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Padalko A, Nair G, Sousa FL. Fusion/fission protein family identification in Archaea. mSystems 2024; 9:e0094823. [PMID: 38700364 DOI: 10.1128/msystems.00948-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 04/02/2024] [Indexed: 05/05/2024] Open
Abstract
The majority of newly discovered archaeal lineages remain without a cultivated representative, but scarce experimental data from the cultivated organisms show that they harbor distinct functional repertoires. To unveil the ecological as well as evolutionary impact of Archaea from metagenomics, new computational methods need to be developed, followed by in-depth analysis. Among them is the genome-wide protein fusion screening performed here. Natural fusions and fissions of genes not only contribute to microbial evolution but also complicate the correct identification and functional annotation of sequences. The products of these processes can be defined as fusion (or composite) proteins, the ones consisting of two or more domains originally encoded by different genes and split proteins, and the ones originating from the separation of a gene in two (fission). Fusion identifications are required for proper phylogenetic reconstructions and metabolic pathway completeness assessments, while mappings between fused and unfused proteins can fill some of the existing gaps in metabolic models. In the archaeal genome-wide screening, more than 1,900 fusion/fission protein clusters were identified, belonging to both newly sequenced and well-studied lineages. These protein families are mainly associated with different types of metabolism, genetic, and cellular processes. Moreover, 162 of the identified fusion/fission protein families are archaeal specific, having no identified fused homolog within the bacterial domain. Our approach was validated by the identification of experimentally characterized fusion/fission cases. However, around 25% of the identified fusion/fission families lack functional annotations for both composite and split states, showing the need for experimental characterization in Archaea.IMPORTANCEGenome-wide fusion screening has never been performed in Archaea on a broad taxonomic scale. The overlay of multiple computational techniques allows the detection of a fine-grained set of predicted fusion/fission families, instead of rough estimations based on conserved domain annotations only. The exhaustive mapping of fused proteins to bacterial organisms allows us to capture fusion/fission families that are specific to archaeal biology, as well as to identify links between bacterial and archaeal lineages based on cooccurrence of taxonomically restricted proteins and their sequence features. Furthermore, the identification of poorly characterized lineage-specific fusion proteins opens up possibilities for future experimental and computational investigations. This approach enhances our understanding of Archaea in general and provides potential candidates for in-depth studies in the future.
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Affiliation(s)
- Anastasiia Padalko
- Genome Evolution and Ecology Group, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Doctoral School of Ecology and Evolution, University of Vienna, Vienna, Austria
| | - Govind Nair
- Genome Evolution and Ecology Group, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Filipa L Sousa
- Genome Evolution and Ecology Group, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
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Oladele P, Ngo J, Chang T, Johnson TA. Temporal dynamics of fecal microbiota community succession in broiler chickens, calves, and piglets under aerobic exposure. Microbiol Spectr 2024; 12:e0408423. [PMID: 38717193 DOI: 10.1128/spectrum.04084-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/16/2024] [Indexed: 06/06/2024] Open
Abstract
Researchers have extensively studied the effect of oxygen on the growth and survival of bacteria. However, the impact of oxygen on bacterial community structure, particularly its ability to select for taxa within the context of a complex microbial community, is still unclear. In a 21-day microcosm experiment, we investigated the effect of aerobic exposure on the fecal community structure and succession pattern in broiler, calf, and piglet feces (n = 10 for each feces type). Bacterial diversity decreased and community structure changed rapidly in the broiler microbiome (P < 0.001), while the fecal community of calves and piglets, which have higher initial diversity, was stable after initial exposure but decreased in diversity after 3 days (P < 0.001). The response to aerobic exposure was host animal specific, but in all three animals, the change in community structure was driven by a decrease in anaerobic species, primarily belonging to Firmicutes and Bacteroidetes (except in broilers where Bacteroidetes increased), along with an increase in aerobic species belonging to Proteobacteria and Actinobacteria. Using random forest regression, we identified microbial features that predict aerobic exposure. In all three animals, host-beneficial Prevotella-related ASVs decreased after exposure, while ASVs belonging to Acinetobacter, Corynbacterium, and Tissierella were increased. The decrease of Prevotella was rapid in broilers but delayed in calves and piglets. Knowing when these pathobionts increase in abundance after aerobic exposure could inform farm sanitation practices and could be important in designing animal experiments that modulate the microbiome.IMPORTANCEThe fecal microbial community is contained within a dynamic ecosystem of interacting microbes that varies in biotic and abiotic components across different animal species. Although oxygen affects bacterial growth, its specific impact on the structure of complex communities, such as those found in feces, and how these effects vary between different animal species are poorly understood. In this study, we demonstrate that the effect of aerobic exposure on the fecal microbiota was host-animal-specific, primarily driven by a decrease in Firmicutes and Bacteroidetes, but accompanied by an increase in Actinobacteria, Proteobacteria, and other pathobionts. Interestingly, we observed that more complex communities from pig and cattle exhibited initial resilience, while a less diverse community from broilers displayed a rapid response to aerobic exposure. Our findings offer insights that can inform farm sanitation practices, as well as experimental design, sample collection, and processing protocols for microbiome studies across various animal species.
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Affiliation(s)
- Paul Oladele
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Jennifer Ngo
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Tiffany Chang
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Timothy A Johnson
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, USA
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Anka IZ, Uren Webster TM, Berbel-Filho WM, Hitchings M, Overland B, Weller S, Garcia de Leaniz C, Consuegra S. Microbiome and epigenetic variation in wild fish with low genetic diversity. Nat Commun 2024; 15:4725. [PMID: 38830879 PMCID: PMC11148108 DOI: 10.1038/s41467-024-49162-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 05/23/2024] [Indexed: 06/05/2024] Open
Abstract
Non-genetic sources of phenotypic variation, such as the epigenome and the microbiome, could be important contributors to adaptive variation for species with low genetic diversity. However, little is known about the complex interaction between these factors and the genetic diversity of the host, particularly in wild populations. Here, we examine the skin microbiome composition of two closely-related mangrove killifish species with different mating systems (self-fertilising and outcrossing) under sympatric and allopatric conditions. This allows us to partition the influence of the genotype and the environment on their microbiome and (previously described) epigenetic profiles. We find the diversity and community composition of the skin microbiome are strongly shaped by the environment and, to a lesser extent, by species-specific influences. Heterozygosity and microbiome alpha diversity, but not epigenetic variation, are associated with the fluctuating asymmetry of traits related to performance (vision) and behaviour (aggression). Our study identifies that a proportion of the epigenetic diversity and microbiome differentiation is unrelated to genetic variation, and we find evidence for an associative relationship between microbiome and epigenetic diversity in these wild populations. This suggests that both mechanisms could potentially contribute to variation in species with low genetic diversity.
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Affiliation(s)
- Ishrat Z Anka
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, Wales, SA2 8PP, UK
- Department of Aquaculture, Chattogram Veterinary and Animal Sciences University, Chattogram, 4225, Bangladesh
| | - Tamsyn M Uren Webster
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, Wales, SA2 8PP, UK
| | - Waldir M Berbel-Filho
- Department of Biology, University of Oklahoma, Norman, OK, 73019, USA
- Department of Biology, University of West Florida, Pensacola, FL, USA
| | - Matthew Hitchings
- Institute of Life Science, Swansea University, Swansea, Wales, SA2 8PP, UK
| | - Benjamin Overland
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, Wales, SA2 8PP, UK
| | - Sarah Weller
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, Wales, SA2 8PP, UK
| | - Carlos Garcia de Leaniz
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, Wales, SA2 8PP, UK
- Marine Research Centre (CIM-UVIGO), Universidade de Vigo, Vigo, Spain
| | - Sofia Consuegra
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, Wales, SA2 8PP, UK.
- Grupo de Biotecnología Acuática, Departamento de Biotecnología y Acuicultura, Instituto de Investigacións Mariñas, IIM-CSIC, Vigo, Spain.
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Geller AM, Shalom M, Zlotkin D, Blum N, Levy A. Identification of type VI secretion system effector-immunity pairs using structural bioinformatics. Mol Syst Biol 2024; 20:702-718. [PMID: 38658795 PMCID: PMC11148199 DOI: 10.1038/s44320-024-00035-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/24/2024] [Accepted: 04/09/2024] [Indexed: 04/26/2024] Open
Abstract
The type VI secretion system (T6SS) is an important mediator of microbe-microbe and microbe-host interactions. Gram-negative bacteria use the T6SS to inject T6SS effectors (T6Es), which are usually proteins with toxic activity, into neighboring cells. Antibacterial effectors have cognate immunity proteins that neutralize self-intoxication. Here, we applied novel structural bioinformatic tools to perform systematic discovery and functional annotation of T6Es and their cognate immunity proteins from a dataset of 17,920 T6SS-encoding bacterial genomes. Using structural clustering, we identified 517 putative T6E families, outperforming sequence-based clustering. We developed a logistic regression model to reliably quantify protein-protein interaction of new T6E-immunity pairs, yielding candidate immunity proteins for 231 out of the 517 T6E families. We used sensitive structure-based annotation which yielded functional annotations for 51% of the T6E families, again outperforming sequence-based annotation. Next, we validated four novel T6E-immunity pairs using basic experiments in E. coli. In particular, we showed that the Pfam domain DUF3289 is a homolog of Colicin M and that DUF943 acts as its cognate immunity protein. Furthermore, we discovered a novel T6E that is a structural homolog of SleB, a lytic transglycosylase, and identified a specific glutamate that acts as its putative catalytic residue. Overall, this study applies novel structural bioinformatic tools to T6E-immunity pair discovery, and provides an extensive database of annotated T6E-immunity pairs.
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Affiliation(s)
- Alexander M Geller
- Department of Plant Pathology and Microbiology, The Institute of Environmental Science, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Maor Shalom
- Department of Plant Pathology and Microbiology, The Institute of Environmental Science, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - David Zlotkin
- Department of Plant Pathology and Microbiology, The Institute of Environmental Science, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Noam Blum
- Department of Plant Pathology and Microbiology, The Institute of Environmental Science, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Asaf Levy
- Department of Plant Pathology and Microbiology, The Institute of Environmental Science, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
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Guo H, Chen Y, Dong W, Lu S, Du Y, Duan L. Fecal Coprococcus, hidden behind abdominal symptoms in patients with small intestinal bacterial overgrowth. J Transl Med 2024; 22:496. [PMID: 38796441 PMCID: PMC11128122 DOI: 10.1186/s12967-024-05316-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 05/20/2024] [Indexed: 05/28/2024] Open
Abstract
BACKGROUND Small intestinal bacterial overgrowth (SIBO) is the presence of an abnormally excessive amount of bacterial colonization in the small bowel. Hydrogen and methane breath test has been widely applied as a non-invasive method for SIBO. However, the positive breath test representative of bacterial overgrowth could also be detected in asymptomatic individuals. METHODS To explore the relationship between clinical symptoms and gut dysbiosis, and find potential fecal biomarkers for SIBO, we compared the microbial profiles between SIBO subjects with positive breath test but without abdominal symptoms (PBT) and healthy controls (HC) using 16S rRNA amplicon sequencing. RESULTS Fecal samples were collected from 63 SIBO who complained of diarrhea, distension, constipation, or abdominal pain, 36 PBT, and 55 HC. For alpha diversity, the Shannon index of community diversity on the genus level showed a tendency for a slight increase in SIBO, while the Shannon index on the predicted function was significantly decreased in SIBO. On the genus level, significantly decreased Bacteroides, increased Coprococcus_2, and unique Butyrivibrio were observed in SIBO. There was a significant positive correlation between saccharolytic Coprococcus_2 and the severity of abdominal symptoms. Differently, the unique Veillonella in the PBT group was related to amino acid fermentation. Interestingly, the co-occurrence network density of PBT was larger than SIBO, which indicates a complicated interaction of genera. Coprococcus_2 showed one of the largest betweenness centrality in both SIBO and PBT microbiota networks. Pathway analysis based on the Kyoto Encyclopedia of Genes and Genome (KEGG) database reflected that one carbon pool by folate and multiple amino acid metabolism were significantly down in SIBO. CONCLUSIONS This study provides valuable insights into the fecal microbiota composition and predicted metabolic functional changes in patients with SIBO. Butyrivibrio and Coprococcus_2, both renowned for their role in carbohydrate fermenters and gas production, contributed significantly to the symptoms of the patients. Coprococcus's abundance hints at its use as a SIBO marker. Asymptomatic PBT individuals show a different microbiome, rich in Veillonella. PBT's complex microbial interactions might stabilize the intestinal ecosystem, but further study is needed due to the core microbiota similarities with SIBO. Predicted folate and amino acid metabolism reductions in SIBO merit additional validation.
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Affiliation(s)
- Huaizhu Guo
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
| | - Yuzhu Chen
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
| | - Wenxin Dong
- Department of Pediatrics, Peking University Third Hospital, Beijing, China
| | - Siqi Lu
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
| | - Yanlin Du
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
| | - Liping Duan
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China.
- International Institute of Population Health, Peking University Health Science Center, Beijing, China.
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Wienhausen G, Moraru C, Bruns S, Tran DQ, Sultana S, Wilkes H, Dlugosch L, Azam F, Simon M. Ligand cross-feeding resolves bacterial vitamin B 12 auxotrophies. Nature 2024; 629:886-892. [PMID: 38720071 DOI: 10.1038/s41586-024-07396-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 04/08/2024] [Indexed: 05/24/2024]
Abstract
Cobalamin (vitamin B12, herein referred to as B12) is an essential cofactor for most marine prokaryotes and eukaryotes1,2. Synthesized by a limited number of prokaryotes, its scarcity affects microbial interactions and community dynamics2-4. Here we show that two bacterial B12 auxotrophs can salvage different B12 building blocks and cooperate to synthesize B12. A Colwellia sp. synthesizes and releases the activated lower ligand α-ribazole, which is used by another B12 auxotroph, a Roseovarius sp., to produce the corrin ring and synthesize B12. Release of B12 by Roseovarius sp. happens only in co-culture with Colwellia sp. and only coincidently with the induction of a prophage encoded in Roseovarius sp. Subsequent growth of Colwellia sp. in these conditions may be due to the provision of B12 by lysed cells of Roseovarius sp. Further evidence is required to support a causative role for prophage induction in the release of B12. These complex microbial interactions of ligand cross-feeding and joint B12 biosynthesis seem to be widespread in marine pelagic ecosystems. In the western and northern tropical Atlantic Ocean, bacteria predicted to be capable of salvaging cobinamide and synthesizing only the activated lower ligand outnumber B12 producers. These findings add new players to our understanding of B12 supply to auxotrophic microorganisms in the ocean and possibly in other ecosystems.
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Affiliation(s)
- Gerrit Wienhausen
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany.
