1
|
Sepúlveda-Alfaro J, Catalán EA, Vallejos OP, Ramos-Tapia I, Madrid-Muñoz C, Mendoza-León MJ, Suazo ID, Rivera-Asin E, Silva PH, Alvarez-Mardones O, Castillo-Godoy DP, Riedel CA, Schinnerling K, Ugalde JA, Soto JA, Bueno SM, Kalergis AM, Melo-Gonzalez F. Human metapneumovirus respiratory infection affects both innate and adaptive intestinal immunity. Front Immunol 2024; 15:1330209. [PMID: 38404579 PMCID: PMC10884822 DOI: 10.3389/fimmu.2024.1330209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/15/2024] [Indexed: 02/27/2024] Open
Abstract
Introduction Respiratory infections are one of the leading causes of morbidity and mortality worldwide, mainly in children, immunocompromised people, and the elderly. Several respiratory viruses can induce intestinal inflammation and alterations in intestinal microbiota composition. Human metapneumovirus (HMPV) is one of the major respiratory viruses contributing to infant mortality in children under 5 years of age worldwide, and the effect of this infection at the gut level has not been studied. Methods Here, we evaluated the distal effects of HMPV infection on intestinal microbiota and inflammation in a murine model, analyzing several post-infection times (days 1, 3, and 5). Six to eight-week-old C57BL/6 mice were infected intranasally with HMPV, and mice inoculated with a non-infectious supernatant (Mock) were used as a control group. Results We did not detect HMPV viral load in the intestine, but we observed significant changes in the transcription of IFN-γ in the colon, analyzed by qPCR, at day 1 post-infection as compared to the control group. Furthermore, we analyzed the frequencies of different innate and adaptive immune cells in the colonic lamina propria, using flow cytometry. The frequency of monocyte populations was altered in the colon of HMPV -infected mice at days 1 and 3, with no significant difference from control mice at day 5 post-infection. Moreover, colonic CD8+ T cells and memory precursor effector CD8+ T cells were significantly increased in HMPV-infected mice at day 5, suggesting that HMPV may also alter intestinal adaptive immunity. Additionally, we did not find alterations in antimicrobial peptide expression, the frequency of colonic IgA+ plasma cells, and levels of fecal IgA. Some minor alterations in the fecal microbiota composition of HMPV -infected mice were detected using 16s rRNA sequencing. However, no significant differences were found in β-diversity and relative abundance at the genus level. Discussion To our knowledge, this is the first report describing the alterations in intestinal immunity following respiratory infection with HMPV infection. These effects do not seem to be mediated by direct viral infection in the intestinal tract. Our results indicate that HMPV can affect colonic innate and adaptive immunity but does not significantly alter the microbiota composition, and further research is required to understand the mechanisms inducing these distal effects in the intestine.
Collapse
Affiliation(s)
- Javiera Sepúlveda-Alfaro
- Millennium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Eduardo A. Catalán
- Millennium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Millennium Institute on Immunology and Immunotherapy, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Omar P. Vallejos
- Millennium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Ignacio Ramos-Tapia
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | | | - María J. Mendoza-León
- Millennium Institute on Immunology and Immunotherapy, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Isidora D. Suazo
- Millennium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Elizabeth Rivera-Asin
- Millennium Institute on Immunology and Immunotherapy, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Pedro H. Silva
- Millennium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Oscar Alvarez-Mardones
- Millennium Institute on Immunology and Immunotherapy, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | | | - Claudia A. Riedel
- Millennium Institute on Immunology and Immunotherapy, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | | | - Juan A. Ugalde
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Jorge A. Soto
- Millennium Institute on Immunology and Immunotherapy, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Susan M. Bueno
- Millennium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alexis M. Kalergis
- Millennium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Felipe Melo-Gonzalez
- Millennium Institute on Immunology and Immunotherapy, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| |
Collapse
|
2
|
Kumbhare SV, Pedroso I, Ugalde JA, Márquez-Miranda V, Sinha R, Almonacid DE. Drug and gut microbe relationships: Moving beyond antibiotics. Drug Discov Today 2023; 28:103797. [PMID: 37806386 DOI: 10.1016/j.drudis.2023.103797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 09/23/2023] [Accepted: 10/04/2023] [Indexed: 10/10/2023]
Abstract
Our understanding of drug-microbe relationships has evolved from viewing microbes as mere drug producers to a dynamic, modifiable system where they can serve as drugs or targets of precision pharmacology. This review highlights recent findings on the gut microbiome, particularly focusing on four aspects of research: (i) drugs for bugs, covering recent strategies for targeting gut pathogens; (ii) bugs as drugs, including probiotics; (iii) drugs from bugs, including postbiotics; and (iv) bugs and drugs, discussing additional types of drug-microbe interactions. This review provides a perspective on future translational research, including efficient companion diagnostics in pharmaceutical interventions.
Collapse
Affiliation(s)
| | | | - Juan A Ugalde
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Valeria Márquez-Miranda
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | | | | |
Collapse
|
3
|
Katz A, Porte L, Weitzel T, Varela C, Muñoz-Rehbein C, Ugalde JA, Grim C, González-Escalona N, Blondel CJ, Bravo V. Whole-genome sequencing reveals changes in genomic diversity and distinctive repertoires of T3SS and T6SS effector candidates in Chilean clinical Campylobacter strains. Front Cell Infect Microbiol 2023; 13:1208825. [PMID: 37520433 PMCID: PMC10374022 DOI: 10.3389/fcimb.2023.1208825] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 06/16/2023] [Indexed: 08/01/2023] Open
Abstract
Campylobacter is the leading cause of bacterial gastroenteritis worldwide and an emerging and neglected pathogen in South America. This zoonotic pathogen colonizes the gastrointestinal tract of a wide range of mammals and birds, with poultry as the most important reservoir for human infections. Apart from its high morbidity rates, the emergence of resistant strains is of global concern. The aims of this work were to determine genetic diversity, presence of antimicrobial resistance determinants and virulence potential of Campylobacter spp. isolated from patients with acute gastrointestinal disease at 'Clinica Alemana', Santiago de Chile. The study considered the isolation of Campylobacter spp., from stool samples during a 20-month period (January 2020 to September 2021). We sequenced (NextSeq, Illumina) and performed an in-depth analysis of the genome sequences of 88 Campylobacter jejuni and 2 Campylobacter coli strains isolated from clinical samples in Chile. We identified a high genetic diversity among C. jejuni strains and the emergence of prevalent clonal complexes, which were not identified in our previous reports. While ~40% of strains harbored a mutation in the gyrA gene associated with fluoroquinolone resistance, no macrolide-resistance determinants were detected. Interestingly, gene clusters encoding virulence factors such as the T6SS or genes associated with long-term sequelae such as Guillain-Barré syndrome showed lineage-relatedness. In addition, our analysis revealed a high degree of variability regarding the presence of fT3SS and T6SS effector proteins in comparison to type strains 81-176, F38011, and NCTC 11168 and 488. Our study provides important insights into the molecular epidemiology of this emerging foodborne pathogen. In addition, the differences observed regarding the repertoire of fT3SS and T6SS effector proteins could have an impact on the pathogenic potential and transmissibility of these Latin American isolates, posing another challenge in characterizing the infection dynamics of this emergent and neglected bacterial pathogen.
