sequences and highly variable loci, and found inconsistencies between the molecular phylogeny and traditional taxonomy of subgenus Seriphidium. The whole chloroplast genomes can serve as molecular markers to infer interspecific relationships in this taxon.
Article
Plant Sciences
Kuan Liu, Rong Wang, Xiu-Xiu Guo, Xue-Jie Zhang, Xiao-Jian Qu, Shou-Jin Fan
Summary: This study sequenced and analyzed the chloroplast genomes of 13 Eragrostideae species, identifying useful molecular markers for phylogenetic analysis. The study revealed Enneapogon as the earliest diverging lineage, Eragrostis as the sister to Uniola including Harpachne, and discussed the classification of Harpachne harpachnoides based on morphological and molecular evidence.
Article
Microbiology
Ekaterina M. Semenova, Denis S. Grouzdev, Diyana S. Sokolova, Tatiyana P. Tourova, Andrey B. Poltaraus, Natalia Potekhina, Polina N. Shishina, Maria A. Bolshakova, Alexander N. Avtukh, Elena A. Ianutsevich, Vera M. Tereshina, Tamara N. Nazina
Summary: This study aimed to determine the diversity of prokaryotes involved in anaerobic oil degradation in oil fields. A new species Actinotalea subterranea was isolated and characterized, and taxonomic revision of the genera Actinotalea and Pseudactinotalea was proposed based on phylogenomic analysis of Actinobacteria.
Article
Biochemistry & Molecular Biology
Jovana Kabic, Katarina Novovic, Dusan Kekic, Anika Trudic, Natasa Opavski, Ivica Dimkic, Branko Jovcic, Ina Gajic
Summary: This study aimed to investigate the prevalence and resistance mechanisms of colistin-resistant Acinetobacter baumannii (ColRAB) isolates in Serbia, assess their genetic relatedness to other circulating A. baumannii isolates in the neighbouring European countries, and analyse the global genomic epidemiology of ColRAB isolates. The findings reveal the central role of the twocomponent regulating system, PmrAB, and increased expression of the pmrC gene in colistin resistance in A. baumannii. The study also highlights the global dissemination of several high-risk clonal lineages of ColRAB isolates.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Plant Sciences
Qiyu Chen, Chunling Chen, Bo Wang, Zehuan Wang, Wenfen Xu, Yuan Huang, Qingwen Sun
Summary: This study assembled and analyzed the chloroplast genomes of the genus Sabia, revealing a relatively conserved genome structure with multiple variable loci. Phylogenetic analysis indicated that the two sections of Sabia did not form separate monophyletic groups. Divergence time calculations showed that the evolutionary branches of Sabia and Meliosma began approximately 85.95 million years ago, with species within Sabia diverging around 7.65 million years ago.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Evolutionary Biology
Nikolas P. Johnston, Thomas Pape, Marcin Piwczynski, James F. Wallman, Brian M. Wiegmann, Brian K. Cassel, Kamran Akbarzadeh, Krzysztof Szpila
Summary: This study used Anchored Hybrid Enrichment (AHE) to investigate the phylogeny of the Miltogramminae subfamily of flesh flies. By analyzing concatenated loci, the study resolved several critical issues in the classification of this group and provided unprecedented insight into their relationships. The findings led to a major update in the classification of Miltogramminae.
SYSTEMATIC ENTOMOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Lei Guo, Xia Wang, Ruihong Wang, Pan Li
Summary: This study focused on the chloroplast genomes of Scrophularia ningpoensis and its adulterants. The research revealed a high degree of conservation in genomic structure and identified potential molecular markers for species identification. Additionally, the study established the phylogenetic relationships of S. ningpoensis and its related species. The findings highlight the importance of chloroplast genomes in identifying medicinal plants and understanding evolutionary processes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Microbiology
Praveen Rahi, Mitesh Khairnar, Ashwini Hagir, Avinash Narayan, Kunal R. Jain, Datta Madamwar, Aabeejjeet Pansare, Yogesh Shouche
Summary: A novel bacterial strain ADMK78(T) was isolated from saline desert soil, identified as a new species named Peteryoungia desertarenae based on phylogenetic analysis, physiological characteristics, and genetic similarities with related species. The study also proposed reclassifications of several Rhizobium species into the genera Peteryoungia and Ciceribacter, based on core gene phylogeny and ANI values.