- Scripps Institution of Oceanography, Marine Biology Research Division, University of California San Diego, La Jolla, CA, USA.
| | - Cristina Moraru
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
- Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Stefan Bruns
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Den Quoc Tran
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Sabiha Sultana
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Heinz Wilkes
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Leon Dlugosch
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Farooq Azam
- Scripps Institution of Oceanography, Marine Biology Research Division, University of California San Diego, La Jolla, CA, USA
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany.
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Oldenburg, Germany.
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Lirette AO, Chen YJ, Freyria NJ, Góngora E, Greer CW, Whyte LG. Characterization of hydrocarbon degraders from Northwest Passage beach sediments and assessment of their ability for bioremediation. Can J Microbiol 2024; 70:163-177. [PMID: 38350082 DOI: 10.1139/cjm-2023-0093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
Global warming-induced sea ice loss in the Canadian Northwest Passage (NWP) will result in more shipping traffic, increasing the risk of oil spills. Microorganisms inhabiting NWP beach sediments may degrade hydrocarbons, offering a potential bioremediation strategy. In this study, the characterization and genomic analyses of 22 hydrocarbon-biodegradative bacterial isolates revealed that they contained a diverse range of key alkane and aromatic hydrocarbon-degradative genes, as well as cold and salt tolerance genes indicating they are highly adapted to the extreme Arctic environment. Some isolates successfully degraded Ultra Low Sulfur Fuel Oil (ULSFO) at temperatures as low as -5 °C and high salinities (3%-10%). Three isolates were grown in liquid medium containing ULSFO as sole carbon source over 3 months and variation of hydrocarbon concentration was measured at three time points to determine their rate of hydrocarbon biodegradation. Our results demonstrate that two isolates (Rhodococcus sp. R1B_2T and Pseudarthrobacter sp. R2D_1T) possess complete degradation pathways and can grow on alkane and aromatic components of ULSFO under Arctic conditions. Overall, these results demonstrate that diverse hydrocarbon-degrading microorganisms exist in the NWP beach sediments, offering a potential bioremediation strategy in the events of a marine fuel spill reaching the shores of the NWP.
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Affiliation(s)
- Antoine-O Lirette
- Department of Natural Resource Sciences, McGill University, QC, Canada
| | - Ya-Jou Chen
- Department of Natural Resource Sciences, McGill University, QC, Canada
| | | | - Esteban Góngora
- Department of Natural Resource Sciences, McGill University, QC, Canada
| | - Charles W Greer
- Department of Natural Resource Sciences, McGill University, QC, Canada
| | - Lyle G Whyte
- Department of Natural Resource Sciences, McGill University, QC, Canada
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Kumar K, Barbora L, Moholkar VS. Genomic insights into clostridia in bioenergy production: Comparison of metabolic capabilities and evolutionary relationships. Biotechnol Bioeng 2024; 121:1298-1313. [PMID: 38047471 DOI: 10.1002/bit.28610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 10/19/2023] [Accepted: 11/16/2023] [Indexed: 12/05/2023]
Abstract
Bacteria from diverse genera, including Acetivibrio, Bacillus, Cellulosilyticum, Clostridium, Desulfotomaculum, Lachnoclostridium, Moorella, Ruminiclostridium, and Thermoanaerobacterium, have attracted significant attention due to their versatile metabolic capabilities encompassing acetogenic, cellulolytic, and C1-metabolic properties, and acetone-butanol-ethanol fermentation. Despite their biotechnological significance, a comprehensive understanding of clostridial physiology and evolution has remained elusive. This study reports an extensive comparative genomic analysis of 48 fully sequenced bacterial genomes from these genera. Our investigation, encompassing pan-genomic analysis, central carbon metabolism comparison, exploration of general genome features, and in-depth scrutiny of Cluster of Orthologous Groups genes, has established a holistic whole-genome-based phylogenetic framework. We have classified these strains into acetogenic, butanol-producing, cellulolytic, CO2-fixating, chemo(litho/organo)trophic, and heterotrophic categories, often exhibiting overlaps. Key outcomes include the identification of misclassified species and the revelation of insights into metabolic features, energy conservation, substrate utilization, stress responses, and regulatory mechanisms. These findings can provide guidance for the development of efficient microbial systems for sustainable bioenergy production. Furthermore, by addressing fundamental questions regarding genetic relationships, conserved genomic features, pivotal enzymes, and essential genes, this study has also contributed to our comprehension of clostridial biology, evolution, and their shared metabolic potential.
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Affiliation(s)
- Karan Kumar
- School of Energy Science and Engineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Lepakshi Barbora
- School of Energy Science and Engineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Vijayanand S Moholkar
- School of Energy Science and Engineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
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Dotan E, Jaschek G, Pupko T, Belinkov Y. Effect of tokenization on transformers for biological sequences. Bioinformatics 2024; 40:btae196. [PMID: 38608190 PMCID: PMC11055402 DOI: 10.1093/bioinformatics/btae196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 02/20/2024] [Accepted: 04/11/2024] [Indexed: 04/14/2024] Open
Abstract
MOTIVATION Deep-learning models are transforming biological research, including many bioinformatics and comparative genomics algorithms, such as sequence alignments, phylogenetic tree inference, and automatic classification of protein functions. Among these deep-learning algorithms, models for processing natural languages, developed in the natural language processing (NLP) community, were recently applied to biological sequences. However, biological sequences are different from natural languages, such as English, and French, in which segmentation of the text to separate words is relatively straightforward. Moreover, biological sequences are characterized by extremely long sentences, which hamper their processing by current machine-learning models, notably the transformer architecture. In NLP, one of the first processing steps is to transform the raw text to a list of tokens. Deep-learning applications to biological sequence data mostly segment proteins and DNA to single characters. In this work, we study the effect of alternative tokenization algorithms on eight different tasks in biology, from predicting the function of proteins and their stability, through nucleotide sequence alignment, to classifying proteins to specific families. RESULTS We demonstrate that applying alternative tokenization algorithms can increase accuracy and at the same time, substantially reduce the input length compared to the trivial tokenizer in which each character is a token. Furthermore, applying these tokenization algorithms allows interpreting trained models, taking into account dependencies among positions. Finally, we trained these tokenizers on a large dataset of protein sequences containing more than 400 billion amino acids, which resulted in over a 3-fold decrease in the number of tokens. We then tested these tokenizers trained on large-scale data on the above specific tasks and showed that for some tasks it is highly beneficial to train database-specific tokenizers. Our study suggests that tokenizers are likely to be a critical component in future deep-network analysis of biological sequence data. AVAILABILITY AND IMPLEMENTATION Code, data, and trained tokenizers are available on https://github.com/technion-cs-nlp/BiologicalTokenizers.
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Affiliation(s)
- Edo Dotan
- The Henry and Marilyn Taub Faculty of Computer Science, Technion – Israel Institute of Technology, Haifa 3200003, Israel
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Gal Jaschek
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, United States
| | - Tal Pupko
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yonatan Belinkov
- The Henry and Marilyn Taub Faculty of Computer Science, Technion – Israel Institute of Technology, Haifa 3200003, Israel
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10
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Blázquez M, Ortiz-Álvarez R, Gasulla F, Pérez-Vargas I, Pérez-Ortega S. Bacterial communities associated with an island radiation of lichen-forming fungi. PLoS One 2024; 19:e0298599. [PMID: 38498492 PMCID: PMC10947700 DOI: 10.1371/journal.pone.0298599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 01/28/2024] [Indexed: 03/20/2024] Open
Abstract
Evolutionary radiations are one of the most striking processes biologists have studied in islands. A radiation is often sparked by the appearance of ecological opportunity, which can originate in processes like trophic niche segregation or the evolution of key innovations. Another recently proposed mechanism is facilitation mediated by the bacterial communities associated with the radiating species. Here we explore the role of the bacterial communities in a radiation of lichen-forming fungi endemic to Macaronesia. Bacterial diversity was quantified by high throughput sequencing of the V1-V2 hyper-variable region of 172 specimens. We characterized the taxonomic and phylogenetic diversity of the bacterial communities associated with the different species, tested for compositional differences between these communities, carried out a functional prediction, explored the relative importance of different factors in bacterial community structure, searched for phylosymbiosis and tried to identify the origin of this pattern. The species of the radiation differed in the composition of their bacterial communities, which were mostly comprised of Alphaproteobacteria and Acidobacteriia, but not in the functionality of those communities. A phylosimbiotic pattern was detected, but it was probably caused by environmental filtering. These findings are congruent with the combined effect of secondary chemistry and mycobiont identity being the main driver of bacterial community structure. Altogether, our results suggest that the associated bacterial communities are not the radiation's main driver. There is one possible exception, however, a species that has an abnormally diverse core microbiome and whose bacterial communities could be subject to a specific environmental filter at the functional level.
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Affiliation(s)
| | | | - Francisco Gasulla
- Department of Life Sciences, Universidad de Alcalá, Alcalá de Henares, Spain
| | - Israel Pérez-Vargas
- Department of Botany, Ecology and Plant Physiology, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
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Gray MJ. The role of metals in hypothiocyanite resistance in Escherichia coli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.583962. [PMID: 38496647 PMCID: PMC10942458 DOI: 10.1101/2024.03.07.583962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The innate immune system employs a variety of antimicrobial oxidants to control and kill host-associated bacteria. Hypothiocyanite/hypothiocyanous acid (-OSCN/HOSCN) is one such antimicrobial oxidant that is synthesized by lactoperoxidase, myeloperoxidase, and eosinophil peroxidase at sites throughout the human body. HOSCN has potent antibacterial activity while being largely non-toxic towards human cells. The molecular mechanisms by which bacteria sense and defend themselves against HOSCN have only recently begun to be elaborated, notably by the discovery of bacterial HOSCN reductase (RclA), an HOSCN-degrading enzyme widely conserved among bacteria that live on epithelial surfaces. In this paper, I show that Ni2+ sensitizes Escherichia coli to HOSCN by inhibiting glutathione reductase, and that inorganic polyphosphate protects E. coli against this effect, probably by chelating Ni2+ ions. I also found that RclA is very sensitive to inhibition by Cu2+ and Zn2+, metals that are accumulated to high levels by innate immune cells, and that, surprisingly, thioredoxin and thioredoxin reductase are not involved in HOSCN stress resistance in E. coli. These results advance our understanding of the contribution of different oxidative stress response and redox buffering pathways to HOSCN resistance in E. coli and illustrate important interactions between metal ions and the enzymes bacteria use to defend themselves against oxidative stress.
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Affiliation(s)
- Michael J. Gray
- Department of Microbiology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
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12
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Leong LEX, Denman SE, Kang S, Mondot S, Hugenholtz P, McSweeney CS. Identification of the mechanism for dehalorespiration of monofluoroacetate in the phylum Synergistota. Anim Biosci 2024; 37:396-403. [PMID: 38186254 PMCID: PMC10838667 DOI: 10.5713/ab.23.0351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/26/2023] [Indexed: 01/09/2024] Open
Abstract
OBJECTIVE Monofluoroacetate (MFA) is a potent toxin that blocks ATP production via the Krebs cycle and causes acute toxicity in ruminants consuming MFA-containing plants. The rumen bacterium, Cloacibacillus porcorum strain MFA1 belongs to the phylum Synergistota and can produce fluoride and acetate from MFA as the end-products of dehalorespiration. The aim of this study was to identify the genomic basis for the metabolism of MFA by this bacterium. METHODS A draft genome sequence for C. porcorum strain MFA1 was assembled and quantitative transcriptomic analysis was performed thus highlighting a candidate operon encoding four proteins that are responsible for the carbon-fluorine bond cleavage. Comparative genome analysis of this operon was undertaken with three other species of closely related Synergistota bacteria. RESULTS Two of the genes in this operon are related to the substrate-binding components of the glycine reductase protein B (GrdB) complex. Glycine shares a similar structure to MFA suggesting a role for these proteins in binding MFA. The remaining two genes in the operon, an antiporter family protein and an oxidoreductase belonging to the radical S-adenosyl methionine superfamily, are hypothesised to transport and activate the GrdB-like protein respectively. Similar operons were identified in a small number of other Synergistota bacteria including type strains of Cloacibacillus porcorum, C. evryensis, and Pyramidobacter piscolens, suggesting lateral transfer of the operon as these genera belong to separate families. We confirmed that all three species can degrade MFA, however, substrate degradation in P. piscolens was notably reduced compared to Cloacibacillus isolates possibly reflecting the loss of the oxidoreductase and antiporter in the P. piscolens operon. CONCLUSION Identification of this unusual anaerobic fluoroacetate metabolism extends the known substrates for dehalorespiration and indicates the potential for substrate plasticity in amino acid-reducing enzymes to include xenobiotics.
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Affiliation(s)
- Lex E X Leong
- CSIRO Agriculture and Food, St Lucia 4067, Queensland Australia
| | - Stuart E Denman
- CSIRO Agriculture and Food, St Lucia 4067, Queensland Australia
| | - Seungha Kang
- CSIRO Agriculture and Food, St Lucia 4067, Queensland Australia
- Current address: The University of Queensland Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane, Queensland 4102, Australia
| | - Stanislas Mondot
- Micalis Institute, INRA, AgroParisTech, University Paris-Saclay, 78350 Jouy-en- Josas, France
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Bioscience, the University of Queensland, St Lucia, 4072 Queensland Australia
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13
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Li J, Li Y, Xiao H, Li W, Ye F, Wang L, Li Y, Wang C, Wu Y, Xuan R, Huang Y, Huang J. The intestinal microflora diversity of aboriginal chickens in Jiangxi province, China. Poult Sci 2024; 103:103198. [PMID: 38016408 PMCID: PMC10696398 DOI: 10.1016/j.psj.2023.103198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 10/06/2023] [Accepted: 10/11/2023] [Indexed: 11/30/2023] Open
Abstract
Intestinal microbiota can coevolve with host to form symbiotic relationship and be participated in the regulation of host physiological function. At present, there is no clear explanation on the effect of intestinal microflora in Jiangxi aboriginal chickens. Here, we investigated the association between gut microbiota and host genome of Jiangxi local chickens using 16S rRNA sequencing and genome-wide association studies (GWAS). The results showed that the breeds and genders had important effects on the intestinal microbiota of chickens. A total of 28 SNPs in 14 regions of the chicken genome were related to the relative abundance of microorganisms in 5 genera: Clostridium_sensu_stricto_1, Enterococcus, Gallibacterium, Turicibacter, and Rikenellaceae_RC9_gut_group. A total of 17 candidate genes were identified composition of chicken microbiome and show an association between the host genome and the chicken intestinal microbiota, which also unveiled the diversity of intestinal microbes in Jiangxi chickens. Given the correlation between chicken genome and intestinal microbe found in the present study, a new idea for the protection of aboriginal chicken genetic resources in China could be provided.