Collapse
Affiliation(s)
- Assaf Katz
- Programa de Biología Celular y Molecular, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Lorena Porte
- Laboratorio Clínico, Clínica Alemana de Santiago, Facultad de Medicina, Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Thomas Weitzel
- Laboratorio Clínico, Clínica Alemana de Santiago, Facultad de Medicina, Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
- Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Carmen Varela
- Laboratorio Clínico, Clínica Alemana de Santiago, Facultad de Medicina, Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Cristina Muñoz-Rehbein
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Juan A. Ugalde
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Christopher Grim
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Narjol González-Escalona
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Carlos J. Blondel
- Instituto de Ciencias Biomédicas, Facultad de Medicina y Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Verónica Bravo
- Centro de Investigaciones Biomédicas y Aplicadas (CIBAP), Escuela de Medicina, Facultad de Ciencias Médicas, Universidad de Santiago de Chile, Santiago, Chile
| |
Collapse
|
4
|
Ruiz-Tagle C, Ugalde JA, Naves R, Araos R, García P, Balcells ME. Reduced microbial diversity of the nasopharyngeal microbiome in household contacts with latent tuberculosis infection. Sci Rep 2023; 13:7301. [PMID: 37147354 PMCID: PMC10160714 DOI: 10.1038/s41598-023-34052-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 04/24/2023] [Indexed: 05/07/2023] Open
Abstract
The upper respiratory tract is an obliged pathway for respiratory pathogens and a healthy microbiota may support the host's mucosal immunity preventing infection. We analyzed the nasopharyngeal microbiome in tuberculosis household contacts (HHCs) and its association with latent tuberculosis infection (TBI). A prospective cohort of HHCs was established and latent TBI status was assessed by serial interferon-γ release assay (IGRA). Nasopharyngeal swabs collected at baseline were processed for 16S rRNA gene sequencing. The 82 participants included in the analysis were classified as: (a) non-TBI [IGRA negative at baseline and follow-up, no active TB (n = 31)], (b) pre-TBI [IGRA negative at baseline but converted to IGRA positive or developed active TB at follow-up (n = 16)], and (c) TBI [IGRA positive at enrollment (n = 35)]. Predominant phyla were Actinobacteriota, Proteobacteria, Firmicutes and Bacteroidota. TBI group had a lower alpha diversity compared to non-TBI (padj = 0.04) and pre-TBI (padj = 0.04). Only TBI and non-TBI had beta diversity differences (padj = 0.035). Core microbiomes' had unique genera, and genus showed differential abundance among groups. HHCs with established latent TBI showed reduced nasopharyngeal microbial diversity with distinctive taxonomical composition. Whether a pre-existing microbiome feature favors, are a consequence, or protects against Mycobacterium tuberculosis needs further investigation.
Collapse
Affiliation(s)
- Cinthya Ruiz-Tagle
- Departamento de Enfermedades Infecciosas del Adulto, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Juan A Ugalde
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de La Vida, Universidad Andrés Bello, Republica 330, Santiago, Chile
| | - Rodrigo Naves
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Rafael Araos
- Instituto de Ciencias E Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
- Advanced Center for Chronic Diseases (ACCDiS), Santiago, Chile
| | - Patricia García
- Laboratorio de Microbiología, Departamento de Laboratorios Clínicos, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - María Elvira Balcells
- Departamento de Enfermedades Infecciosas del Adulto, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile.
| |
Collapse
|
5
|
Zárate A, Molina V, Valdés J, Icaza G, Vega SE, Castillo A, Ugalde JA, Dorador C. Spatial co-occurrence patterns of benthic microbial assemblage in response to trace metals in the Atacama Desert Coastline. Front Microbiol 2023; 13:1020491. [PMID: 36726571 PMCID: PMC9885135 DOI: 10.3389/fmicb.2022.1020491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 12/31/2022] [Indexed: 01/17/2023] Open
Abstract
Taxonomic and functional microbial communities may respond differently to anthropogenic coastal impacts, but ecological quality monitoring assessments using environmental DNA and RNA (eDNA/eRNA) in response to pollution are poorly understood. In the present study, we investigated the utility of the co-occurrence network approach's to comprehensively explore both structure and potential functions of benthic marine microbial communities and their responses to Cu and Fe fractioning from two sediment deposition coastal zones of northern Chile via 16S rRNA gene metabarcoding. The results revealed substantial differences in the microbial communities, with the predominance of two distinct module hubs based on study zone. This indicates that habitat influences microbial co-occurrence networks. Indeed, the discriminant analysis allowed us to identify keystone taxa with significant differences in eDNA and eRNA comparison between sampled zones, revealing that Beggiatoaceae, Carnobacteriaceae, and Nitrosococcaceae were the primary representatives from Off Loa, whereas Enterobacteriaceae, Corynebacteriaceae, Latescibacteraceae, and Clostridiaceae were the families responsible for the observed changes in Mejillones Bay. The quantitative evidence from the multivariate analyses supports that the benthic microbial assemblages' features were linked to specific environments associated with Cu and Fe fractions, mainly in the Bay. Furthermore, the predicted functional microbial structure suggested that transporters and DNA repair allow the communities to respond to metals and endure the interacting variable environmental factors like dissolved oxygen, temperature, and salinity. Moreover, some active taxa recovered are associated with anthropogenic impact, potentially harboring antibiotic resistance and other threats in the coastal zone. Overall, the method of scoping eRNA in parallel with eDNA applied here has the capacity to significantly enhance the spatial and functional understanding of real-time microbial assemblages and, in turn, would have the potential to increase the acuity of biomonitoring programs key to responding to immediate management needs for the marine environment.