ARCHIVES OF MICROBIOLOGY
(2021)
Article
Biology
Xiu-Xiu Guo, Xiao-Jian Qu, Xue-Jie Zhang, Shou-Jin Fan
Summary: This study focuses on the plastomes of Aristidoideae, a subfamily in the family Poaceae. The plastomes of two species, Aristida adscensionis and Stipagrostis pennata, were newly sequenced and compared with a total of 16 Aristidoideae plastomes. The plastomes were found to be conservative in terms of genome size, gene number, structure, and IR boundary. Repeat sequence analysis showed that forward and palindrome repeats were the most common types. The study also analyzed codon usage and identified highly variable regions. The phylogenetic analysis supported the monophyly of Aristidoideae and the relationship between the three genera. The divergence between different species may be associated with factors such as carbon fixation patterns, geographical distributions, and ploidy. This study contributes to our understanding of the phylogeny and evolution of Aristidoideae.
Article
Microbiology
Hao You, Lin Xu, Yan-Hui Kong, Cong Sun, Peng Zhou, Xue-Wei Xu
Summary: A novel aerobic bacterium, designated as Sphingomicrobium nitratireducens sp. nov., was isolated from a tidal flat sediment in southern China. This strain showed unique morphological, physiological, and genetic characteristics, and belonged to the genus Sphingomicrobium.
ARCHIVES OF MICROBIOLOGY
(2022)
Article
Microbiology
Lin Xu, Jun-Jie Ying, Yuan-Chun Fang, Ran Zhang, Jia Hua, Min Wu, Bing-Nan Han, Cong Sun
Summary: Three strains of Halomonas were isolated from stems of Populus euphratica and characterized by their unique biological features and genomic composition. Based on phenotypic, chemotaxonomic, phylogenetic and genomic analyses, these strains represent a novel species within the genus Halomonas.
ARCHIVES OF MICROBIOLOGY
(2022)
Article
Microbiology
Peter Kaempfer, Stefanie P. Glaeser, John A. McInroy, Dominique Clermont, Andre Lipski, Alexis Criscuolo
Summary: A new species of the genus Neobacillus, Neobacillus rhizosphaerae, was isolated from the roots/rhizosphere of maize. It exhibited lower similarity to other Neobacillus species and had slight physiological and biochemical differences. Additionally, the reclassification of Bacillus dielmonensis as Neobacillus dielmonensis was proposed based on phylogenomic and conserved signature indel analyses.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Microbiology
Xue Yu, Wei Zhang, Gaosen Zhang, Yujie Wu, Shiyu Wu, Mao Tian, Wei Ding, Ali Bahadur, Tuo Chen, Guangxiu Liu
Summary: A novel species of Arthrobacter, capable of producing a water-soluble blue pigment, was discovered in the soil of Mt. Everest. This species shows significant genetic distance to its closest relatives and has high tolerance to hydrogen peroxide.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Microbiology
Carlos Cortes-Albayay, Vartul Sangal, Hans-Peter Klenk, Imen Nouioui
Summary: This study compared the biodegradation capabilities of several mycobacterial species for chlorinated ethenes, finding multiple genes involved in the process and confirming the formation of a novel clade, classified as Mycolicibacterium vinylchloridicum sp. nov.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Bram Danneels, Monique Blignaut, Guillaume Marti, Simon Sieber, Peter Vandamme, Marion Meyer, Aurelien Carlier
Summary: The symbiotic relationships between plants of the Rubiaceae and Primulaceae families and Burkholderia bacteria are unique and intimate. This study assembled and analyzed 17 new endophyte genomes, revealing that all endophytes, despite their taxonomic diversity, contained gene clusters linked to the production of specialized metabolites. Acquisition of secondary metabolite gene clusters through horizontal gene transfer is proposed to be a prerequisite for the evolution of a stable association between these endophytes and their hosts.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Review
Entomology
Mary Morgan-Richards, Craig J. Marshall, Patrick J. Biggs, Steven A. Trewick
Summary: The alpine insect fauna of Aotearoa/New Zealand can survive freezing at any time of the year, and the role of microbes living in their guts in facilitating this freezing tolerance is considered. Many bacteria and fungi produce ice-nucleating agents that mediate ice crystal formation, which can have both positive and negative impacts on insects. Insects that are freeze-tolerant start freezing at high sub-zero temperatures, producing small ice crystals with the help of ice-nucleating agents. Gut microbes in New Zealand insects may provide ice-nucleating active compounds that moderate freezing, and there could be potential transmission pathways of shared gut fauna. Despite years of research, the role of exogenous ice-nucleating agents in freeze-tolerant insects has been neglected.