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Affiliation(s)
- Jiawei Li
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Yuping Li
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Huiyuan Xiao
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Wen Li
- Changsheng Town People's Government of Ningdu County, Ganzhou, China
| | - Fengchun Ye
- Jiangxi Yifeng County Qiaoxi Veterinary Station, Yichun, China
| | - Liping Wang
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Yuhang Li
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Cong Wang
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Yan Wu
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Rui Xuan
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Yuxuan Huang
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China
| | - Jianhua Huang
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, China.
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14
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Dutta RK, Abu YF, Tao J, Chupikova I, Oleas J, Singh PK, Vitari NA, Qureshi R, Ramakrishnan S, Roy S. Altered gut microbiome drives heightened pain sensitivity in a murine model of metastatic triple-negative breast cancer. Am J Cancer Res 2024; 14:274-299. [PMID: 38323292 PMCID: PMC10839306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 12/25/2023] [Indexed: 02/08/2024] Open
Abstract
The microbiota residing in the gut environment is essential for host homeostasis. Increasing evidence suggests that microbial perturbation (dysbiosis) regulates cancer initiation and progression at local and distant sites. Here, we have identified microbial dysbiosis with the depletion of commensal bacteria as a host-intrinsic factor associated with metastatic dissemination to the bone. Using a mouse model of triple-negative mammary cancer, we demonstrate that a pre-established disruption of microbial homeostasis using an antibiotic cocktail increases tumor growth, enhanced circulating tumor cells, and subsequent dissemination to the bone. We found that the presence of pathogenic bacteria and loss of commensal bacteria in an antibiotic-induced gut environment is associated with sustained inflammation. Increased secretion of G-CSF and MMP-9 in intestinal tissues, followed by increased neutrophil infiltration and severe systemic inflammation in tumor-bearing mice, indicates the direct consequence of a dysbiotic microbiome. Increased neutrophil infiltration to the bone metastatic niche facilitates extravasation and transendothelial migration of tumor cells. It provides a novel, pre-established, and favorable environment to form an immunosuppressive pre-metastatic niche. The presence of tumor cells in immunosuppressive metastatic tumor niche disrupts the balance between osteoblasts and osteoclasts, promotes osteoclast differentiation, and remodels the bone structure. Excessive bone resorption by osteoclasts causes bone degradation and ultimately causes extreme pain in a bone metastatic mouse model. In clinical settings, bone metastasis is associated with intractable severe pain that severely compromises the quality of life in these patients.
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Affiliation(s)
- Rajib K Dutta
- Department of Surgery, University of MiamiMiami, FL 33136, USA
| | - Yaa F Abu
- Department of Surgery, University of MiamiMiami, FL 33136, USA
- Department of Microbiology and Immunology, University of MiamiMiami, FL 33136, USA
| | - Junyi Tao
- Department of Surgery, University of MiamiMiami, FL 33136, USA
| | - Irina Chupikova
- Department of Surgery, University of MiamiMiami, FL 33136, USA
| | - Janneth Oleas
- Department of Surgery, University of MiamiMiami, FL 33136, USA
| | - Praveen K Singh
- Department of Surgery, University of MiamiMiami, FL 33136, USA
| | - Nicolas A Vitari
- Department of Surgery, University of MiamiMiami, FL 33136, USA
- Department of Microbiology and Immunology, University of MiamiMiami, FL 33136, USA
| | - Rehana Qureshi
- Department of Pathology, University of MiamiMiami, FL 33136, USA
| | | | - Sabita Roy
- Department of Surgery, University of MiamiMiami, FL 33136, USA
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15
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Turunen J, Tejesvi MV, Paalanne N, Pokka T, Amatya SB, Mishra S, Kaisanlahti A, Reunanen J, Tapiainen T. Investigating prenatal and perinatal factors on meconium microbiota: a systematic review and cohort study. Pediatr Res 2024; 95:135-145. [PMID: 37591927 PMCID: PMC10798900 DOI: 10.1038/s41390-023-02783-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/30/2023] [Accepted: 07/29/2023] [Indexed: 08/19/2023]
Abstract
BACKGROUND The first-pass meconium has been suggested as a proxy for the fetal gut microbiota because it is formed in utero. This systematic review and cohort study investigated how pre- and perinatal factors influence the composition of the meconium microbiota. METHODS We performed the systematic review using Covidence by searching PubMed, Scopus, and Web of Science databases with the search terms "meconium microbiome" and "meconium microbiota". In the cohort study, we performed 16 S rRNA gene sequencing on 393 meconium samples and analyzed the sequencing data using QIIME2. RESULTS Our systematic review identified 69 studies exploring prenatal factors, immediate perinatal factors, and microbial composition in relation to subsequent health of infants but gave only limited comparative evidence regarding factors related to the composition of the meconium microbiota. The cohort study pointed to a low-biomass microbiota consisting of the phyla Firmicutes, Proteobacteria and Actinobacteriota and the genera Staphylococcus, Escherichia-Shigella and Lactobacillus, and indicated that immediate perinatal factors affected the composition of the meconium microbiota more than did prenatal factors. CONCLUSIONS This finding supports the idea that the meconium microbiota mostly starts developing during delivery. IMPACT It is unclear when the first-pass meconium microbiota develops, and what are the sources of the colonization. In this systematic review, we found 69 studies exploring prenatal factors, immediate perinatal factors, and microbial composition relative to subsequent health of infants, but there was no consensus on the factors affecting the meconium microbiota development. In this cohort study, immediate perinatal factors markedly affected the meconium microbiota development while prenatal factors had little effect on it. As the meconium microbiota composition was influenced by immediate perinatal factors, the present study supports the idea that the initial gut microbiota develops mainly during delivery.
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Affiliation(s)
- Jenni Turunen
- Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland.
- Biocenter Oulu, University of Oulu, Oulu, Finland.
| | - Mysore V Tejesvi
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Ecology and Genetics, Faculty of Science, University of Oulu, Oulu, Finland
| | - Niko Paalanne
- Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
| | - Tytti Pokka
- Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland
- Research Service Unit, Oulu University Hospital, Oulu, Finland
| | - Sajeen Bahadur Amatya
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Research Unit of Translational Medicine, University of Oulu, Oulu, Finland
| | - Surbhi Mishra
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Research Unit of Translational Medicine, University of Oulu, Oulu, Finland
| | - Anna Kaisanlahti
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Research Unit of Translational Medicine, University of Oulu, Oulu, Finland
| | - Justus Reunanen
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Research Unit of Translational Medicine, University of Oulu, Oulu, Finland
| | - Terhi Tapiainen
- Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
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16
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Carhuaricra-Huaman D, Setubal JC. Step-by-Step Bacterial Genome Comparison. Methods Mol Biol 2024; 2802:107-134. [PMID: 38819558 DOI: 10.1007/978-1-0716-3838-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Thanks to advancements in genome sequencing and bioinformatics, thousands of bacterial genome sequences are available in public databases. This presents an opportunity to study bacterial diversity in unprecedented detail. This chapter describes a complete bioinformatics workflow for comparative genomics of bacterial genomes, including genome annotation, pangenome reconstruction and visualization, phylogenetic analysis, and identification of sequences of interest such as antimicrobial-resistance genes, virulence factors, and phage sequences. The workflow uses state-of-the-art, open-source tools. The workflow is presented by means of a comparative analysis of Salmonella enterica serovar Typhimurium genomes. The workflow is based on Linux commands and scripts, and result visualization relies on the R environment. The chapter provides a step-by-step protocol that researchers with basic expertise in bioinformatics can easily follow to conduct investigations on their own genome datasets.
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Affiliation(s)
- Dennis Carhuaricra-Huaman
- Programa de Pós-Graduação Interunidades em Bioinformática, Instituto de Matemática e Estatística, Universidade de São Paulo, Sao Paulo, SP, Brazil
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratory of Biology and Molecular Genetics, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, San Borja, Lima, Peru
| | - João Carlos Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Sao Paulo, SP, Brazil.
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17
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Zhang H, Dierkes RF, Perez-Garcia P, Costanzi E, Dittrich J, Cea PA, Gurschke M, Applegate V, Partus K, Schmeisser C, Pfleger C, Gohlke H, Smits SHJ, Chow J, Streit WR. The metagenome-derived esterase PET40 is highly promiscuous and hydrolyses polyethylene terephthalate (PET). FEBS J 2024; 291:70-91. [PMID: 37549040 DOI: 10.1111/febs.16924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 07/24/2023] [Accepted: 08/07/2023] [Indexed: 08/09/2023]
Abstract
Polyethylene terephthalate (PET) is a widely used synthetic polymer and known to contaminate marine and terrestrial ecosystems. Only few PET-active microorganisms and enzymes (PETases) are currently known, and it is debated whether degradation activity for PET originates from promiscuous enzymes with broad substrate spectra that primarily act on natural polymers or other bulky substrates, or whether microorganisms evolved their genetic makeup to accepting PET as a carbon source. Here, we present a predicted diene lactone hydrolase designated PET40, which acts on a broad spectrum of substrates, including PET. It is the first esterase with activity on PET from a GC-rich Gram-positive Amycolatopsis species belonging to the Pseudonocardiaceae (Actinobacteria). It is highly conserved within the genera Amycolatopsis and Streptomyces. PET40 was identified by sequence-based metagenome search using a PETase-specific hidden Markov model. Besides acting on PET, PET40 has a versatile substrate spectrum, hydrolyzing δ-lactones, β-lactam antibiotics, the polyester-polyurethane Impranil® DLN, and various para-nitrophenyl ester substrates. Molecular docking suggests that the PET degradative activity is likely a result of the promiscuity of PET40, as potential binding modes were found for substrates encompassing mono(2-hydroxyethyl) terephthalate, bis(2-hydroxyethyl) terephthalate, and a PET trimer. We also solved the crystal structure of the inactive PET40 variant S178A to 1.60 Å resolution. PET40 is active throughout a wide pH (pH 4-10) and temperature range (4-65 °C) and remarkably stable in the presence of 5% SDS, making it a promising enzyme as a starting point for further investigations and optimization approaches.
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Affiliation(s)
- Hongli Zhang
- Department of Microbiology and Biotechnology, University of Hamburg, Germany
| | - Robert F Dierkes
- Department of Microbiology and Biotechnology, University of Hamburg, Germany
| | - Pablo Perez-Garcia
- Department of Microbiology and Biotechnology, University of Hamburg, Germany
- Molecular Microbiology, Institute for General Microbiology, Kiel University, Germany
| | - Elisa Costanzi
- Center for Structural Studies, Heinrich Heine University, Düsseldorf, Germany
| | - Jonas Dittrich
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University, Düsseldorf, Germany
| | - Pablo A Cea
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University, Düsseldorf, Germany
| | - Marno Gurschke
- Department of Microbiology and Biotechnology, University of Hamburg, Germany
| | - Violetta Applegate
- Center for Structural Studies, Heinrich Heine University, Düsseldorf, Germany
| | - Kristina Partus
- Department of Microbiology and Biotechnology, University of Hamburg, Germany
| | - Christel Schmeisser
- Department of Microbiology and Biotechnology, University of Hamburg, Germany
| | - Christopher Pfleger
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University, Düsseldorf, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University, Düsseldorf, Germany
- Institute of Bio- and Geosciences (IBG-4: Bioinformatics), John von Neumann Institute for Computing and Jülich Supercomputing Centre, Forschungszentrum Jülich GmbH, Germany
| | - Sander H J Smits
- Center for Structural Studies, Heinrich Heine University, Düsseldorf, Germany
- Institute of Biochemistry, Heinrich Heine University, Düsseldorf, Germany
| | - Jennifer Chow
- Department of Microbiology and Biotechnology, University of Hamburg, Germany
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, University of Hamburg, Germany
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18
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Maggiori C, Fernández-Martínez MA, Bourdages LJ, Sánchez-García L, Moreno-Paz M, Sobrado JM, Carrizo D, Vicente-Retortillo Á, Goordial J, Whyte LG. Biosignature Detection and MinION Sequencing of Antarctic Cryptoendoliths After Exposure to Mars Simulation Conditions. ASTROBIOLOGY 2024; 24:44-60. [PMID: 38153386 DOI: 10.1089/ast.2023.0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
In the search for life in our Solar System, Mars remains a promising target based on its proximity and similarity to Earth. When Mars transitioned from a warmer, wetter climate to its current dry and freezing conditions, any putative extant life probably retreated into habitable refugia such as the subsurface or the interior of rocks. Terrestrial cryptoendolithic microorganisms (i.e., those inhabiting rock interiors) thus represent possible modern-day Mars analogs, particularly those from the hyperarid McMurdo Dry Valleys in Antarctica. As DNA is a strong definitive biosignature, given that there is no known abiotic chemistry that can polymerize nucleobases, we investigated DNA detection with MinION sequencing in Antarctic cryptoendoliths after an ∼58-sol exposure in MARTE, a Mars environmental chamber capable of simulating martian temperature, pressure, humidity, ultraviolet (UV) radiation, and atmospheric composition, in conjunction with protein and lipid detection. The MARTE conditions resulted in changes in community composition and DNA, proteins, and cell membrane-derived lipids remained detectable postexposure. Of the multitude of extreme environmental conditions on Mars, UV radiation (specifically UVC) is the most destructive to both cells and DNA. As such, we further investigated if a UVC exposure corresponding to ∼278 martian years would impede DNA detection via MinION sequencing. The MinION was able to successfully detect and sequence DNA after this UVC radiation exposure, suggesting its utility for life detection in future astrobiology missions focused on finding relatively recently exposed biomarkers inside possible martian refugia.
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Affiliation(s)
- Catherine Maggiori
- Department of Biology, Georgetown University, Washington, District of Columbia, USA
| | - Miguel Angel Fernández-Martínez
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Ste. Anne-de-Bellevue, Quebec, Canada
- Department of Ecology, Universidad Autónoma de Madrid, Ciudad Universitaria de Cantoblanco, Madrid, Spain
| | - Louis-Jacques Bourdages
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Ste. Anne-de-Bellevue, Quebec, Canada
| | | | | | | | | | | | - Jacqueline Goordial
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Lyle G Whyte
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Ste. Anne-de-Bellevue, Quebec, Canada
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19
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Sannino DR, Arroyo FA, Pepe-Ranney C, Chen W, Volland JM, Elisabeth NH, Angert ER. The exceptional form and function of the giant bacterium Ca. Epulopiscium viviparus revolves around its sodium motive force. Proc Natl Acad Sci U S A 2023; 120:e2306160120. [PMID: 38109545 PMCID: PMC10756260 DOI: 10.1073/pnas.2306160120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 11/09/2023] [Indexed: 12/20/2023] Open
Abstract
Epulopiscium spp. are the largest known heterotrophic bacteria; a large cigar-shaped individual is a million times the volume of Escherichia coli. To better understand the metabolic potential and relationship of Epulopiscium sp. type B with its host Naso tonganus, we generated a high-quality draft genome from a population of cells taken from a single fish. We propose the name Candidatus Epulopiscium viviparus to describe populations of this best-characterized Epulopiscium species. Metabolic reconstruction reveals more than 5% of the genome codes for carbohydrate active enzymes, which likely degrade recalcitrant host-diet algal polysaccharides into substrates that may be fermented to acetate, the most abundant short-chain fatty acid in the intestinal tract. Moreover, transcriptome analyses and the concentration of sodium ions in the host intestinal tract suggest that the use of a sodium motive force (SMF) to drive ATP synthesis and flagellar rotation is integral to symbiont metabolism and cellular biology. In natural populations, genes encoding both F-type and V-type ATPases and SMF generation via oxaloacetate decarboxylation are among the most highly expressed, suggesting that ATPases synthesize ATP and balance ion concentrations across the cell membrane. High expression of these and other integral membrane proteins may allow for the growth of its extensive intracellular membrane system. Further, complementary metabolism between microbe and host is implied with the potential provision of nitrogen and B vitamins to reinforce this nutritional symbiosis. The few features shared by all bacterial behemoths include extreme polyploidy, polyphosphate synthesis, and thus far, they have all resisted cultivation in the lab.