Collapse
Affiliation(s)
- Ana Zárate
- Doctorado en Ciencias Aplicadas mención Sistemas Marinos Costeros, Universidad de Antofagasta, Antofagasta, Chile,Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta and Centro de Bioingeniería y Biotecnología (CeBiB), Universidad de Antofagasta, Antofagasta, Chile,Laboratorio de Biotecnología en Ambientes Extremos, Centro de Excelencia en Medicina Traslacional, Universidad de la Frontera, Temuco, Chile,*Correspondence: Ana Zárate, ✉
| | - Verónica Molina
- Departamento de Ciencias y Geografía, Facultad de Ciencias Naturales y Exactas y HUB Ambiental UPLA, Universidad de Playa Ancha, Valparaíso, Chile,Centro de Investigación Oceanográfica COPAS COASTAL, Universidad de Concepción, Concepción, Chile,Verónica Molina, ✉
| | - Jorge Valdés
- Laboratorio de Sedimentología y Paleoambientes, Facultad de Ciencias del Mar y de Recursos Biológicos, Instituto de Ciencias Naturales A. von Humboldt, Universidad de Antofagasta, Antofagasta, Chile
| | - Gonzalo Icaza
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta and Centro de Bioingeniería y Biotecnología (CeBiB), Universidad de Antofagasta, Antofagasta, Chile
| | | | - Alexis Castillo
- Centro de Investigación y Estudios Avanzados del Maule, Vicerrectoría de Investigación de Investigación y Posgrado, Universidad Católica del Maule, Campus San Miguel, Talca, Chile,J’EAI CHARISMA (IRD-France, UMNG-Colombia, UA-Chile, UCM-Chile, UCH-Chile, IGP-Peru, UPCH-Peru) and Nucleo Milenio UPWELL, Concepción, Chile
| | - Juan A. Ugalde
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta and Centro de Bioingeniería y Biotecnología (CeBiB), Universidad de Antofagasta, Antofagasta, Chile,Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile,Cristina Dorador, ✉
| |
Collapse
|
6
|
Contreras-Gómez MJ, Martinez JRW, Rivas L, Riquelme-Neira R, Ugalde JA, Wozniak A, García P, Munita JM, Olivares-Pacheco J, Alcalde-Rico M. Role of the multi-drug efflux systems on the baseline susceptibility to ceftazidime/avibactam and ceftolozane/tazobactam in clinical isolates of non-carbapenemase-producing carbapenem-resistant Pseudomonas aeruginosa. Front Pharmacol 2022; 13:1007162. [PMID: 36263116 PMCID: PMC9574371 DOI: 10.3389/fphar.2022.1007162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 09/13/2022] [Indexed: 11/19/2022] Open
Abstract
Carbapenem-resistant Pseudomonas aeruginosa (CRPA) is one of the pathogens that urgently needs new drugs and new alternatives for its control. The primary strategy to combat this bacterium is combining treatments of beta-lactam with a beta-lactamase inhibitor. The most used combinations against P. aeruginosa are ceftazidime/avibactam (CZA) and ceftolozane/tazobactam (C/T). Although mechanisms leading to CZA and C/T resistance have already been described, among which are the resistance-nodulation-division (RND) efflux pumps, the role that these extrusion systems may play in CZA, and C/T baseline susceptibility of clinical isolates remains unknown. For this purpose, 161 isolates of non-carbapenemase-producing (Non-CP) CRPA were selected, and susceptibility tests to CZA and C/T were performed in the presence and absence of the RND efflux pumps inhibitor, Phenylalanine-arginine β-naphthylamide (PAβN). In the absence of PAβN, C/T showed markedly higher activity against Non-CP-CRPA isolates than observed for CZA. These results were even more evident in isolates classified as extremely-drug resistant (XDR) or with difficult-to-treat resistance (DTR), where CZA decreased its activity up to 55.2% and 20.0%, respectively, whereas C/T did it up to 82.8% (XDR), and 73.3% (DTR). The presence of PAβN showed an increase in both CZA (37.6%) and C/T (44.6%) activity, and 25.5% of Non-CP-CRPA isolates increased their susceptibility to these two combined antibiotics. However, statistical analysis showed that only the C/T susceptibility of Non-CP-CRPA isolates was significantly increased. Although the contribution of RND activity to CZA and C/T baseline susceptibility was generally low (two-fold decrease of minimal inhibitory concentrations [MIC]), a more evident contribution was observed in a non-minor proportion of the Non-CP-CRPA isolates affected by PAβN [CZA: 25.4% (15/59); C/T: 30% (21/70)]. These isolates presented significantly higher MIC values for C/T. Therefore, we conclude that RND efflux pumps are participating in the phenomenon of baseline susceptibility to CZA and, even more, to C/T. However, the genomic diversity of clinical isolates is so great that deeper analyzes are necessary to determine which elements are directly involved in this phenomenon.
Collapse
Affiliation(s)
- María José Contreras-Gómez
- Grupo de Resistencia Antimicrobiana en Bacterias Patógenas y Ambientales (GRABPA), Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
- Genomics and Resistant Microbes Group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina, Clínica Alemana, Universidad Del Desarrollo, Santiago, Chile
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
| | - José R. W. Martinez
- Genomics and Resistant Microbes Group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina, Clínica Alemana, Universidad Del Desarrollo, Santiago, Chile
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Lina Rivas
- Genomics and Resistant Microbes Group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina, Clínica Alemana, Universidad Del Desarrollo, Santiago, Chile
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Roberto Riquelme-Neira
- Genomics and Resistant Microbes Group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina, Clínica Alemana, Universidad Del Desarrollo, Santiago, Chile
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
- Núcleo de Investigaciones Aplicadas en Ciencias Veterinarias y Agronómicas, Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Santiago, Chile
| | - Juan A. Ugalde
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Aniela Wozniak
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
- Laboratory of Microbiology, Department of Clinical Laboratories, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Clinical Laboratories Network, Red de Salud UC-CHRISTUS, Santiago, Chile
| | - Patricia García
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
- Laboratory of Microbiology, Department of Clinical Laboratories, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Clinical Laboratories Network, Red de Salud UC-CHRISTUS, Santiago, Chile
| | - José M. Munita
- Genomics and Resistant Microbes Group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina, Clínica Alemana, Universidad Del Desarrollo, Santiago, Chile
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
- *Correspondence: José M. Munita, ; Jorge Olivares-Pacheco, ; Manuel Alcalde-Rico,
| | - Jorge Olivares-Pacheco
- Grupo de Resistencia Antimicrobiana en Bacterias Patógenas y Ambientales (GRABPA), Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
- *Correspondence: José M. Munita, ; Jorge Olivares-Pacheco, ; Manuel Alcalde-Rico,
| | - Manuel Alcalde-Rico
- Grupo de Resistencia Antimicrobiana en Bacterias Patógenas y Ambientales (GRABPA), Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
- Genomics and Resistant Microbes Group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina, Clínica Alemana, Universidad Del Desarrollo, Santiago, Chile
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
- *Correspondence: José M. Munita, ; Jorge Olivares-Pacheco, ; Manuel Alcalde-Rico,
| |
Collapse
|
7
|
Wu J, Danko D, Afshinnekoo E, Bezdan D, Bhattacharyya M, Castro-Nallar E, Chmielarczyk A, Hazrin-Chong NH, Deng Y, Dias-Neto E, Frolova A, Mason-Buck G, Iraola G, Jang S, Łabaj P, Lee PKH, Nieto-Caballero M, Osuolale OO, Ouzounis CA, Perlin MH, Prithiviraj B, Rascovan N, Różańska A, Schriml LM, Semmler T, Suzuki H, Ugalde JA, Young B, Werner J, Zambrano MM, Zhao Y, Mason C, Shi T. Annotating unknown species of urban microorganisms on a global scale unveils novel functional diversity and local environment association. Environ Res 2022; 207:112183. [PMID: 34637759 DOI: 10.1016/j.envres.2021.112183] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Abstract
In urban ecosystems, microbes play a key role in maintaining major ecological functions that directly support human health and city life. However, the knowledge about the species composition and functions involved in urban environments is still limited, which is largely due to the lack of reference genomes in metagenomic studies comprises more than half of unclassified reads. Here we uncovered 732 novel bacterial species from 4728 samples collected from various common surface with the matching materials in the mass transit system across 60 cities by the MetaSUB Consortium. The number of novel species is significantly and positively correlated with the city population, and more novel species can be identified in the skin-associated samples. The in-depth analysis of the new gene catalog showed that the functional terms have a significant geographical distinguishability. Moreover, we revealed that more biosynthetic gene clusters (BGCs) can be found in novel species. The co-occurrence relationship between BGCs and genera and the geographical specificity of BGCs can also provide us more information for the synthesis pathways of natural products. Expanded the known urban microbiome diversity and suggested additional mechanisms for taxonomic and functional characterization of the urban microbiome. Considering the great impact of urban microbiomes on human life, our study can also facilitate the microbial interaction analysis between human and urban environment.