Article
Biochemistry & Molecular Biology
Amanda Hettiarachchi, Margo Cnockaert, Marie Joossens, David Laureys, Jessika De Clippeleer, Nicolas J. Vereecken, Denis Michez, Guy Smagghe, Dirk C. de Graaf, Peter Vandamme
Summary: This study analyzed the cultivable bacterial communities of different compartments in the invasive insect Vespa velutina, as well as the nest samples, using both cultivation and 16S rRNA amplicon sequencing. The bacterial symbionts in Vespa velutina were dominated by Convivina, Fructobacillus, Lactiplantibacillus, Lactococcus, Sphingomonas, and Spiroplasma. Lactococcus lactis and Lactiplantibacillus plantarum were generalist core lactic acid bacteria (LAB) symbionts, while Convivina species and Fructobacillus fructosus were highly specialized core LAB symbionts with reduced genome sizes. Sphingomonas and Spiroplasma were non-LAB core symbionts, but they were not isolated. Convivina bacteria were particularly enriched in the hornet crop and included Convivina intestini, a species adapted to amino acid metabolism, and Convivina praedatoris sp. nov., which was adapted to carbohydrate metabolism.
INSECT MOLECULAR BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Tina Tuerlings, Amanda Hettiarachchi, Marie Joossens, Benoit Geslin, Nicolas J. J. Vereecken, Denis Michez, Guy Smagghe, Peter Vandamme
Summary: The study characterized the gut microbiota of invasive bee Megachile sculpturalis from native and invaded regions. The microbiota communities in bees from invaded regions were similar and different from those in Japan. Core amplicon sequence variants (ASVs) represented micro-organisms commonly present in bee-associated niches. The absence of known bee pathogens and presence of microparasite infections suggest a potential role of pathogen pressure and natural enemies in the invasion success of M. sculpturalis.
INSECT MOLECULAR BIOLOGY
(2023)
Article
Food Science & Technology
Louise Vermote, Jonas De Roos, Margo Cnockaert, Peter Vandamme, Stefan Weckx, Luc De Vuyst
Summary: Belgian lambic beers are produced using traditional craftsmanship, relying on wooden barrels for spontaneous fermentation and maturation. These barrels play a crucial role in establishing a stable microbial ecosystem, minimizing batch-to-batch variations, and preventing flavor deviations. They provide an inoculation source of necessary microorganisms and a microaerobic environment for successful lambic beer production.
INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY
(2023)
Article
Microbiology
Juan Guzman, Miyoung Won, Anja Poehlein, Atena Sadat Sombolestani, Daniela Mayorga-Ch, David Laureys, Jessika De Clippeleer, Peter Kaempfer, Rolf Daniel, Andreas Vilcinskas, Peter Vandamme, Soon- Wo Kwon
Summary: In this study, two strains of bacteria were isolated from wasps in Germany and Korea. Molecular and phenotypic analysis showed that these strains are closely related to known species but also have distinct characteristics. Therefore, it is proposed to name these strains Aristophania vespae.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2023)
Article
Microbiology
Sam C. Mahoney-Kurpe, Nikola Palevich, Samantha J. Noel, Dragana Gagic, Patrick J. Biggs, Priya Soni, Peter M. Reid, Satoshi Koike, Yasuo Kobayashi, Peter H. Janssen, Graeme T. Attwood, Christina D. Moon
Summary: This study characterized two strains of bacteria from an abundant but uncharacterized group of rumen bacteria, which belong to a novel family of the order 'Christensenellales'. These strains, named R-7T and WTE2008T, showed high sequence similarity in their 16S rRNA gene sequences and shared an average nucleotide identity of 83.6% in their genome sequences. The strains also exhibited differences in carbon source utilization and fermentation end products.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Peter Vandamme, Charlotte Peeters, Amanda Hettiarachchi, Margo Cnockaert, Aurelien Carlier
Summary: Strain LMG 31809 T was isolated from a top soil sample in Belgium and classified as a rare biosphere bacterium that occurs at low abundances in multiple soil and water ecosystems. It represents a new species within a new genus, Govania unica gen. nov., sp. nov, belonging to the class Alphaproteobacteria. The strain is strictly aerobic and uses organic acids and possibly aromatic compounds as growth substrates. Its whole-genome sequence has a size of 3.21 Mbp with a G + C content of 58.99 mol%.
SYSTEMATIC AND APPLIED MICROBIOLOGY
(2023)
Article
Infectious Diseases
Ali Heydari, Nick D. Kim, Patrick J. Biggs, Jacqui Horswell, Gerty J. H. P. Gielen, Alma Siggins, Matthew D. Taylor, Collette Bromhead, Barry R. Palmer
Summary: The accumulation of heavy metals in agricultural soil from superphosphate fertilisers can cause soil bacteria to develop resistance to heavy metals and antibiotics. This study investigated the co-selection of heavy metal and antibiotic resistance in uncontaminated soil incubated with cadmium, zinc, and mercury for 6 weeks. The microbial communities exposed to heavy metals were found to differ significantly from the control group across various taxonomic levels.