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Affiliation(s)
| | | | - Charles Pepe-Ranney
- Soil & Crop Sciences Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY14853
| | - Wenbo Chen
- Department of Microbiology, Cornell University, Ithaca, NY14853
| | - Jean-Marie Volland
- Laboratory for Research in Complex Systems, Menlo Park, CA94025
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Nathalie H. Elisabeth
- Department of Energy Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA94720
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20
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Yang Y, Han Z, Gao Z, Chen J, Song C, Xu J, Wang H, Huang A, Shi J, Gu J. Metagenomic and targeted metabolomic analyses reveal distinct phenotypes of the gut microbiota in patients with colorectal cancer and type 2 diabetes mellitus. Chin Med J (Engl) 2023; 136:2847-2856. [PMID: 36959686 PMCID: PMC10686596 DOI: 10.1097/cm9.0000000000002421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Indexed: 03/25/2023] Open
Abstract
BACKGROUND Type 2 diabetes mellitus (T2DM) is an independent risk factor for colorectal cancer (CRC), and the patients with CRC and T2DM have worse survival. The human gut microbiota (GM) is linked to the development of CRC and T2DM, respectively. However, the GM characteristics in patients with CRC and T2DM remain unclear. METHODS We performed fecal metagenomic and targeted metabolomics studies on 36 samples from CRC patients with T2DM (DCRC group, n = 12), CRC patients without diabetes (CRC group, n = 12), and healthy controls (Health group, n = 12). We analyzed the fecal microbiomes, characterized the composition and function based on the metagenomics of DCRC patients, and detected the short-chain fatty acids (SCFAs) and bile acids (BAs) levels in all fecal samples. Finally, we performed a correlation analysis of the differential bacteria and metabolites between different groups. RESULTS Compared with the CRC group, LefSe analysis showed that there is a specific GM community in DCRC group, including an increased abundance of Eggerthella , Hungatella , Peptostreptococcus , and Parvimonas , and decreased Butyricicoccus , Lactobacillus , and Paraprevotella . The metabolomics analysis results revealed that the butyric acid level was lower but the deoxycholic acid and 12-keto-lithocholic acid levels were higher in the DCRC group than other groups ( P < 0.05). The correlation analysis showed that the dominant bacterial abundance in the DCRC group ( Parvimonas , Desulfurispora , Sebaldella , and Veillonellales , among others) was negatively correlated with butyric acid, hyodeoxycholic acid, ursodeoxycholic acid, glycochenodeoxycholic acid, chenodeoxycholic acid, cholic acid and glycocholate. However, the abundance of mostly inferior bacteria was positively correlated with these metabolic acid levels, including Faecalibacterium , Thermococci , and Cellulophaga . CONCLUSIONS Unique fecal microbiome signatures exist in CRC patients with T2DM compared to those with non-diabetic CRC. Alterations in GM composition and SCFAs and secondary BAs levels may promote CRC development.
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Affiliation(s)
- Yong Yang
- Department of Gastrointestinal Surgery, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education, Beijing), Peking University Cancer Hospital and Institute, Beijing 100142, China
- Department of Gastrointestinal Surgery, Peking University Shougang Hospital, Beijing 100144, China
| | - Zihan Han
- Department of Gastrointestinal Oncology, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Zhaoya Gao
- Department of Gastrointestinal Surgery, Peking University Shougang Hospital, Beijing 100144, China
| | - Jiajia Chen
- Department of Gastrointestinal Surgery, Peking University Shougang Hospital, Beijing 100144, China
| | - Can Song
- Peking-Tsinghua Center for Life Science, Peking University International Cancer Center, Beijing 100142, China
| | - Jingxuan Xu
- Department of Gastrointestinal Surgery, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education, Beijing), Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Hanyang Wang
- Department of Gastrointestinal Surgery, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education, Beijing), Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - An Huang
- Department of Gastrointestinal Surgery, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education, Beijing), Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Jingyi Shi
- Department of Gastrointestinal Surgery, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education, Beijing), Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Jin Gu
- Department of Gastrointestinal Surgery, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education, Beijing), Peking University Cancer Hospital and Institute, Beijing 100142, China
- Department of Gastrointestinal Surgery, Peking University Shougang Hospital, Beijing 100144, China
- Peking-Tsinghua Center for Life Science, Peking University International Cancer Center, Beijing 100142, China
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21
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Patel V, Lynn-Bell N, Chevignon G, Kucuk RA, Higashi CHV, Carpenter M, Russell JA, Oliver KM. Mobile elements create strain-level variation in the services conferred by an aphid symbiont. Environ Microbiol 2023; 25:3333-3348. [PMID: 37864320 DOI: 10.1111/1462-2920.16520] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 09/27/2023] [Indexed: 10/22/2023]
Abstract
Heritable, facultative symbionts are common in arthropods, often functioning in host defence. Despite moderately reduced genomes, facultative symbionts retain evolutionary potential through mobile genetic elements (MGEs). MGEs form the primary basis of strain-level variation in genome content and architecture, and often correlate with variability in symbiont-mediated phenotypes. In pea aphids (Acyrthosiphon pisum), strain-level variation in the type of toxin-encoding bacteriophages (APSEs) carried by the bacterium Hamiltonella defensa correlates with strength of defence against parasitoids. However, co-inheritance creates difficulties for partitioning their relative contributions to aphid defence. Here we identified isolates of H. defensa that were nearly identical except for APSE type. When holding H. defensa genotype constant, protection levels corresponded to APSE virulence module type. Results further indicated that APSEs move repeatedly within some H. defensa clades providing a mechanism for rapid evolution in anti-parasitoid defences. Strain variation in H. defensa also correlates with the presence of a second symbiont Fukatsuia symbiotica. Predictions that nutritional interactions structured this coinfection were not supported by comparative genomics, but bacteriocin-containing plasmids unique to co-infecting strains may contribute to their common pairing. In conclusion, strain diversity, and joint capacities for horizontal transfer of MGEs and symbionts, are emergent players in the rapid evolution of arthropods.
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Affiliation(s)
- Vilas Patel
- Department of Entomology, University of Georgia, Athens, Georgia, USA
| | - Nicole Lynn-Bell
- Department of Entomology, University of Georgia, Athens, Georgia, USA
| | - Germain Chevignon
- Laboratoire de Génétique et Pathologie des Mollusques Marins, IFREMER, La Tremblade, France
| | - Roy A Kucuk
- Department of Entomology, University of Georgia, Athens, Georgia, USA
| | | | - Melissa Carpenter
- Department of Biodiversity, Earth, and Environmental Science, Drexel University, Philadelphia, Pennsylvania, USA
| | - Jacob A Russell
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, USA
| | - Kerry M Oliver
- Department of Entomology, University of Georgia, Athens, Georgia, USA
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22
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Peters MK, Astafyeva Y, Han Y, Macdonald JFH, Indenbirken D, Nakel J, Virdi S, Westhoff G, Streit WR, Krohn I. Novel marine metalloprotease-new approaches for inhibition of biofilm formation of Stenotrophomonas maltophilia. Appl Microbiol Biotechnol 2023; 107:7119-7134. [PMID: 37755512 PMCID: PMC10638167 DOI: 10.1007/s00253-023-12781-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/30/2023] [Accepted: 09/07/2023] [Indexed: 09/28/2023]
Abstract
Many marine organisms produce bioactive molecules with unique characteristics to survive in their ecological niches. These enzymes can be applied in biotechnological processes and in the medical sector to replace aggressive chemicals that are harmful to the environment. Especially in the human health sector, there is a need for new approaches to fight against pathogens like Stenotrophomonas maltophilia which forms thick biofilms on artificial joints or catheters and causes serious diseases. Our approach was to use enrichment cultures of five marine resources that underwent sequence-based screenings in combination with deep omics analyses in order to identify enzymes with antibiofilm characteristics. Especially the supernatant of the enrichment culture of a stony coral caused a 40% reduction of S. maltophilia biofilm formation. In the presence of the supernatant, our transcriptome dataset showed a clear stress response (upregulation of transcripts for metal resistance, antitoxins, transporter, and iron acquisition) to the treatment. Further investigation of the enrichment culture metagenome and proteome indicated a series of potential antimicrobial enzymes. We found an impressive group of metalloproteases in the proteome of the supernatant that is responsible for the detected anti-biofilm effect against S. maltophilia. KEY POINTS: • Omics-based discovery of novel marine-derived antimicrobials for human health management by inhibition of S. maltophilia • Up to 40% reduction of S. maltophilia biofilm formation by the use of marine-derived samples • Metalloprotease candidates prevent biofilm formation of S. maltophilia K279a by up to 20.
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Affiliation(s)
- Marie Kristin Peters
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany
| | - Yekaterina Astafyeva
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany
| | - Yuchen Han
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany
| | - Jascha F H Macdonald
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany
| | - Daniela Indenbirken
- Technology Platform Next Generation Sequencing, Leibniz Institute of Virology, Martinistraße 52, 20251, Hamburg, Germany
| | - Jacqueline Nakel
- Technology Platform Next Generation Sequencing, Leibniz Institute of Virology, Martinistraße 52, 20251, Hamburg, Germany
| | - Sanamjeet Virdi
- Technology Platform Next Generation Sequencing, Leibniz Institute of Virology, Martinistraße 52, 20251, Hamburg, Germany
| | - Guido Westhoff
- Tierpark Hagenbeck, Gemeinnützige Gesellschaft mbH, Lokstedter Grenzstraße 2, 22527, Hamburg, Germany
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany
| | - Ines Krohn
- Department of Microbiology and Biotechnology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr.18, 22609, Hamburg, Germany.
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23
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Salerno KM, Domenico J, Le NQ, Balakrishnan K, McQuillen RJ, Stiles CD, Solov'yov IA, Martino CF. Long-Time Oxygen and Superoxide Localization in Arabidopsis thaliana Cryptochrome. J Chem Inf Model 2023; 63:6756-6767. [PMID: 37874902 DOI: 10.1021/acs.jcim.3c00325] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
Cryptochromes are proteins that are highly conserved across species and in many instances bind the flavin adenine dinucleotide (FAD) cofactor within their photolyase-homology region (PHR) domain. The FAD cofactor has multiple redox states that help catalyze reactions, and absorbs photons at about 450 nm, a feature linked to the light-related functions of cryptochrome proteins. Reactive oxygen species (ROS) are produced from redox reactions involving molecular oxygen and are involved in a myriad of biological processes. Superoxide O2•- is an exemplary ROS that may be formed through electron transfer from FAD to O2, generating an electron radical pair. Although the formation of a superoxide-FAD radical pair has been speculated, it is still unclear if the required process steps could be realized in cryptochrome. Here, we present results from molecular dynamics (MD) simulations of oxygen interacting with the PHR domain of Arabidopsis thaliana cryptochrome 1 (AtCRY1). Using MD simulation trajectories, oxygen binding locations are characterized through both the O2-FAD intermolecular distance and the local protein environment. Oxygen unbinding times are characterized through replica simulations of the bound oxygen. Simulations reveal that oxygen molecules can localize at certain sites within the cryptochrome protein for tens of nanoseconds, and superoxide molecules can localize for significantly longer. This relatively long-duration molecule binding suggests the possibility of an electron-transfer reaction leading to superoxide formation. Estimates of electron-transfer rates using the Marcus theory are performed for the identified potential binding sites. Molecular oxygen binding results are compared with recent results demonstrating long-time oxygen binding within the electron-transfer flavoprotein (ETF), another FAD binding protein.
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Affiliation(s)
- K Michael Salerno
- Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, Maryland 20723, United States
| | - Janna Domenico
- Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, Maryland 20723, United States
| | - Nam Q Le
- Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, Maryland 20723, United States
| | - Krithika Balakrishnan
- Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, Maryland 20723, United States
| | - Ryan J McQuillen
- Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, Maryland 20723, United States
| | - Christopher D Stiles
- Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, Maryland 20723, United States
| | - Ilia A Solov'yov
- Institute of Physics, Carl von Ossietzky University Oldenburg, Carl von Ossietzky Straße 9-11, 26129 Oldenburg, Germany
- Centre for Nanoscale Dynamics (CENAD), Carl von Ossietzky Universität Oldenburg, Carl von Ossietzky Straße 9-11, 26129 Oldenburg, Germany
- Centre for Neurosensory Science, Carl von Ossietzky Universität Oldenburg, Carl von Ossietzky Straße 9-11, 26129 Oldenburg, Germany
| | - Carlos F Martino
- Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, Maryland 20723, United States
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24
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Pavia MJ, Finn D, Macedo-Tafur F, Tello-Espinoza R, Penaccio C, Bouskill N, Cadillo-Quiroz H. Genes and genome-resolved metagenomics reveal the microbial functional make up of Amazon peatlands under geochemical gradients. Environ Microbiol 2023; 25:2388-2403. [PMID: 37501535 DOI: 10.1111/1462-2920.16469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 07/12/2023] [Indexed: 07/29/2023]
Abstract
The Pastaza-Marañón Foreland Basin (PMFB) holds the most extensive tropical peatland area in South America. PMFB peatlands store ~7.07 Gt of organic carbon interacting with multiple microbial heterotrophic, methanogenic, and other aerobic/anaerobic respirations. Little is understood about the contribution of distinct microbial community members inhabiting tropical peatlands. Here, we studied the metagenomes of three geochemically distinct peatlands spanning minerotrophic, mixed, and ombrotrophic conditions. Using gene- and genome-centric approaches, we evaluate the functional potential of the underlying microbial communities. Abundance analyses show significant differences in C, N, P, and S acquisition genes. Furthermore, community interactions mediated by toxin-antitoxin and CRISPR-Cas systems were enriched in oligotrophic soils, suggesting that non-metabolic interactions may exert additional controls in low-nutrient environments. Additionally, we reconstructed 519 metagenome-assembled genomes spanning 28 phyla. Our analyses detail key differences across the geochemical gradient in the predicted microbial populations involved in degradation of organic matter, and the cycling of N and S. Notably, we observed differences in the nitric oxide (NO) reduction strategies between sites with high and low N2 O fluxes and found phyla putatively capable of both NO and sulfate reduction. Our findings detail how gene abundances and microbial populations are influenced by geochemical differences in tropical peatlands.