Collapse
Affiliation(s)
- Jun Wu
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - David Danko
- Weill Cornell Medicine, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, USA
| | - Ebrahim Afshinnekoo
- Weill Cornell Medicine, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, USA
| | - Daniela Bezdan
- Weill Cornell Medicine, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, USA
| | - Malay Bhattacharyya
- Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India; Centre for Artificial Intelligence and Machine Learning, Indian Statistical Institute, Kolkata, India
| | - Eduardo Castro-Nallar
- Universidad Andrés Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Argentina
| | | | - Nur Hazlin Hazrin-Chong
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor, Malaysia
| | - Youping Deng
- University of Hawaii, John A. Burns School of Mecidine, USA
| | - Emmanuel Dias-Neto
- Medical Genomics Group, A.C. Camargo Cancer Center and LIM-27 Faculdade de Medicina, USP, São Paulo, Brazil
| | - Alina Frolova
- Institute of Molecular Biology and Genetics of National Academy of Science of Ukraine, Ukraine
| | - Gabriella Mason-Buck
- Department of Analytical, Environmental and Forensic Sciences, King's College London, UK
| | - Gregorio Iraola
- Microbial Genomics Laboratory, Institut Pasteur de Montevideo, Uruguay; Center for Integrative Biology, Universidad Mayor, Santiago de Chile, Chile; Wellcome Sanger Institute, Hinxton, United Kingdom
| | | | - Paweł Łabaj
- Małopolska Centre of Biotechnology, Jagiellonian University, Poland
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Marina Nieto-Caballero
- University of Colorado at Boulder, Civil, Environmental and Architectural Department, Boulder, 80303, USA
| | - Olayinka O Osuolale
- Applied Environmental Metagenomics and Infectious Diseases Research (AEMIDR), Department of Biological Sciences, Elizade University, Nigeria
| | - Christos A Ouzounis
- BCPL-CPERI, Centre for Research & Technology Hellas, Thessalonica, GR, 57001, Greece
| | - Michael H Perlin
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY, 40292, USA
| | - Bharath Prithiviraj
- Reckitt Health, Montvale, NJ, USA; Dept. of Biology, City University of New York, Brooklyn, 11210, NY, USA
| | - Nicolás Rascovan
- Aix-Marseille Université, IRD, AP-HM, IHU Méditerranée Infection, France
| | - Anna Różańska
- Jagiellonian University, Faculty of Medicine, Department of Microbiology, Poland
| | - Lynn M Schriml
- University of Maryland School of Medicine, Institute for Genome Sciences, USA
| | | | - Haruo Suzuki
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, Japan
| | - Juan A Ugalde
- Millennium Initiative for Collaborative Research on Bacterial Resistance, Germany
| | - Ben Young
- Weill Cornell Medicine, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, USA
| | - Johannes Werner
- High Performance and Cloud Computing Group, Zentrum für Datenverarbeitung (ZDV), Eberhard Karls University of Tübingen, Wächterstraße 76, 72074, Tübingen, Germany
| | | | - Yongxiang Zhao
- Biological Targeting Diagnosis and Therapy Research Center, Guangxi Medical University, Nanning, 530021, China
| | - Christopher Mason
- Weill Cornell Medicine, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, USA
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China; Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University & Capital Medical University, Beijing, 100083, China.
| |
Collapse
|
8
|
Vásquez-Ponce F, Higuera-Llantén S, Parás-Silva J, Gamboa-Acuña N, Cortés J, Opazo-Capurro A, Ugalde JA, Alcalde-Rico M, Olivares-Pacheco J. Genetic characterization of clinically relevant class 1 integrons carried by multi-drug resistant bacteria (MDRB) isolated from the gut microbiota of highly antibiotic treated Salmo salar. J Glob Antimicrob Resist 2022; 29:55-62. [DOI: 10.1016/j.jgar.2022.02.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/08/2022] [Accepted: 02/07/2022] [Indexed: 11/30/2022] Open
|
9
|
Danko D, Bezdan D, Afshin EE, Ahsanuddin S, Bhattacharya C, Butler DJ, Chng KR, Donnellan D, Hecht J, Jackson K, Kuchin K, Karasikov M, Lyons A, Mak L, Meleshko D, Mustafa H, Mutai B, Neches RY, Ng A, Nikolayeva O, Nikolayeva T, Png E, Ryon KA, Sanchez JL, Shaaban H, Sierra MA, Thomas D, Young B, Abudayyeh OO, Alicea J, Bhattacharyya M, Blekhman R, Castro-Nallar E, Cañas AM, Chatziefthimiou AD, Crawford RW, De Filippis F, Deng Y, Desnues C, Dias-Neto E, Dybwad M, Elhaik E, Ercolini D, Frolova A, Gankin D, Gootenberg JS, Graf AB, Green DC, Hajirasouliha I, Hastings JJA, Hernandez M, Iraola G, Jang S, Kahles A, Kelly FJ, Knights K, Kyrpides NC, Łabaj PP, Lee PKH, Leung MHY, Ljungdahl PO, Mason-Buck G, McGrath K, Meydan C, Mongodin EF, Moraes MO, Nagarajan N, Nieto-Caballero M, Noushmehr H, Oliveira M, Ossowski S, Osuolale OO, Özcan O, Paez-Espino D, Rascovan N, Richard H, Rätsch G, Schriml LM, Semmler T, Sezerman OU, Shi L, Shi T, Siam R, Song LH, Suzuki H, Court DS, Tighe SW, Tong X, Udekwu KI, Ugalde JA, Valentine B, Vassilev DI, Vayndorf EM, Velavan TP, Wu J, Zambrano MM, Zhu J, Zhu S, Mason CE. A global metagenomic map of urban microbiomes and antimicrobial resistance. Cell 2021; 184:3376-3393.e17. [PMID: 34043940 PMCID: PMC8238498 DOI: 10.1016/j.cell.2021.05.002] [Citation(s) in RCA: 129] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/05/2021] [Accepted: 04/29/2021] [Indexed: 01/14/2023]
Abstract
We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.