Article
Biotechnology & Applied Microbiology
Nanzhen Qiao, Julia Bechtner, Margo Cnockaert, Eliza Depoorter, Christian Diaz-Munoz, Peter Vandamme, Luc De Vuyst, Michael G. Ganzle
Summary: This study characterized the genus Periweissella through phylogenetic analysis and genomic analysis, revealing its evolutionary relationship with closely related genera Weissella and Furfurilactobacillus. The study also determined the genetic and physiological traits of the genus. Results showed that Periweissella is the link between rod-shaped heterofermentative lactobacilli and the coccoid Leuconostoc clade, and it is the only heterofermentative genus in the Lactobacillaceae that comprises predominantly motile strains.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Ecology
Amanda Hettiarachchi, Margo Cnockaert, Marie Joossens, Antoine Gekiere, Ivan Meeus, Nicolas J. Vereecken, Denis Michez, Guy Smagghe, Peter Vandamme
Summary: We characterized the microbial communities in different parts of four wild solitary bee species and found that the dominant bacteria were endosymbionts such as Wolbachia and Spiroplasma. Other bacterial and yeast genera were associated with environmental sources. The bacterial communities varied between bee species, gut compartments, and ovaries, suggesting a selective process influenced by floral and host traits. Many of the gut symbionts identified in this study exhibited metabolic versatility.
Article
Biotechnology & Applied Microbiology
Atena Sadat Sombolestani, Dries Bongaerts, Eliza Depoorter, Ilse Cleenwerck, Anneleen D. Wieme, Scott J. Britton, Stefan Weckx, Luc De Vuyst, Peter Vandamme
Summary: Polyphasic taxonomic and comparative genomic analyses revealed a novel species among acetic acid bacteria, named Brytella acorum gen. nov., sp. nov., represented by lambic beer isolates including strain LMG 32668T and the kombucha isolate LMG 32879. This species has Acidomonas methanolica as its closest phylogenomic neighbor and possesses metabolic characteristics typical of acetic acid bacteria. The absence of glycolysis pathway and the presence of both aerobic respiration and oxidative fermentation for energy metabolism are notable features. Antibiotic resistance genes and virulence factors are absent.
SYSTEMATIC AND APPLIED MICROBIOLOGY
(2023)
Article
Ecology
Joseph Guhlin, Marissa F. Le Lec, Jana Wold, Emily Koot, David Winter, Patrick J. Biggs, Stephanie J. Galla, Lara Urban, Yasmin Foster, Murray P. Cox, Andrew Digby, Lydia R. Uddstrom, Daryl Eason, Deidre Vercoe, Tane Davis, Jason T. Howard, Erich D. Jarvis, Fiona E. Robertson, Bruce C. Robertson, Neil J. Gemmell, Tammy E. Steeves, Anna W. Santure, Peter K. Dearden
Summary: The study investigated the genetic variation and phenotypic influences in the critically endangered kakapo parrot using whole-genome sequence data and phenotype data. Associations were found between genic regions and traits such as growth and disease susceptibility. The study also showed that active management has maintained genetic diversity and evolutionary potential in the species. The findings provide insights for future conservation management decisions for the kakapo.
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Biology
Luc Cornet, Benoit Durieu, Frederik Baert, Elizabet D'hooge, David Colignon, Loic Meunier, Valerian Lupo, Ilse Cleenwerck, Heide-Marie Daniel, Leen Rigouts, Damien Sirjacobs, Stephane Declerck, Peter Vandamme, Annick Wilmotte, Denis Baurain, Pierre Becker
Summary: A bioinformatics toolbox called GEN-ERA has been developed by the Belgian Coordinated Collections of Microorganisms. It allows researchers to perform robust phylogenomic analyses on bacteria and small eukaryotes without specific training in bioinformatics. The toolbox provides workflows for genome downloading, quality assessment, contamination estimation, tree reconstruction, average nucleotide identity comparisons, and metabolic modeling. It has been tested on various microorganisms and used in a case study on Gloeobacterales for microbial taxonomy.
Article
Environmental Sciences
Leon Marshall, Nicolas Leclercq, Timothy Weekers, Insafe El Abdouni, Luisa G. Carvalheiro, Michael Kuhlmann, Denis Michez, Pierre Rasmont, Stuart P. M. Roberts, Guy Smagghe, Peter Vandamme, Thomas Wood, Nicolas J. Vereecken
Summary: Visitation by wild bee species is essential for apple production, but they are vulnerable to climate change. We modeled the distribution range shifts of key apple-pollinating bee species under different climate change scenarios and found that overall contractions in range are limited. However, under the worst-case scenario, some countries such as France and Italy may experience significant loss in bee populations and potential pollination services. Climate change is not the only threat to apple pollination, and future deficits will also depend on orchard management and ecological infrastructure.
GLOBAL ENVIRONMENTAL CHANGE-HUMAN AND POLICY DIMENSIONS
(2023)