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Affiliation(s)
- Michael J Pavia
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Damien Finn
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Franco Macedo-Tafur
- Laboratory of Soil Research, Research Institute of Amazonia's Natural Resources, National University of the Peruvian Amazon, Iquitos, Loreto, Peru
| | - Rodil Tello-Espinoza
- Laboratory of Soil Research, Research Institute of Amazonia's Natural Resources, National University of the Peruvian Amazon, Iquitos, Loreto, Peru
- School of Forestry, National University of the Peruvian Amazon, Iquitos, Loreto, Peru
| | - Christa Penaccio
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Nicholas Bouskill
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Hinsby Cadillo-Quiroz
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
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25
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Blikstad C, Dugan EJ, Laughlin TG, Turnšek JB, Liu MD, Shoemaker SR, Vogiatzi N, Remis JP, Savage DF. Identification of a carbonic anhydrase-Rubisco complex within the alpha-carboxysome. Proc Natl Acad Sci U S A 2023; 120:e2308600120. [PMID: 37862384 PMCID: PMC10614612 DOI: 10.1073/pnas.2308600120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/28/2023] [Indexed: 10/22/2023] Open
Abstract
Carboxysomes are proteinaceous organelles that encapsulate key enzymes of CO2 fixation-Rubisco and carbonic anhydrase-and are the centerpiece of the bacterial CO2 concentrating mechanism (CCM). In the CCM, actively accumulated cytosolic bicarbonate diffuses into the carboxysome and is converted to CO2 by carbonic anhydrase, producing a high CO2 concentration near Rubisco and ensuring efficient carboxylation. Self-assembly of the α-carboxysome is orchestrated by the intrinsically disordered scaffolding protein, CsoS2, which interacts with both Rubisco and carboxysomal shell proteins, but it is unknown how the carbonic anhydrase, CsoSCA, is incorporated into the α-carboxysome. Here, we present the structural basis of carbonic anhydrase encapsulation into α-carboxysomes from Halothiobacillus neapolitanus. We find that CsoSCA interacts directly with Rubisco via an intrinsically disordered N-terminal domain. A 1.98 Å single-particle cryoelectron microscopy structure of Rubisco in complex with this peptide reveals that CsoSCA binding is predominantly mediated by a network of hydrogen bonds. CsoSCA's binding site overlaps with that of CsoS2, but the two proteins utilize substantially different motifs and modes of binding, revealing a plasticity of the Rubisco binding site. Our results advance the understanding of carboxysome biogenesis and highlight the importance of Rubisco, not only as an enzyme but also as a central hub for mediating assembly through protein interactions.
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Affiliation(s)
- Cecilia Blikstad
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala75120, Sweden
| | - Eli J. Dugan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Thomas G. Laughlin
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Julia B. Turnšek
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Mira D. Liu
- Department of Chemistry, University of California, Berkeley, CA94720
| | - Sophie R. Shoemaker
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Nikoleta Vogiatzi
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala75120, Sweden
| | - Jonathan P. Remis
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
| | - David F. Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- HHMI, University of California, Berkeley, CA94720
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26
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Jenkins DJ, Woolston BM, Hood-Pishchany MI, Pelayo P, Konopaski AN, Quinn Peters M, France MT, Ravel J, Mitchell CM, Rakoff-Nahoum S, Whidbey C, Balskus EP. Bacterial amylases enable glycogen degradation by the vaginal microbiome. Nat Microbiol 2023; 8:1641-1652. [PMID: 37563289 PMCID: PMC10465358 DOI: 10.1038/s41564-023-01447-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 07/11/2023] [Indexed: 08/12/2023]
Abstract
The human vaginal microbiota is frequently dominated by lactobacilli and transition to a more diverse community of anaerobic microbes is associated with health risks. Glycogen released by lysed epithelial cells is believed to be an important nutrient source in the vagina. However, the mechanism by which vaginal bacteria metabolize glycogen is unclear, with evidence implicating both bacterial and human enzymes. Here we biochemically characterize six glycogen-degrading enzymes (GDEs), all of which are pullanases (PulA homologues), from vaginal bacteria that support the growth of amylase-deficient Lactobacillus crispatus on glycogen. We reveal variations in their pH tolerance, substrate preferences, breakdown products and susceptibility to inhibition. Analysis of vaginal microbiome datasets shows that these enzymes are expressed in all community state types. Finally, we confirm the presence and activity of bacterial and human GDEs in cervicovaginal fluid. This work establishes that bacterial GDEs can participate in the breakdown of glycogen, providing insight into metabolism that may shape the vaginal microbiota.
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Affiliation(s)
- Dominick J Jenkins
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Benjamin M Woolston
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Department of Chemical Engineering, Northeastern University, Boston, MA, USA
| | - M Indriati Hood-Pishchany
- Division of Infectious Diseases and Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Paula Pelayo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | | | - M Quinn Peters
- Department of Chemistry, Seattle University, Seattle, WA, USA
| | - Michael T France
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Caroline M Mitchell
- Vincent Center for Reproductive Biology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Seth Rakoff-Nahoum
- Division of Infectious Diseases and Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA.
- Department of Microbiology, Harvard Medical School, Boston, MA, USA.
| | | | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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27
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Guo B, Frigon D. Cellular RNA levels define heterotrophic substrate-uptake rate sub-guilds in activated sludge microbial communities. Interface Focus 2023; 13:20220080. [PMID: 37303744 PMCID: PMC10251117 DOI: 10.1098/rsfs.2022.0080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 01/23/2023] [Indexed: 06/13/2023] Open
Abstract
A heterotrophic-specialist model was proposed previously to divide wastewater treatment plant (WWTP) heterotrophs into sub-guilds of consumers of readily or slowly degradable substrates (RDS or SDS, respectively). The substrate degradation rate model coupled to metabolic considerations predicted that RNA and polyhydroxyalkanoate (PHA) levels would be positively correlated in the activated sludge communities with high RNA and PHA occurring in RDS-consumers, and low RNA with no PHA accumulation occurring in SDS-consumers because their external substrates are always present. This prediction was verified in previous studies and in the current one. Thus, RNA and PHA levels were used as biomarkers of the RDS- and SDS-consumer sub-guilds for cell sorting using flow cytometry of samples from three WWTPs. Subsequently, 16S rRNA gene amplicon sequencing revealed that the sorted groups were highly similar over time and among WWTPs, and demonstrated a clear segregation by RNA levels. Predicted ecophysiological traits based on 16S rRNA phylogeny suggested that the high-RNA population showed RDS-consumer traits such as higher rrn copy numbers per genome. Using a mass-flow immigration model, it appeared that the high-RNA populations exhibited high immigration rates more frequently than low-RNA populations, but the differences in frequencies were less with increasing solids residence times.
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Affiliation(s)
- Bing Guo
- Department of Civil Engineering and Applied Mechanics, McGill University, 817 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0C3
- Centre for Environmental Health and Engineering (CEHE), Department of Civil and Environmental Engineering, University of Surrey, Guildford GU2 7XH, UK
| | - Dominic Frigon
- Department of Civil Engineering and Applied Mechanics, McGill University, 817 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0C3
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28
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Touchette D, Maggiori C, Altshuler I, Tettenborn A, Bourdages LJ, Magnuson E, Blenner-Hassett O, Raymond-Bouchard I, Ellery A, Whyte LG. Microbial Characterization of Arctic Glacial Ice Cores with a Semiautomated Life Detection System. ASTROBIOLOGY 2023; 23:756-768. [PMID: 37126945 DOI: 10.1089/ast.2022.0130] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The search for extant microbial life will be a major focus of future astrobiology missions; however, no direct extant life detection instrumentation is included in current missions to Mars. In this study, we developed the semiautomated MicroLife detection platform that collects and processes environmental samples, detects biosignatures, and characterizes microbial activity. This platform is composed of a drill for sample collection, a redox dye colorimetric system for microbial metabolic activity detection and assessment (μMAMA [microfluidics Microbial Activity MicroAssay]), and a MinION sequencer for biosignature detection and characterization of microbial communities. The MicroLife platform was field-tested on White Glacier on Axel Heiberg Island in the Canadian high Arctic, with two extracted ice cores. The μMAMA successfully detected microbial metabolism from the ice cores within 1 day of incubation. The MinION sequencing of the ice cores and the positive μMAMA card identified a microbial community consistent with cold and oligotrophic environments. Furthermore, isolation and identification of microbial isolates from the μMAMA card corroborated the MinION sequencing. Together, these analyses support the MicroLife platform's efficacy in identifying microbes natively present in cryoenvironments and detecting their metabolic activity. Given our MicroLife platform's size and low energy requirements, it could be incorporated into a future landed platform or rovers for life detection.
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Affiliation(s)
- David Touchette
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Canada
- McGill Space Institute, Montréal, Canada
- Environmental Engineering Institute, River Ecosystems Laboratory, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Catherine Maggiori
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Canada
- McGill Space Institute, Montréal, Canada
| | - Ianina Altshuler
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Canada
- Environmental Engineering Institute, MACE Laboratory, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Alex Tettenborn
- Department of Mechanical and Aerospace Engineering, Carleton University, Ottawa, Canada
| | - Louis-Jacques Bourdages
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Canada
- Department of Mechanical Engineering, Faculty of Engineering, McGill University, Montréal, Canada
| | - Elisse Magnuson
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Canada
| | - Olivia Blenner-Hassett
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Canada
- McGill Space Institute, Montréal, Canada
| | - Isabelle Raymond-Bouchard
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Canada
- McGill Space Institute, Montréal, Canada
| | - Alex Ellery
- Department of Mechanical and Aerospace Engineering, Carleton University, Ottawa, Canada
| | - Lyle G Whyte
- Department of Natural Resource Sciences, McGill University, Sainte-Anne-de-Bellevue, Canada
- McGill Space Institute, Montréal, Canada
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29
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Arnold A, Alexander J, Liu G, Stokes JM. Applications of machine learning in microbial natural product drug discovery. Expert Opin Drug Discov 2023; 18:1259-1272. [PMID: 37651150 DOI: 10.1080/17460441.2023.2251400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/21/2023] [Indexed: 09/01/2023]
Abstract
INTRODUCTION Natural products (NPs) are a desirable source of new therapeutics due to their structural diversity and evolutionarily optimized bioactivities. NPs and their derivatives account for roughly 70% of approved pharmaceuticals. However, the rate at which novel NPs are discovered has decreased. To accelerate the microbial NP discovery process, machine learning (ML) is being applied to numerous areas of NP discovery and development. AREAS COVERED This review explores the utility of ML at various phases of the microbial NP drug discovery pipeline, discussing concrete examples throughout each major phase: genome mining, dereplication, and biological target prediction. Moreover, the authors discuss how ML approaches can be applied to semi-synthetic approaches to drug discovery. EXPERT OPINION Despite the important role that microbial NPs play in the development of novel drugs, their discovery has declined due to challenges associated with the conventional discovery process. ML is positioned to overcome these limitations given its ability to model complex datasets and generalize to novel chemical and sequence space. Unsurprisingly, ML comes with its own limitations that must be considered for its successful implementation. The authors stress the importance of continuing to build high quality and open access NP datasets to further increase the utility of ML in NP discovery.
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Affiliation(s)
- Autumn Arnold
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, OntarioCanada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton,Ontario, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario Canada
| | - Jeremie Alexander
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, OntarioCanada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton,Ontario, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario Canada
| | - Gary Liu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, OntarioCanada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton,Ontario, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario Canada
| | - Jonathan M Stokes
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, OntarioCanada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton,Ontario, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario Canada
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30
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Page CA, Pérez-Díaz IM, Pan M, Barrangou R. Genome-Wide Comparative Analysis of Lactiplantibacillus pentosus Isolates Autochthonous to Cucumber Fermentation Reveals Subclades of Divergent Ancestry. Foods 2023; 12:2455. [PMID: 37444193 DOI: 10.3390/foods12132455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/07/2023] [Accepted: 06/13/2023] [Indexed: 07/15/2023] Open
Abstract
Lactiplantibacillus pentosus, commonly isolated from commercial cucumber fermentation, is a promising candidate for starter culture formulation due to its ability to achieve complete sugar utilization to an end pH of 3.3. In this study, we conducted a comparative genomic analysis encompassing 24 L. pentosus and 3 Lactiplantibacillus plantarum isolates autochthonous to commercial cucumber fermentation and 47 lactobacillales reference genomes to determine species specificity and provide insights into niche adaptation. Results showed that metrics such as average nucleotide identity score, emulated Rep-PCR-(GTG)5, computed multi-locus sequence typing (MLST), and multiple open reading frame (ORF)-based phylogenetic trees can robustly and consistently distinguish the two closely related species. Phylogenetic trees based on the alignment of 587 common ORFs separated the L. pentosus autochthonous cucumber isolates from olive fermentation isolates into clade A and B, respectively. The L. pentosus autochthonous clade partitions into subclades A.I, A.II, and A.III, suggesting substantial intraspecies diversity in the cucumber fermentation habitat. The hypervariable sequences within CRISPR arrays revealed recent evolutionary history, which aligns with the L. pentosus subclades identified in the phylogenetic trees constructed. While L. plantarum autochthonous to cucumber fermentation only encode for Type II-A CRISPR arrays, autochthonous L. pentosus clade B codes for Type I-E and L. pentosus clade A hosts both types of arrays. L. pentosus 7.8.2, for which phylogeny could not be defined using the varied methods employed, was found to uniquely encode for four distinct Type I-E CRISPR arrays and a Type II-A array. Prophage sequences in varied isolates evidence the presence of adaptive immunity in the candidate starter cultures isolated from vegetable fermentation as observed in dairy counterparts. This study provides insight into the genomic features of industrial Lactiplantibacillus species, the level of species differentiation in a vegetable fermentation habitat, and diversity profile of relevance in the selection of functional starter cultures.