Collapse
Affiliation(s)
- David Danko
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Daniela Bezdan
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA; Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany; NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany
| | - Evan E Afshin
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | | | - Chandrima Bhattacharya
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Daniel J Butler
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Kern Rei Chng
- Genome Institute of Singapore, A(∗)STAR, Singapore, Singapore
| | - Daisy Donnellan
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Jochen Hecht
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Katelyn Jackson
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Katerina Kuchin
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Mikhail Karasikov
- ETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Abigail Lyons
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Lauren Mak
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Dmitry Meleshko
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Harun Mustafa
- ETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Beth Mutai
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Kenya Medical Research Institute - Kisumu, Kisumu, Kenya
| | - Russell Y Neches
- Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Amanda Ng
- Genome Institute of Singapore, A(∗)STAR, Singapore, Singapore
| | | | | | - Eileen Png
- Genome Institute of Singapore, A(∗)STAR, Singapore, Singapore
| | - Krista A Ryon
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Jorge L Sanchez
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Heba Shaaban
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Maria A Sierra
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Dominique Thomas
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Ben Young
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Omar O Abudayyeh
- Massachusetts Institute of Technology, McGovern Institute for Brain Research, Cambridge, MA, USA
| | - Josue Alicea
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Malay Bhattacharyya
- Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India; Centre for Artificial Intelligence and Machine Learning, Indian Statistical Institute, Kolkata, India
| | | | - Eduardo Castro-Nallar
- Universidad Andres Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Santiago, Chile
| | - Ana M Cañas
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Aspassia D Chatziefthimiou
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | | | - Francesca De Filippis
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Naples, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Youping Deng
- University of Hawaii John A. Burns School of Medicine, Honolulu, HI, USA
| | - Christelle Desnues
- Aix-Marseille Université, Mediterranean Institute of Oceanology, Université de Toulon, CNRS, IRD, UM 110, Marseille, France
| | - Emmanuel Dias-Neto
- Medical Genomics group, A.C.Camargo Cancer Center, São Paulo - SP, Brazil
| | - Marius Dybwad
- Norwegian Defence Research Establishment FFI, Kjeller, Norway
| | - Eran Elhaik
- Department of Biology, Lund University, Lund, Sweden
| | - Danilo Ercolini
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Naples, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Alina Frolova
- Institute of Molecular Biology and Genetics of National Academy of Sciences of Ukraine, Kyiv, Ukraine; Kyiv Academic University, Kyiv, Ukraine
| | - Dennis Gankin
- Massachusetts Institute of Technology, McGovern Institute for Brain Research, Cambridge, MA, USA
| | - Jonathan S Gootenberg
- Massachusetts Institute of Technology, McGovern Institute for Brain Research, Cambridge, MA, USA
| | | | - David C Green
- Department of Analytical, Environmental and Forensic Sciences, King's College London, London, UK
| | - Iman Hajirasouliha
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Jaden J A Hastings
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | | | - Gregorio Iraola
- Microbial Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay; Center for Integrative Biology, Universidad Mayor, Santiago de Chile, Santiago, Chile; Wellcome Sanger Institute, Hinxton, UK
| | | | - Andre Kahles
- ETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland; Kyiv Academic University, Kyiv, Ukraine; C+, Research Center in Technologies for Society, School of Engineering, Universidad del Desarrollo, Santiago, Chile
| | - Frank J Kelly
- Department of Analytical, Environmental and Forensic Sciences, King's College London, London, UK
| | - Kaymisha Knights
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Nikos C Kyrpides
- Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Paweł P Łabaj
- State Key Laboratory of Genetic Engineering (SKLGE) and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China; Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland; Boku University Viennna, Vienna, Austria
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Marcus H Y Leung
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Per O Ljungdahl
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Gabriella Mason-Buck
- Department of Analytical, Environmental and Forensic Sciences, King's College London, London, UK
| | - Ken McGrath
- Microba, 388 Queen St, Brisbane City, QLD 4000, Australia
| | - Cem Meydan
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Emmanuel F Mongodin
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA
| | | | | | | | - Houtan Noushmehr
- University of São Paulo, Ribeirão Preto Medical School, Ribeirão Preto - SP, Brazil
| | - Manuela Oliveira
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - Stephan Ossowski
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany; NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany
| | - Olayinka O Osuolale
- Applied Environmental Metagenomics and Infectious Diseases Research (AEMIDR), Department of Biological Sciences, Elizade University, Ilara-Mokin, Nigeria
| | - Orhan Özcan
- Acibadem Mehmet Ali Aydınlar University, Istanbul, Turkey
| | - David Paez-Espino
- Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nicolás Rascovan
- Microbial Paleogenomics Unit, Institut Pasteur, CNRS UMR2000, Paris 75015, France
| | - Hugues Richard
- Sorbonne University, Faculty of Science, Institute of Biology Paris-Seine, Laboratory of Computational and Quantitative Biology, Paris, France; Robert Koch Institute, Berlin, Germany
| | - Gunnar Rätsch
- ETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Lynn M Schriml
- University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA
| | | | | | - Leming Shi
- Center for Pharmacogenomics, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China; State Key Laboratory of Genetic Engineering (SKLGE) and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Tieliu Shi
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Rania Siam
- University of Medicine and Health Sciences, St. Kitts, West Indies and American University in Cairo, Cairo, Egypt
| | - Le Huu Song