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Affiliation(s)
- Clinton A Page
- United States Department of Agriculture, Agricultural Research Service, SEA Food Science and Market Quality and Handling Research Unit, 322 Schaub Hall, Box 7624, Raleigh, NC 27695-7624, USA
| | - Ilenys M Pérez-Díaz
- United States Department of Agriculture, Agricultural Research Service, SEA Food Science and Market Quality and Handling Research Unit, 322 Schaub Hall, Box 7624, Raleigh, NC 27695-7624, USA
| | - Meichen Pan
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, 322 Schaub Hall, Box 7624, Raleigh, NC 27695-7624, USA
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, 322 Schaub Hall, Box 7624, Raleigh, NC 27695-7624, USA
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Patwardhan S, Phan J, Smedile F, Vetriani C. The Genome of Varunaivibrio sulfuroxidans Strain TC8 T, a Metabolically Versatile Alphaproteobacterium from the Tor Caldara Gas Vents in the Tyrrhenian Sea. Microorganisms 2023; 11:1366. [PMID: 37374867 DOI: 10.3390/microorganisms11061366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/02/2023] [Accepted: 05/15/2023] [Indexed: 06/29/2023] Open
Abstract
Varunaivibrio sulfuroxidans type strain TC8T is a mesophilic, facultatively anaerobic, facultatively chemolithoautotrophic alphaproteobacterium isolated from a sulfidic shallow-water marine gas vent located at Tor Caldara, Tyrrhenian Sea, Italy. V. sulfuroxidans belongs to the family Thalassospiraceae within the Alphaproteobacteria, with Magnetovibrio blakemorei as its closest relative. The genome of V. sulfuroxidans encodes the genes involved in sulfur, thiosulfate and sulfide oxidation, as well as nitrate and oxygen respiration. The genome encodes the genes involved in carbon fixation via the Calvin-Benson-Bassham cycle, in addition to genes involved in glycolysis and the TCA cycle, indicating a mixotrophic lifestyle. Genes involved in the detoxification of mercury and arsenate are also present. The genome also encodes a complete flagellar complex, one intact prophage and one CRISPR, as well as a putative DNA uptake mechanism mediated by the type IVc (aka Tad pilus) secretion system. Overall, the genome of Varunaivibrio sulfuroxidans highlights the organism's metabolic versatility, a characteristic that makes this strain well-adapted to the dynamic environmental conditions of sulfidic gas vents.
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Affiliation(s)
- Sushmita Patwardhan
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901, USA
| | - Jonathan Phan
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Francesco Smedile
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901, USA
| | - Costantino Vetriani
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901, USA
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
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Sun Y, Lu J, Yang J, Liu Y, Liu L, Zeng F, Niu Y, Dong L, Yang F. Construction of a caries diagnosis model based on microbiome novelty score. HUA XI KOU QIANG YI XUE ZA ZHI = HUAXI KOUQIANG YIXUE ZAZHI = WEST CHINA JOURNAL OF STOMATOLOGY 2023; 41:208-217. [PMID: 37056188 PMCID: PMC10427253 DOI: 10.7518/hxkq.2023.2022301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 12/30/2022] [Indexed: 04/15/2023]
Abstract
OBJECTIVES This study aimed to analyze the bacteria in dental caries and establish an optimized dental-ca-ries diagnosis model based on 16S ribosomal RNA (rRNA) data of oral flora. METHODS We searched the public databa-ses of microbiomes including NCBI, MG-RAST, EMBL-EBI, and QIITA and collected data involved in the relevant research on human oral microbiomes worldwide. The samples in the caries dataset (1 703) were compared with healthy ones (20 540) by using the microbial search engine (MSE) to obtain the microbiome novelty score (MNS) and construct a caries diagnosis model based on this index. Nonparametric multivariate ANOVA was used to analyze and compare the impact of different host factors on the oral flora MNS, and the model was optimized by controlling related factors. Finally, the effect of the model was evaluated by receiver operating characteristic (ROC) curve analysis. RESULTS 1) The oral microbiota distribution obviously differed among people with various oral-health statuses, and the species richness and species diversity index decreased. 2) ROC curve was used to evaluate the caries data set, and the area under ROC curve was AUC=0.67. 3) Among the five hosts' factors including caries status, country, age, decayed missing filled tooth (DMFT) indices, and sampling site displayed the strongest effect on MNS of samples (P=0.001). 4) The AUC of the model was 0.87, 0.74, 0.74, and 0.75 in high caries, medium caries, low caries samples in Chinese children, and mixed dental plaque samples after controlling host factors, respectively. CONCLUSIONS The model based on the analysis of 16S rRNA data of oral flora had good diagnostic efficiency.
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Affiliation(s)
- Yanfei Sun
- School of Stomatology, Qingdao University, Qingdao 266003, China
- Dept. of Pediatric Dentistry, Center of Stomatology, Municipal Hospital, Qingdao 266071, China
| | - Jie Lu
- Dept. of Stomatology, Pujiang Stomatological Hospital, Jinhua 322299, China
| | - Jiazhen Yang
- Dept. of Pediatric Dentistry, Stomatological Hospital of Qingdao, Qingdao 266000, China
| | - Yuhan Liu
- Central Laboratory, Stomatological Hospital of Qing-dao, Qingdao 266000, China
| | - Lu Liu
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Fei Zeng
- Dept. of Stomatology, Affiliated Hospital of Jining Medical University, Jining 272000, China
| | - Yufen Niu
- Dept. of Pediatric Dentistry, Center of Stomatology, Municipal Hospital, Qingdao 266071, China
- School of Stomatology, Dalian Medical University, Dalian 116044, China
| | - Lei Dong
- Dept. of Pediatric Dentistry, Center of Stomatology, Municipal Hospital, Qingdao 266071, China
- School of Stomatology, Dalian Medical University, Dalian 116044, China
| | - Fang Yang
- School of Stomatology, Qingdao University, Qingdao 266003, China
- Dept. of Pediatric Dentistry, Center of Stomatology, Municipal Hospital, Qingdao 266071, China
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Najjari A, Boussetta A, Youssef N, Linares-Pastén JA, Mahjoubi M, Belloum R, Sghaier H, Cherif A, Ouzari HI. Physiological and genomic insights into abiotic stress of halophilic archaeon Natrinema altunense 4.1R isolated from a saline ecosystem of Tunisian desert. Genetica 2023; 151:133-152. [PMID: 36795306 PMCID: PMC9995536 DOI: 10.1007/s10709-023-00182-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 02/02/2023] [Indexed: 02/17/2023]
Abstract
Halophilic archaea are polyextremophiles with the ability to withstand fluctuations in salinity, high levels of ultraviolet radiation, and oxidative stress, allowing them to survive in a wide range of environments and making them an excellent model for astrobiological research. Natrinema altunense 4.1R is a halophilic archaeon isolated from the endorheic saline lake systems, Sebkhas, located in arid and semi-arid regions of Tunisia. It is an ecosystem characterized by periodic flooding from subsurface groundwater and fluctuating salinities. Here, we assess the physiological responses and genomic characterization of N. altunense 4.1R to UV-C radiation, as well as osmotic and oxidative stresses. Results showed that the 4.1R strain is able to survive up to 36% of salinity, up to 180 J/m2 to UV-C radiation, and at 50 mM of H2O2, a resistance profile similar to Halobacterium salinarum, a strain often used as UV-C resistant model. In order to understand the genetic determinants of N. altunense 4.1R survival strategy, we sequenced and analyzed its genome. Results showed multiple gene copies of osmotic stress, oxidative stress, and DNA repair response mechanisms supporting its survivability at extreme salinities and radiations. Indeed, the 3D molecular structures of seven proteins related to responses to UV-C radiation (excinucleases UvrA, UvrB, and UvrC, and photolyase), saline stress (trehalose-6-phosphate synthase OtsA and trehalose-phosphatase OtsB), and oxidative stress (superoxide dismutase SOD) were constructed by homology modeling. This study extends the abiotic stress range for the species N. altunense and adds to the repertoire of UV and oxidative stress resistance genes generally known from haloarchaeon.
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Affiliation(s)
- Afef Najjari
- Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092, Tunis, Tunisie
| | - Ayoub Boussetta
- Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092, Tunis, Tunisie
| | - Noha Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Javier A Linares-Pastén
- Department of Biotechnology, Faculty of Engineering, Lunds Tekniska Högskola (LTH), Lund University, P. O. Box 124, 22100, Lund, Sweden.
| | - Mouna Mahjoubi
- University of Manouba, ISBST, LR11-ES31 BVBGR, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia
| | - Rahma Belloum
- Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092, Tunis, Tunisie
| | - Haitham Sghaier
- Laboratory "Energy and Matter for Development of Nuclear Sciences" (LR16CNSTN02), National Center for Nuclear Sciences and Technology (CNSTN), Ariana, Tunisia
| | - Ameur Cherif
- University of Manouba, ISBST, LR11-ES31 BVBGR, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia
| | - Hadda Imene Ouzari
- Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092, Tunis, Tunisie
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Meng J, Tao J, Abu Y, Sussman DA, Girotra M, Franceschi D, Roy S. HIV-Positive Patients on Antiretroviral Therapy Have an Altered Mucosal Intestinal but Not Oral Microbiome. Microbiol Spectr 2023; 11:e0247222. [PMID: 36511710 PMCID: PMC9927552 DOI: 10.1128/spectrum.02472-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 11/27/2022] [Indexed: 12/15/2022] Open
Abstract
This study characterized compositional and functional shifts in the intestinal and oral microbiome in HIV-positive patients on antiretroviral therapy compared to HIV-negative individuals. Seventy-nine specimens were collected from 5 HIV-positive and 12 control subjects from five locations (colon brush, colon wash, terminal ileum [TI] brush, TI wash, and saliva) during colonoscopy and at patient visits. Microbiome composition was characterized using 16S rRNA sequencing, and microbiome function was predicted using bioinformatics tools (PICRUSt and BugBase). Our analysis indicated that the β-diversity of all intestinal samples (colon brush, colon wash, TI brush, and TI wash) from patients with HIV was significantly different from patients without HIV. Specifically, bacteria from genera Prevotella, Fusobacterium, and Megasphaera were more abundant in samples from HIV-positive patients. On the other hand, bacteria from genera Ruminococcus, Blautia, and Clostridium were more abundant in samples from HIV-negative patients. Additionally, HIV-positive patients had higher abundances of biofilm-forming and pathogenic bacteria. Furthermore, pathways related to translation and nucleotide metabolism were elevated in HIV-positive patients, whereas pathways related to lipid and carbohydrate metabolism were positively correlated with samples from HIV-negative patients. Our analyses further showed variations in microbiome composition in HIV-positive and negative patients by sampling site. Samples from colon wash, colon brush, and TI wash were significant between groups, while samples from TI brush and saliva were not significant. Taken together, here, we report altered intestinal microbiome composition and predicted function in patients with HIV compared to uninfected patients, though we found no changes in the oral microbiome. IMPORTANCE Over 37 million people worldwide are living with HIV. Although the availability of antiretroviral therapy has significantly reduced the number of AIDS-related deaths, individuals living with HIV are at increased risk for opportunistic infections. We now know that HIV interacts with the trillions of bacteria, fungi, and viruses in the human body termed the microbiome. Only a limited number of previous studies have compared variations in the oral and gastrointestinal microbiome with HIV infection. Here, we detail how the oral and gastrointestinal microbiome changes with HIV infection, having used 5 different sampling sites to gain a more comprehensive view of these changes by location. Our results show site-specific changes in the intestinal microbiome associated with HIV infection. Additionally, we show that while there were significant changes in the intestinal microbiome, there were no significant changes in the oral microbiome.
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Affiliation(s)
- Jingjing Meng
- Department of Surgery, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida, USA
| | - Junyi Tao
- Department of Surgery, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida, USA
| | - Yaa Abu
- Department of Surgery, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida, USA
| | - Daniel Andrew Sussman
- Department of Gastroenterology, University of Miami Medical Group, Miami, Florida, USA
| | - Mohit Girotra
- Department of Gastroenterology, University of Miami Medical Group, Miami, Florida, USA
| | - Dido Franceschi
- Department of Surgery, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida, USA
| | - Sabita Roy
- Department of Surgery, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida, USA
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Genomics discovery of giant fungal viruses from subsurface oceanic crustal fluids. ISME COMMUNICATIONS 2023; 3:10. [PMID: 36732595 PMCID: PMC9894930 DOI: 10.1038/s43705-022-00210-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 12/12/2022] [Accepted: 12/22/2022] [Indexed: 02/04/2023]
Abstract
The oceanic igneous crust is a vast reservoir for microbial life, dominated by diverse and active bacteria, archaea, and fungi. Archaeal and bacterial viruses were previously detected in oceanic crustal fluids at the Juan de Fuca Ridge (JdFR). Here we report the discovery of two eukaryotic Nucleocytoviricota genomes from the same crustal fluids by sorting and sequencing single virions. Both genomes have a tRNATyr gene with an intron (20 bps) at the canonical position between nucleotide 37 and 38, a common feature in eukaryotic and archaeal tRNA genes with short introns (<100 bps), and fungal genes acquired through horizontal gene transfer (HGT) events. The dominance of Ascomycota fungi as the main eukaryotes in crustal fluids and the evidence for HGT point to these fungi as the putative hosts, making these the first putative fungi-Nucleocytoviricota specific association. Our study suggests active host-viral dynamics for the only eukaryotic group found in the subsurface oceanic crust and raises important questions about the impact of viral infection on the productivity and biogeochemical cycling in this ecosystem.
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Kuo J, Liu D, Lin CH. Functional Prediction of Microbial Communities in Sediment Microbial Fuel Cells. Bioengineering (Basel) 2023; 10:bioengineering10020199. [PMID: 36829693 PMCID: PMC9951962 DOI: 10.3390/bioengineering10020199] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/25/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
Sediment microbial fuel cells (MFCs) were developed in which the complex substrates present in the sediment could be oxidized by microbes for electron production. In this study, the functional prediction of microbial communities of anode-associated soils in sediment MFCs was investigated based on 16S rRNA genes. Four computational approaches, including BugBase, Functional Annotation of Prokaryotic Taxa (FAPROTAX), the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2), and Tax4Fun2, were applied. A total of 67, 9, 37, and 38 functional features were statistically significant. Among these functional groups, the function related to the generation of precursor metabolites and energy was the only one included in all four computational methods, and the sum total of the proportion was 93.54%. The metabolism of cofactor, carrier, and vitamin biosynthesis was included in the three methods, and the sum total of the proportion was 29.94%. The results suggested that the microbial communities usually contribute to energy metabolism, or the metabolism of cofactor, carrier, and vitamin biosynthesis might reveal the functional status in the anode of sediment MFCs.
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Affiliation(s)
- Jimmy Kuo
- Department of Planning and Research, National Museum of Marine Biology and Aquarium, Pingtung 94450, Taiwan
- Graduate Institute of Marine Biology, National Dong Hwa University, Pingtung 94450, Taiwan
| | - Daniel Liu
- Department of Biomedical Sciences, Da-Yeh University, 168 University Road, Dacun, Changhua 51591, Taiwan
| | - Chorng-Horng Lin
- Department of Biomedical Sciences, Da-Yeh University, 168 University Road, Dacun, Changhua 51591, Taiwan
- Correspondence: ; Tel.: +886-4-8511888
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Allemann MN, Presley GN, Elkins JG, Michener JK. Sphingobium lignivorans sp. nov., isolated from river sediment downstream of a paper mill. Int J Syst Evol Microbiol 2023; 73. [PMID: 36790427 DOI: 10.1099/ijsem.0.005704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
Abstract
A bacterial isolate, B1D3AT, was isolated from river sediment collected from the Hiwassee River near Calhoun, TN, by enrichment culturing with a model 5-5' lignin dimer, dehydrodivanillate, as its sole carbon source. B1D3AT was also shown to utilize several model lignin-derived monomers and dimers as sole carbon sources in a variety of minimal media. Cells were Gram-stain-negative, aerobic, motile, rod-shaped and formed yellow/cream-coloured colonies on rich agar. Optimal growth occurred at 30 °C, pH 7-8, and in the absence of NaCl. The major fatty acids of B1D3AT were C18 : 1 ω7c and C17 : 1 ω6c. The predominant hydroxy fatty acids were C14 : 0 2-OH and C15 : 0 2-OH. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidyldimethylethanolamine and sphingoglycolipid. B1D3AT contained spermidine as the only major polyamine. The major isoprenoid quinone was Q-10 with minor amounts of Q-9 and Q-11. The genomic DNA G+C content of B1D3AT was 65.6 mol%. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 49 core, universal genes defined by Clusters of Orthologous Groups gene families indicated that B1D3AT was a member of the genus Sphingobium. B1D3AT was most closely related to Sphingobium sp. SYK-6, with a 100 % 16S rRNA gene sequence similarity. B1D3AT showed 78.1-89.9 % average nucleotide identity and 19.5-22.2% digital DNA-DNA hybridization identity with other type strains from the genus Sphingobium. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain B1D3AT should be classified as representing a novel species of the genus Sphingobium, for which the name Sphingobium lignivorans sp. nov. is proposed. The type strain is strain B1D3AT (ATCC TSD-279T=DSM 111877T).
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Affiliation(s)
- Marco N Allemann
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Gerald N Presley
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.,Present address: Wood Science and Engineering, Oregon State University, Corvallis, OR 97331, USA
| | - James G Elkins
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Joshua K Michener
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
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Fan X, Gu C, Jin Z, Cai J, Bian Y, Wang F, Chen H, Jiang X. Major biotransformation of phthalic acid esters in Eisenia fetida: Mechanistic insights and association with catalytic enzymes and intestinal symbionts. ENVIRONMENT INTERNATIONAL 2023; 171:107712. [PMID: 36577298 DOI: 10.1016/j.envint.2022.107712] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/22/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
Phthalic acid esters (PAEs) are an important group of organic pollutants that are widely used as plasticizers in the environment. The PAEs in soil organisms are likely to be biotransformed into a variety of metabolites, and the combined toxicity of PAEs and their metabolites might be more serious than PAEs alone. However, there are only a few studies on PAE biotransformation by terrestrial animals, e.g. earthworms. Herein, the key biotransformation pathways of PAEs and their association with catalytic enzymes and intestinal symbionts in earthworms were studied using in vivo and in vitro incubation approaches. The widely distributed PAE in soil, dibutyl phthalate (DBP), was proven to be biotransformed rapidly together with apparent bioaccumulation in earthworms. The biotransformation of PAE congeners with medium or long side chains appeared to be faster compared with those with short side chains. DBP was biotransformed into butyl methyl phthalate (BMP), monobutyl phthalate (MBP), and phthalic acid (PA) through esterolysis and transesterification. Besides, the generation of small quantities of low-molecular weight metabolites via β-oxidation, decarboxylation or ring-cleavage, was also observed, especially when the appropriate proportion of NADPH coenzyme was applied to transfer electrons for oxidases. Interestingly, the esterolysis of PAEs was mainly regulated by the cytoplasmic carboxylesterase (CarE) in earthworms, with a Michaelis constant (Km) of 0.416 mM in the catalysis of DBP. The stronger esterolysis in non-intestinal tissues indicated that the CarE was primarily secreted by non-intestinal tissues of earthworms. Additionally, the intestinal symbiotic bacteria of earthworms could respond to PAE stress, leading to the changes in their diversity and composition. The enrichment of some genera e.g. Bacillus and Paracoccus, and the enhancement of metabolism function, e.g. amino acids, energy, lipids biosynthesis and oxidase secretion, indicated their important role in the degradation of PAEs.
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Affiliation(s)
- Xiuli Fan
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of the Chinese Academy of Sciences, Beijing 100049, PR China
| | - Chenggang Gu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of the Chinese Academy of Sciences, Beijing 100049, PR China.
| | - Zhihua Jin
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of the Chinese Academy of Sciences, Beijing 100049, PR China
| | - Jun Cai
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of the Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yongrong Bian
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of the Chinese Academy of Sciences, Beijing 100049, PR China
| | - Fang Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of the Chinese Academy of Sciences, Beijing 100049, PR China
| | - Hong Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Xin Jiang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; University of the Chinese Academy of Sciences, Beijing 100049, PR China
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Olo Ndela E, Roux S, Henke C, Sczyrba A, Sime Ngando T, Varsani A, Enault F. Reekeekee- and roodoodooviruses, two different Microviridae clades constituted by the smallest DNA phages. Virus Evol 2022; 9:veac123. [PMID: 36694818 PMCID: PMC9865509 DOI: 10.1093/ve/veac123] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/19/2022] [Accepted: 12/22/2022] [Indexed: 12/25/2022] Open
Abstract
Small circular single-stranded DNA viruses of the Microviridae family are both prevalent and diverse in all ecosystems. They usually harbor a genome between 4.3 and 6.3 kb, with a microvirus recently isolated from a marine Alphaproteobacteria being the smallest known genome of a DNA phage (4.248 kb). A subfamily, Amoyvirinae, has been proposed to classify this virus and other related small Alphaproteobacteria-infecting phages. Here, we report the discovery, in meta-omics data sets from various aquatic ecosystems, of sixteen complete microvirus genomes significantly smaller (2.991-3.692 kb) than known ones. Phylogenetic analysis reveals that these sixteen genomes represent two related, yet distinct and diverse, novel groups of microviruses-amoyviruses being their closest known relatives. We propose that these small microviruses are members of two tentatively named subfamilies Reekeekeevirinae and Roodoodoovirinae. As known microvirus genomes encode many overlapping and overprinted genes that are not identified by gene prediction software, we developed a new methodology to identify all genes based on protein conservation, amino acid composition, and selection pressure estimations. Surprisingly, only four to five genes could be identified per genome, with the number of overprinted genes lower than that in phiX174. These small genomes thus tend to have both a lower number of genes and a shorter length for each gene, leaving no place for variable gene regions that could harbor overprinted genes. Even more surprisingly, these two Microviridae groups had specific and different gene content, and major differences in their conserved protein sequences, highlighting that these two related groups of small genome microviruses use very different strategies to fulfill their lifecycle with such a small number of genes. The discovery of these genomes and the detailed prediction and annotation of their genome content expand our understanding of ssDNA phages in nature and are further evidence that these viruses have explored a wide range of possibilities during their long evolution.
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Affiliation(s)
| | | | - Christian Henke
- Computational Metagenomics, Bielefeld University, Universitätsstraße 27, Bielefeld 30501, Germany,Center for Biotechnology, Bielefeld University, Universitätsstraße 27, Bielefeld 33615, Germany
| | - Alexander Sczyrba
- Computational Metagenomics, Bielefeld University, Universitätsstraße 27, Bielefeld 30501, Germany,Center for Biotechnology, Bielefeld University, Universitätsstraße 27, Bielefeld 33615, Germany
| | - Télesphore Sime Ngando
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Genome et Environnement, Clermont-Ferrand F-63000, France
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Fregulia P, Campos MM, Dias RJP, Liu J, Guo W, Pereira LGR, Machado MA, Faza DRDLR, Guan LL, Garnsworthy PC, Neves ALA. Taxonomic and predicted functional signatures reveal linkages between the rumen microbiota and feed efficiency in dairy cattle raised in tropical areas. Front Microbiol 2022; 13:1025173. [PMID: 36523842 PMCID: PMC9745175 DOI: 10.3389/fmicb.2022.1025173] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 11/07/2022] [Indexed: 08/27/2023] Open
Abstract
Ruminants digest plant biomass more efficiently than monogastric animals due to their symbiotic relationship with a complex microbiota residing in the rumen environment. What remains unclear is the relationship between the rumen microbial taxonomic and functional composition and feed efficiency (FE), especially in crossbred dairy cattle (Holstein x Gyr) raised under tropical conditions. In this study, we selected twenty-two F1 Holstein x Gyr heifers and grouped them according to their residual feed intake (RFI) ranking, high efficiency (HE) (n = 11) and low efficiency (LE) (n = 11), to investigate the effect of FE on the rumen microbial taxa and their functions. Rumen fluids were collected using a stomach tube apparatus and analyzed using amplicon sequencing targeting the 16S (bacteria and archaea) and 18S (protozoa) rRNA genes. Alpha-diversity and beta-diversity analysis revealed no significant difference in the rumen microbiota between the HE and LE animals. Multivariate analysis (sPLS-DA) showed a clear separation of two clusters in bacterial taxonomic profiles related to each FE group, but in archaeal and protozoal profiles, the clusters overlapped. The sPLS-DA also revealed a clear separation in functional profiles for bacteria, archaea, and protozoa between the HE and LE animals. Microbial taxa were differently related to HE (e.g., Howardella and Shuttleworthia) and LE animals (e.g., Eremoplastron and Methanobrevibacter), and predicted functions were significatively different for each FE group (e.g., K03395-signaling and cellular process was strongly related to HE animals, and K13643-genetic information processing was related to LE animals). This study demonstrates that differences in the rumen microbiome relative to FE ranking are not directly observed from diversity indices (Faith's Phylogenetic Diversity, Pielou's Evenness, Shannon's diversity, weighted UniFrac distance, Jaccard index, and Bray-Curtis dissimilarity), but from targeted identification of specific taxa and microbial functions characterizing each FE group. These results shed light on the role of rumen microbial taxonomic and functional profiles in crossbred Holstein × Gyr dairy cattle raised in tropical conditions, creating the possibility of using the microbial signature of the HE group as a biological tool for the development of biomarkers that improve FE in ruminants.
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Affiliation(s)
- Priscila Fregulia
- Laboratório de Protozoologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
- Programa de Pós-Graduação em Biodiversidade e Conservação da Natureza, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | - Mariana Magalhães Campos
- Brazilian Agricultural Research Corporation (Empresa Brasileira de Pesquisa Agropecuária, EMBRAPA), National Center for Research on Dairy Cattle, Juiz de Fora, Minas Gerais, Brazil
| | - Roberto Júnio Pedroso Dias
- Laboratório de Protozoologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
- Programa de Pós-Graduação em Biodiversidade e Conservação da Natureza, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | - Junhong Liu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Wei Guo
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China
| | - Luiz Gustavo Ribeiro Pereira
- Brazilian Agricultural Research Corporation (Empresa Brasileira de Pesquisa Agropecuária, EMBRAPA), National Center for Research on Dairy Cattle, Juiz de Fora, Minas Gerais, Brazil
| | - Marco Antônio Machado
- Brazilian Agricultural Research Corporation (Empresa Brasileira de Pesquisa Agropecuária, EMBRAPA), National Center for Research on Dairy Cattle, Juiz de Fora, Minas Gerais, Brazil
| | - Daniele Ribeiro de Lima Reis Faza
- Brazilian Agricultural Research Corporation (Empresa Brasileira de Pesquisa Agropecuária, EMBRAPA), National Center for Research on Dairy Cattle, Juiz de Fora, Minas Gerais, Brazil
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Phil C. Garnsworthy
- School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - André Luis Alves Neves
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
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Bairoliya S, Goel A, Mukherjee M, Koh Zhi Xiang J, Cao B. Monochloramine Induces Release of DNA and RNA from Bacterial Cells: Quantification, Sequencing Analyses, and Implications. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:15791-15804. [PMID: 36215406 DOI: 10.1021/acs.est.2c06632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Monochloramine (MCA) is a widely used secondary disinfectant to suppress microbial growth in drinking water distribution systems. In monochloraminated drinking water, a significant amount of extracellular DNA (eDNA) has been reported, which has many implications ranging from obscuring DNA-based drinking water microbiome analyses to posing potential health concerns. To address this, it is imperative for us to know the origin of the eDNA in drinking water. Using Pseudomonas aeruginosa as a model organism, we report for the first time that MCA induces the release of nucleic acids from both biofilms and planktonic cells. Upon exposure to 2 mg/L MCA, massive release of DNA from suspended cells in both MilliQ water and 0.9% NaCl was directly visualized using live cell imaging in a CellASIC ONIX2 microfluidic system. Exposing established biofilms to MCA also resulted in DNA release from the biofilms, which was confirmed by increased detection of eDNA in the effluent. Intriguingly, massive release of RNA was also observed, and the extracellular RNA (eRNA) was also found to persist in water for days. Sequencing analyses of the eDNA revealed that it could be used to assemble the whole genome of the model organism, while in the water, certain fragments of the genome were more persistent than others. RNA sequencing showed that the eRNA contains non-coding RNA and mRNA, implying its role as a possible signaling molecule in environmental systems and a snapshot of the past metabolic state of the bacterial cells.
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Affiliation(s)
- Sakcham Bairoliya
- Singapore Centre for Environmental Life Sciences Engineering, Interdisciplinary Graduate Program, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Ave, Singapore 639798, Singapore
| | - Apoorva Goel
- Singapore Centre for Environmental Life Sciences Engineering, Interdisciplinary Graduate Program, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Manisha Mukherjee
- Singapore Centre for Environmental Life Sciences Engineering, Interdisciplinary Graduate Program, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Ave, Singapore 639798, Singapore
| | - Jonas Koh Zhi Xiang
- Singapore Centre for Environmental Life Sciences Engineering, Interdisciplinary Graduate Program, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Bin Cao
- Singapore Centre for Environmental Life Sciences Engineering, Interdisciplinary Graduate Program, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
- School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Ave, Singapore 639798, Singapore
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Letourneau J, Holmes ZC, Dallow EP, Durand HK, Jiang S, Carrion VM, Gupta SK, Mincey AC, Muehlbauer MJ, Bain JR, David LA. Ecological memory of prior nutrient exposure in the human gut microbiome. THE ISME JOURNAL 2022; 16:2479-2490. [PMID: 35871250 PMCID: PMC9563064 DOI: 10.1038/s41396-022-01292-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 04/20/2023]
Abstract
Many ecosystems have been shown to retain a memory of past conditions, which in turn affects how they respond to future stimuli. In microbial ecosystems, community disturbance has been associated with lasting impacts on microbiome structure. However, whether microbial communities alter their response to repeated stimulus remains incompletely understood. Using the human gut microbiome as a model, we show that bacterial communities retain an "ecological memory" of past carbohydrate exposures. Memory of the prebiotic inulin was encoded within a day of supplementation among a cohort of human study participants. Using in vitro gut microbial models, we demonstrated that the strength of ecological memory scales with nutrient dose and persists for days. We found evidence that memory is seeded by transcriptional changes among primary degraders of inulin within hours of nutrient exposure, and that subsequent changes in the activity and abundance of these taxa are sufficient to enhance overall community nutrient metabolism. We also observed that ecological memory of one carbohydrate species impacts microbiome response to other carbohydrates, and that an individual's habitual exposure to dietary fiber was associated with their gut microbiome's efficiency at digesting inulin. Together, these findings suggest that the human gut microbiome's metabolic potential reflects dietary exposures over preceding days and changes within hours of exposure to a novel nutrient. The dynamics of this ecological memory also highlight the potential for intra-individual microbiome variation to affect the design and interpretation of interventions involving the gut microbiome.