- 108 Military Central Hospital, Hanoi, Vietnam; Vietnamese-German Center for Medical Research (VG-CARE), Hanoi, Vietnam
| | | | - Denise Syndercombe Court
- Department of Analytical, Environmental and Forensic Sciences, King's College London, London, UK
| | | | - Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Klas I Udekwu
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden; SciLife EVP, Department of Aquatic Sciences Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Juan A Ugalde
- Millennium Initiative for Collaborative Research on Bacterial Resistance, Santiago, Chile; C+, Research Center in Technologies for Society, School of Engineering, Universidad del Desarrollo, Santiago, Chile
| | - Brandon Valentine
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Dimitar I Vassilev
- Faculty of Mathematics and Informatics, Sofia University "St. Kliment Ohridski," Sofia, Bulgaria
| | - Elena M Vayndorf
- Institute of Arctic Biology, University of Alaska, Fairbanks, Fairbanks, AK, USA
| | - Thirumalaisamy P Velavan
- Institute of Tropical Medicine, Univeristätsklinikum Tübingen, Tübingen, Germany; Faculty of Medicine, Duy Tan University, Da Nang, Vietnam
| | - Jun Wu
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | | | - Jifeng Zhu
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
| | - Sibo Zhu
- State Key Laboratory of Genetic Engineering (SKLGE) and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China; Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China
| | - Christopher E Mason
- Weill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA; The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
| |
Collapse
|
10
|
Moreno-Pino M, Ugalde JA, Valdés JH, Rodríguez-Marconi S, Parada-Pozo G, Trefault N. Bacteria Isolated From the Antarctic Sponge Iophon sp. Reveals Mechanisms of Symbiosis in Sporosarcina, Cellulophaga, and Nesterenkonia. Front Microbiol 2021; 12:660779. [PMID: 34177840 PMCID: PMC8222686 DOI: 10.3389/fmicb.2021.660779] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/21/2021] [Indexed: 11/13/2022] Open
Abstract
Antarctic sponges harbor a diverse range of microorganisms that perform unique metabolic functions for nutrient cycles. Understanding how microorganisms establish functional sponge-microbe interactions in the Antarctic marine ecosystem provides clues about the success of these ancient animals in this realm. Here, we use a culture-dependent approach and genome sequencing to investigate the molecular determinants that promote a dual lifestyle in three bacterial genera Sporosarcina, Cellulophaga, and Nesterenkonia. Phylogenomic analyses showed that four sponge-associated isolates represent putative novel bacterial species within the Sporosarcina and Nesterenkonia genera and that the fifth bacterial isolate corresponds to Cellulophaga algicola. We inferred that isolated sponge-associated bacteria inhabit similarly marine sponges and also seawater. Comparative genomics revealed that these sponge-associated bacteria are enriched in symbiotic lifestyle-related genes. Specific adaptations related to the cold Antarctic environment are features of the bacterial strains isolated here. Furthermore, we showed evidence that the vitamin B5 synthesis-related gene, panE from Nesterenkonia E16_7 and E16_10, was laterally transferred within Actinobacteria members. Together, these findings indicate that the genomes of sponge-associated strains differ from other related genomes based on mechanisms that may contribute to the life in association with sponges and the extreme conditions of the Antarctic environment.
Collapse
Affiliation(s)
- Mario Moreno-Pino
- GEMA Center for Genomics, Ecology and Environment, Faculty of Sciences, Universidad Mayor, Santiago, Chile
| | - Juan A. Ugalde
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Jorge H. Valdés
- Center for Genomics and Bioinformatics, Faculty of Sciences, Universidad Mayor, Santiago, Chile
| | - Susana Rodríguez-Marconi
- GEMA Center for Genomics, Ecology and Environment, Faculty of Sciences, Universidad Mayor, Santiago, Chile
| | - Génesis Parada-Pozo
- GEMA Center for Genomics, Ecology and Environment, Faculty of Sciences, Universidad Mayor, Santiago, Chile
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology and Environment, Faculty of Sciences, Universidad Mayor, Santiago, Chile
| |
Collapse
|
11
|
Peoples LM, Kyaw TS, Ugalde JA, Mullane KK, Chastain RA, Yayanos AA, Kusube M, Methé BA, Bartlett DH. Distinctive gene and protein characteristics of extremely piezophilic Colwellia. BMC Genomics 2020; 21:692. [PMID: 33023469 PMCID: PMC7542103 DOI: 10.1186/s12864-020-07102-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 09/24/2020] [Indexed: 01/05/2023] Open
Abstract
Background The deep ocean is characterized by low temperatures, high hydrostatic pressures, and low concentrations of organic matter. While these conditions likely select for distinct genomic characteristics within prokaryotes, the attributes facilitating adaptation to the deep ocean are relatively unexplored. In this study, we compared the genomes of seven strains within the genus Colwellia, including some of the most piezophilic microbes known, to identify genomic features that enable life in the deep sea. Results Significant differences were found to exist between piezophilic and non-piezophilic strains of Colwellia. Piezophilic Colwellia have a more basic and hydrophobic proteome. The piezophilic abyssal and hadal isolates have more genes involved in replication/recombination/repair, cell wall/membrane biogenesis, and cell motility. The characteristics of respiration, pilus generation, and membrane fluidity adjustment vary between the strains, with operons for a nuo dehydrogenase and a tad pilus only present in the piezophiles. In contrast, the piezosensitive members are unique in having the capacity for dissimilatory nitrite and TMAO reduction. A number of genes exist only within deep-sea adapted species, such as those encoding d-alanine-d-alanine ligase for peptidoglycan formation, alanine dehydrogenase for NADH/NAD+ homeostasis, and a SAM methyltransferase for tRNA modification. Many of these piezophile-specific genes are in variable regions of the genome near genomic islands, transposases, and toxin-antitoxin systems. Conclusions We identified a number of adaptations that may facilitate deep-sea radiation in members of the genus Colwellia, as well as in other piezophilic bacteria. An enrichment in more basic and hydrophobic amino acids could help piezophiles stabilize and limit water intrusion into proteins as a result of high pressure. Variations in genes associated with the membrane, including those involved in unsaturated fatty acid production and respiration, indicate that membrane-based adaptations are critical for coping with high pressure. The presence of many piezophile-specific genes near genomic islands highlights that adaptation to the deep ocean may be facilitated by horizontal gene transfer through transposases or other mobile elements. Some of these genes are amenable to further study in genetically tractable piezophilic and piezotolerant deep-sea microorganisms.