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Affiliation(s)
- Jeffrey Letourneau
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Zachary C Holmes
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Eric P Dallow
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Heather K Durand
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Sharon Jiang
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Verónica M Carrion
- Duke Office of Clinical Research, Duke University School of Medicine, Durham, NC, USA
| | - Savita K Gupta
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Adam C Mincey
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | - Michael J Muehlbauer
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | - James R Bain
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Medicine (Endocrinology), Duke University School of Medicine, Durham, NC, USA
| | - Lawrence A David
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA.
- Program in Computational Biology and Bioinformatics, Duke University School of Medicine, Durham, NC, USA.
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43
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Mucilaginibacter rivuli sp. nov., isolated from a water rivulet. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Strain HMF5004T was isolated from a rivulet located in Yongin, Republic of Korea. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain HMF5004T belonged to the genus
Mucilaginibacter
. Strain HMF5004T was closely related to
Mucilaginibacter paludis
(97.7%) and
Mucilaginibacter gracilis
(97.2%). The values of average nucleotide identity and digital DNA–DNA hybridization between strain HMF5004T and
M. paludis
were 72.8 and 19.2 %, respectively. Cells of strain HMF5004T were Gram-stain-negative, rod-shaped, non-motile, catalase-positive and oxidase-positive. The DNA G+C content of strain HMF5004T was 42.4 mol%. Strain HMF5004T had menaquinone-7 as a major quinone. The major cellular fatty acids included iso-C15 : 0, summed feature 3 (C16 : 1
ω7c and/or C16 : 1
ω6c) and anteiso-C15 : 0. The polar lipids of strain HMF5004T contained phosphatidylethanolamine, five unidentified aminolipids, one unidentified aminophospholipid and four unidentified polar lipids. On the basis of the evidence presented in this polyphasic taxonomic study, strain HMF5004T is considered to represent a novel species for which the name Mucilaginibacter rivuli sp. nov. is proposed. The type strain is HMF5004T (=KCTC 82633T=NBRC 115091T).
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Abstract
N-glycans are common posttranslational modifications on plant proteins, particularly secreted proteins. As plants are the major component of the human diet, and especially in high-fiber diets, plant N-glycans are prominent in the gut. Despite their ubiquity in the gut, the degradation of plant N-glycans by the microbiota has not been described. Here we used a functional analysis approach, coupled to detailed biochemistry and structural biology, to reveal a pathway for the degradation of plant N-glycans encoded by the human gut microbiota. The work reveals insight into how our gut microbes use plant N-glycans as a nutrient source and also provides tools to modify plant N-glycans to mitigate allergic responses, either from foods or plant-expressed therapeutics. The major nutrients available to the human colonic microbiota are complex glycans derived from the diet. To degrade this highly variable mix of sugar structures, gut microbes have acquired a huge array of different carbohydrate-active enzymes (CAZymes), predominantly glycoside hydrolases, many of which have specificities that can be exploited for a range of different applications. Plant N-glycans are prevalent on proteins produced by plants and thus components of the diet, but the breakdown of these complex molecules by the gut microbiota has not been explored. Plant N-glycans are also well characterized allergens in pollen and some plant-based foods, and when plants are used in heterologous protein production for medical applications, the N-glycans present can pose a risk to therapeutic function and stability. Here we use a novel genome association approach for enzyme discovery to identify a breakdown pathway for plant complex N-glycans encoded by a gut Bacteroides species and biochemically characterize five CAZymes involved, including structures of the PNGase and GH92 α-mannosidase. These enzymes provide a toolbox for the modification of plant N-glycans for a range of potential applications. Furthermore, the keystone PNGase also has activity against insect-type N-glycans, which we discuss from the perspective of insects as a nutrient source.
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The Relationship of Tumor Microbiome and Oral Bacteria and Intestinal Dysbiosis in Canine Mammary Tumor. Int J Mol Sci 2022; 23:ijms231810928. [PMID: 36142841 PMCID: PMC9503607 DOI: 10.3390/ijms231810928] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 12/15/2022] Open
Abstract
Canine mammary tumor (CMT) is the most common tumor in dogs, with 50% of malignant cases, and lacks an effective therapeutic schedule, hence its early diagnosis is of great importance to achieve a good prognosis. Microbiota is believed to play important roles in systemic diseases, including cancers. In this study, 91 tumors, 21 oral and fecal samples in total were collected from dogs with CMTs, and 31 oral and 21 fecal samples from healthy dogs were collected as control. The intratumoral, oral and gut bacterial community of dogs with CMTs and healthy dogs was profiled by 16S rRNA high-throughput sequencing and bioinformatic methods. The predominant intratumoral microbes were Ralstonia, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Pseudomonas, unidentified_Chloroplast and Bacteroides at the genus level. In addition, our findings demonstrated striking changes in the composition of the oral and gut bacterium community in the dogs suffered from CMTs compared to the healthy dogs, with a significant increase of Bacteroides which also was the significant microbial biomarker in the oral and gut bacterium community. It showed that the Bacteroides was shared in the intratumoral, oral and intestinal bacterial microbiomes, confirming that microbiota might travel from the mouth to the intestine and finally to the distant mammary tumor tissue. This study provides a new microbiological idea for the treatment of canine mammary tumors, and also provides a theoretical basis for the study of human breast cancer.
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46
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Salerno KM, Domenico J, Le NQ, Stiles CD, Solov’yov IA, Martino CF. Long-Time Oxygen Localization in Electron Transfer Flavoprotein. J Chem Inf Model 2022; 62:4191-4199. [PMID: 35998902 PMCID: PMC9472800 DOI: 10.1021/acs.jcim.2c00430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Indexed: 11/30/2022]
Abstract
Reactive oxygen species (ROS) exert a wide range of biological effects from beneficial regulatory function to deleterious oxidative stress. The electron transfer flavoprotein (ETF) is ubiquitous to life and is associated with aerobic metabolism and ROS production due to its location in the mitochondria. Quantifying oxygen localization within the ETF complex is critical for understanding the potential for electron transfer and radical pair formation between flavin adenine dinucleotide (FAD) cofactor and superoxide during ROS formation. Our study employed all-atom molecular dynamics simulations and identified several novel, long-lived oxygen binding sites within the ETF complex that appear near the FAD cofactor. Site locations, the local electrostatic environment, and characteristic oxygen binding times for each site were evaluated to establish factors that may lead to possible charge transfer reactions and superoxide formation within the ETF complex. The study revealed that some oxygen binding sites are naturally linked to protein domain features, suggesting opportunities to engineer and control ROS production and subsequent dynamics.
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Affiliation(s)
- K. Michael Salerno
- The
Johns Hopkins University Applied Physics
Laboratory, 11100 Johns
Hopkins Road, Laurel, Maryland 20723, United States
| | - Janna Domenico
- The
Johns Hopkins University Applied Physics
Laboratory, 11100 Johns
Hopkins Road, Laurel, Maryland 20723, United States
| | - Nam Q. Le
- The
Johns Hopkins University Applied Physics
Laboratory, 11100 Johns
Hopkins Road, Laurel, Maryland 20723, United States
| | - Christopher D. Stiles
- The
Johns Hopkins University Applied Physics
Laboratory, 11100 Johns
Hopkins Road, Laurel, Maryland 20723, United States
| | - Ilia A. Solov’yov
- Institute
of Physics, Carl von Ossietzky University
Oldenburg, Carl von Ossietzky
Straße 9-11, 26129 Oldenburg, Germany
- Centre
for Neurosensory Science, Carl von Ossietzky
University Oldenburg, Carl von Ossietzky Straße 9-11, 26129 Oldenburg, Germany
| | - Carlos F. Martino
- The
Johns Hopkins University Applied Physics
Laboratory, 11100 Johns
Hopkins Road, Laurel, Maryland 20723, United States
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Oral Absorbent AST-120 Is Associated with Compositional and Functional Adaptations of Gut Microbiota and Modification of Serum Short and Medium-Chain Fatty Acids in Advanced CKD Patients. Biomedicines 2022; 10:biomedicines10092234. [PMID: 36140334 PMCID: PMC9496242 DOI: 10.3390/biomedicines10092234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/18/2022] [Accepted: 09/05/2022] [Indexed: 11/30/2022] Open
Abstract
Background: Animal studies have demonstrated that an oral absorbent AST-120 modulates gut environment. However, this phenomenon remains unclear in humans. This study aimed to assess the effects of AST-120 on the gut microbiota, related functional capability and metabolomic profiling in advanced chronic kidney diseases (CKD) patients. Methods: Eight advanced CKD patients with AST-120 (CKD+AST), 24 CKD patients (CKD), and 24 non-CKD controls were enrolled. We analyzed 16S rRNA pyrosequencing of feces and serum metabolomics profiling. Results: The CKD+AST group exhibited dispersed microbial community structure (β-diversity, p < 0.001) compared to other groups. The relative abundances of at least 16 genera were significantly different amongst the three groups. Increases of fatty acids-producing bacteria (Clostridium_sensu_stricto_1, Ruminococcus_2, Eubacterium_nodatum and Phascolarctobacterium) associated with elevated serum acetic acid and octanoic acid levels were found in CKD+AST group. Analysis of microbial gene function indicated that pathway modules relevant to metabolisms of lipids, amino acids and carbohydrates were differentially enriched between CKD+AST and CKD groups. Specifically, enrichments of gene markers of the biosynthesis of fatty acids were noted in the CKD+AST group. Conclusion: Advanced CKD patients exhibited significant gut dysbiosis. AST-120 can partially restore the gut microbiota and intervenes in a possible signature of short- and medium-chain fatty acids metabolism.
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48
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Avalon NE, Murray AE, Baker BJ. Integrated Metabolomic-Genomic Workflows Accelerate Microbial Natural Product Discovery. Anal Chem 2022; 94:11959-11966. [PMID: 35994737 PMCID: PMC9453739 DOI: 10.1021/acs.analchem.2c02245] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The pairing of analytical chemistry with genomic techniques represents a new wave in natural product chemistry. With an increase in the availability of sequencing and assembly of microbial genomes, interrogation into the biosynthetic capability of producers with valuable secondary metabolites is possible. However, without the development of robust, accessible, and medium to high throughput tools, the bottleneck in pairing metabolic potential and compound isolation will continue. Several innovative approaches have proven useful in the nascent stages of microbial genome-informed drug discovery. Here, we consider a number of these approaches which have led to prioritization of strain targets and have mitigated rediscovery rates. Likewise, we discuss integration of principles of comparative evolutionary studies and retrobiosynthetic predictions to better understand biosynthetic mechanistic details and link genome sequence to structure. Lastly, we discuss advances in engineering, chemistry, and molecular networking and other computational approaches that are accelerating progress in the field of omic-informed natural product drug discovery. Together, these strategies enhance the synergy between cutting edge omics, chemical characterization, and computational technologies that pitch the discovery of natural products with pharmaceutical and other potential applications to the crest of the wave where progress is ripe for rapid advances.
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Affiliation(s)
- Nicole E Avalon
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Alison E Murray
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, Nevada 89512, United States
| | - Bill J Baker
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
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Draft Genome Sequences of Two Desiccation-Tolerant Strains, Bradyrhizobium japonicum TXVA and TXEA, Isolated from the Root Nodules of Soybean Grown in Texas. Microbiol Resour Announc 2022; 11:e0046722. [PMID: 35916509 PMCID: PMC9387295 DOI: 10.1128/mra.00467-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Two Bradyrhizobium japonicum strains, TXVA and TXEA, were isolated for their desiccation tolerance and symbiotic performance with soybean as biofertilizers. Their genomes were sequenced and annotated using the Department of Energy Joint Genome Institute annotation pipeline. Sequencing yielded chromosomes of 9,193,770 and 9,339,455 bp for TXVA and TXEA, respectively.
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50
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Ma J, Chen F, Xu H, Liu J, Chen CC, Zhang Z, Jiang H, Li Y, Pan K. Fate of face masks after being discarded into seawater: Aging and microbial colonization. JOURNAL OF HAZARDOUS MATERIALS 2022; 436:129084. [PMID: 35596986 PMCID: PMC9069998 DOI: 10.1016/j.jhazmat.2022.129084] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/30/2022] [Accepted: 05/03/2022] [Indexed: 05/06/2023]
Abstract
Billions of discarded masks have entered the oceans since the outbreak of the COVID-19 pandemic. Current reports mostly discuss the potential of masks as plastic pollution, but there has been no study on the fate of this emerging plastic waste in the marine environment. Therefore, we exposed masks in natural seawater and evaluated their aging and effects on the microbial community using a combination of physicochemical and biological techniques. After 30-day exposure in natural seawater, the masks suffered from significant aging. Microbial colonizers such as Rhodobacteraceae Flavobacteriaceae, Vibrionaceae and fouling organisms like calcareous tubeworms Hydroides elegans were massively present on the masks. The roughness and modulus of the mask fiber increased 3 and 5 times, respectively, and the molecular weight decreased 7%. The growth of biofouling organisms caused the masks negatively buoyant after 14-30 days. Our study sheds some light on the fate of discarded masks in a coastal area and provides fundamental data to manage this important plastic waste during COVID-19 pandemic.
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Affiliation(s)
- Jie Ma
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060 Guangdong, China
| | - Fengyuan Chen
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060 Guangdong, China
| | - Huo Xu
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060 Guangdong, China
| | - Jingli Liu
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060 Guangdong, China
| | - Ciara Chun Chen
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060 Guangdong, China
| | - Zhen Zhang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060 Guangdong, China
| | - Hao Jiang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074 Hubei, China
| | - Yanping Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060 Guangdong, China
| | - Ke Pan
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060 Guangdong, China.
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