Collapse
Affiliation(s)
- Logan M Peoples
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093-0202, USA.,Flathead Lake Biological Station, University of Montana, Polson, MT, 59860, USA
| | - Than S Kyaw
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093-0202, USA
| | - Juan A Ugalde
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Kelli K Mullane
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093-0202, USA
| | - Roger A Chastain
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093-0202, USA
| | - A Aristides Yayanos
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093-0202, USA
| | - Masataka Kusube
- Department of Material Science, National Institute of Technology, Wakayama College, 77 Noshima, Nada-cho, Gobo, Wakayama, 644-0023, Japan
| | - Barbara A Methé
- Center for Microbiome and Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Douglas H Bartlett
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093-0202, USA.
| |
Collapse
|
12
|
Araos R, Battaglia T, Ugalde JA, Rojas-Herrera M, Blaser MJ, D'Agata EMC. Fecal Microbiome Characteristics and the Resistome Associated With Acquisition of Multidrug-Resistant Organisms Among Elderly Subjects. Front Microbiol 2019; 10:2260. [PMID: 31611867 PMCID: PMC6777474 DOI: 10.3389/fmicb.2019.02260] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 09/17/2019] [Indexed: 11/13/2022] Open
Abstract
Infections caused by multidrug-resistant organisms (MDRO) lead to considerable morbidity and mortality. The elderly population residing in nursing homes are a major reservoir of MDRO. Our objective was to characterize the fecal microbiome of 82 elderly subjects from 23 nursing homes and compare their resistome to that of healthy young persons. Comparisons of microbiome composition and the resistome between subjects who acquired MDRO or not were analyzed to characterize specific microbiome disruption indices (MDI) associated with MDRO acquisition. An approach based on both 16S rRNA amplicon and whole metagenome shotgun (WMS) sequencing data was used. The microbiome of the study cohort was substantially perturbed, with Bacteroides, Firmicutes, and Proteobacteria predominating. Compared to healthy persons, the cohort of elderly persons had an increased number, abundance, and diversity of antimicrobial resistance genes. High proportions of study subjects harbored genes for multidrug-efflux pumps (96%) and linezolid resistance (52%). Among the 302 antimicrobial resistance gene families identified in any subject, 60% were exclusively detected within the study cohort, including Class D beta-lactamase genes. Subjects who acquired MDRO or not had significant differences in bacterial taxa; Odoribacter laneus, and Akkermansia muciniphila were significantly greater among subjects who did not acquire MDRO whereas Blautia hydrogenotrophica predominated among subjects who acquired MDRO. These findings suggest that specific MDI may identify persons at high risk of acquiring MDRO.
Collapse
Affiliation(s)
- Rafael Araos
- Instituto de Ciencias e Innovación en Medicina, and Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Thomas Battaglia
- Centre for Integrative Bioinformatics (IBIVU), VU University of Amsterdam, Amsterdam, Netherlands
| | - Juan A Ugalde
- Instituto de Ciencias e Innovación en Medicina, and Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Marcelo Rojas-Herrera
- Instituto de Ciencias e Innovación en Medicina, and Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Martin J Blaser
- Center for Advanced Biotechnology and Medicine, Rutgers University, New Brunswick, NJ, United States
| | - Erika M C D'Agata
- Rhode Island Hospital, Brown University, Providence, RI, United States
| |
Collapse
|
13
|
Bik EM, Bird SW, Bustamante JP, Leon LE, Nieto PA, Addae K, Alegría-Mera V, Bravo C, Bravo D, Cardenas JP, Carson GA, Caughey A, Covarrubias PC, Pérez-Donoso J, Gass G, Gupta SL, Harman K, Hongo DMB, Jiménez JC, Kraal L, Melis-Arcos F, Morales EH, Morton A, Navas CF, Nuñez H, Olivares E, Órdenes-Aenishanslins N, Ossandon FJ, Phan R, Pino R, Soto-Liebe K, Varas I, Vera-Wolf P, Walton NA, Almonacid DE, Goddard AD, Ugalde JA, Zneimer S, Richman J, Apte ZS. A novel sequencing-based vaginal health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis. PLoS One 2019; 14:e0215945. [PMID: 31042762 PMCID: PMC6493738 DOI: 10.1371/journal.pone.0215945] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 04/12/2019] [Indexed: 11/18/2022] Open
Abstract
The composition of the vaginal microbiome, including both the presence of pathogens involved in sexually transmitted infections (STI) as well as commensal microbiota, has been shown to have important associations for a woman's reproductive and general health. Currently, healthcare providers cannot offer comprehensive vaginal microbiome screening, but are limited to the detection of individual pathogens, such as high-risk human papillomavirus (hrHPV), the predominant cause of cervical cancer. There is no single test on the market that combines HPV, STI, and microbiome screening. Here, we describe a novel inclusive vaginal health assay that combines self-sampling with sequencing-based HPV detection and genotyping, vaginal microbiome analysis, and STI-associated pathogen detection. The assay includes genotyping and detection of 14 hrHPV types, 5 low-risk HPV types (lrHPV), as well as the relative abundance of 31 bacterial taxa of clinical importance, including Lactobacillus, Sneathia, Gardnerella, and 3 pathogens involved in STI, with high sensitivity, specificity, and reproducibility. For each of these taxa, reference ranges were determined in a group of 50 self-reported healthy women. The HPV sequencing portion of the test was evaluated against the digene High-Risk HPV HC2 DNA test. For hrHPV genotyping, agreement was 95.3% with a kappa of 0.804 (601 samples); after removal of samples in which the digene hrHPV probe showed cross-reactivity with lrHPV types, the sensitivity and specificity of the hrHPV genotyping assay were 94.5% and 96.6%, respectively, with a kappa of 0.841. For lrHPV genotyping, agreement was 93.9% with a kappa of 0.788 (148 samples), while sensitivity and specificity were 100% and 92.9%, respectively. This novel assay could be used to complement conventional cervical cancer screening, because its self-sampling format can expand access among women who would otherwise not participate, and because of its additional information about the composition of the vaginal microbiome and the presence of pathogens.
Collapse
Affiliation(s)
| | - Sara W. Bird
- uBiome, San Francisco, CA, United States of America
| | | | - Luis E. Leon
- uBiome, San Francisco, CA, United States of America
| | | | - Kwasi Addae
- uBiome, San Francisco, CA, United States of America
| | | | | | | | | | | | - Adam Caughey
- uBiome, San Francisco, CA, United States of America
| | | | | | - Graham Gass
- uBiome, San Francisco, CA, United States of America
| | | | - Kira Harman
- uBiome, San Francisco, CA, United States of America
| | | | | | | | | | | | | | | | - Harold Nuñez
- uBiome, San Francisco, CA, United States of America
| | | | | | | | - Richard Phan
- uBiome, San Francisco, CA, United States of America
| | - Raul Pino
- uBiome, San Francisco, CA, United States of America
| | | | | | | | | | | | | | | | | | | | - Zachary S. Apte
- uBiome, San Francisco, CA, United States of America
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, United States of America
- * E-mail:
| |
Collapse
|
14
|
Plominsky AM, Henríquez-Castillo C, Delherbe N, Podell S, Ramirez-Flandes S, Ugalde JA, Santibañez JF, van den Engh G, Hanselmann K, Ulloa O, De la Iglesia R, Allen EE, Trefault N. Distinctive Archaeal Composition of an Artisanal Crystallizer Pond and Functional Insights Into Salt-Saturated Hypersaline Environment Adaptation. Front Microbiol 2018; 9:1800. [PMID: 30154761 PMCID: PMC6102401 DOI: 10.3389/fmicb.2018.01800] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 07/17/2018] [Indexed: 11/23/2022] Open
Abstract
Hypersaline environments represent some of the most challenging settings for life on Earth. Extremely halophilic microorganisms have been selected to colonize and thrive in these extreme environments by virtue of a broad spectrum of adaptations to counter high salinity and osmotic stress. Although there is substantial data on microbial taxonomic diversity in these challenging ecosystems and their primary osmoadaptation mechanisms, less is known about how hypersaline environments shape the genomes of microbial inhabitants at the functional level. In this study, we analyzed the microbial communities in five ponds along the discontinuous salinity gradient from brackish to salt-saturated environments and sequenced the metagenome of the salt (halite) precipitation pond in the artisanal Cáhuil Solar Saltern system. We combined field measurements with spectrophotometric pigment analysis and flow cytometry to characterize the microbial ecology of the pond ecosystems, including primary producers and applied metagenomic sequencing for analysis of archaeal and bacterial taxonomic diversity of the salt crystallizer harvest pond. Comparative metagenomic analysis of the Cáhuil salt crystallizer pond against microbial communities from other salt-saturated aquatic environments revealed a dominance of the archaeal genus Halorubrum and showed an unexpectedly low abundance of Haloquadratum in the Cáhuil system. Functional comparison of 26 hypersaline microbial metagenomes revealed a high proportion of sequences associated with nucleotide excision repair, helicases, replication and restriction-methylation systems in all of them. Moreover, we found distinctive functional signatures between the microbial communities from salt-saturated (>30% [w/v] total salinity) compared to sub-saturated hypersaline environments mainly due to a higher representation of sequences related to replication, recombination and DNA repair in the former. The current study expands our understanding of the diversity and distribution of halophilic microbial populations inhabiting salt-saturated habitats and the functional attributes that sustain them.
Collapse
Affiliation(s)
- Alvaro M Plominsky
- Department of Oceanography, Faculty of Natural and Oceanographic Sciences, Universidad de Concepción, Concepción, Chile.,Instituto Milenio de Oceanografía, Concepción, Chile
| | - Carlos Henríquez-Castillo
- Department of Oceanography, Faculty of Natural and Oceanographic Sciences, Universidad de Concepción, Concepción, Chile.,Instituto Milenio de Oceanografía, Concepción, Chile
| | - Nathalie Delherbe
- Biology Department, Cell and Molecular Biology Joint Doctoral Program with UC San Diego, San Diego State University, San Diego, CA, United States
| | - Sheila Podell
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
| | - Salvador Ramirez-Flandes
- Instituto Milenio de Oceanografía, Concepción, Chile.,Programa de Doctorado en Ingeniería de Sistemas Complejos, Universidad Adolfo Ibáñez, Santiago, Chile
| | - Juan A Ugalde
- uBiome, Inc., San Francisco, CA, United States.,Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
| | - Juan F Santibañez
- Department of Oceanography, Faculty of Natural and Oceanographic Sciences, Universidad de Concepción, Concepción, Chile
| | | | - Kurt Hanselmann
- Department of Earth Sciences, ETH Zürich, Zurich, Switzerland
| | - Osvaldo Ulloa
- Department of Oceanography, Faculty of Natural and Oceanographic Sciences, Universidad de Concepción, Concepción, Chile.,Instituto Milenio de Oceanografía, Concepción, Chile
| | - Rodrigo De la Iglesia
- Department of Molecular Genetics and Microbiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Eric E Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States.,Division of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology and Environment, Faculty of Sciences, Universidad Mayor, Santiago, Chile
| |
Collapse
|
15
|
Undabarrena A, Salvà-Serra F, Jaén-Luchoro D, Castro-Nallar E, Mendez KN, Valencia R, Ugalde JA, Moore ERB, Seeger M, Cámara B. Complete genome sequence of the marine Rhodococcus sp. H-CA8f isolated from Comau fjord in Northern Patagonia, Chile. Mar Genomics 2018; 40:13-17. [PMID: 32420876 DOI: 10.1016/j.margen.2018.01.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/18/2018] [Accepted: 01/29/2018] [Indexed: 01/18/2023]
Abstract
Rhodococcus sp. H-CA8f was isolated from marine sediments obtained from the Comau fjord, located in Northern Chilean Patagonia. Whole-genome sequencing was achieved using PacBio RS II platform, comprising one closed, complete chromosome of 6,19 Mbp with a 62.45% G + C content. The chromosome harbours several metabolic pathways providing a wide catabolic potential, where the upper biphenyl route is described. Also, Rhodococcus sp. H-CA8f bears one linear mega-plasmid of 301 Kbp and 62.34% of G + C content, where genomic analyses demonstrated that it is constituted mostly by putative ORFs with unknown functions, representing a novel genetic feature. These genetic characteristics provide relevant insights regarding Chilean marine actinobacterial strains.
Collapse
Affiliation(s)
- A Undabarrena
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - F Salvà-Serra
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden; Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
| | - D Jaén-Luchoro
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden; Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
| | - E Castro-Nallar
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
| | - K N Mendez
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
| | - R Valencia
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - J A Ugalde
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile; uBiome, Inc., San Francisco, CA, United States
| | - E R B Moore
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden; Culture Collection University of Gothenburg (CCUG), Gothenburg, Sweden
| | - M Seeger
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - B Cámara
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile.
| |
Collapse
|
16
|
Bik EM, Ugalde JA, Cousins J, Goddard AD, Richman J, Apte ZS. Microbial biotransformations in the human distal gut. Br J Pharmacol 2017; 175:4404-4414. [PMID: 29116650 PMCID: PMC6255956 DOI: 10.1111/bph.14085] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 09/26/2017] [Accepted: 10/04/2017] [Indexed: 12/20/2022] Open
Abstract
The human distal gut is home to a rich and dense microbial community with representatives of all three domains of life which are intricately connected with our physiology and health. The combined genomes of these microbes, collectively called the human microbiome, vastly expand the metabolic capacities of our own genome, allowing us to break down and extract energy from dietary compounds that human enzymes cannot digest. In addition, the variable composition of these communities and their biotransformations might explain inter-individual differences in toxicities, tolerances and efficacies for certain drugs. Recent advances in sequencing technologies and bioinformatics have provided exciting new insights into the genomes of our microbial symbionts, their functional capacities and the interactions between these microbes and their human host. This review summarizes the metabolic conversions of dietary components and pharmaceuticals that take place in the human distal gut, as well as their implications for human health. LINKED ARTICLES: This article is part of a themed section on When Pharmacology Meets the Microbiome: New Targets for Therapeutics? To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v175.24/issuetoc.
Collapse
Affiliation(s)
| | | | | | | | | | - Zachary S Apte
- uBiome, Inc., San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| |
Collapse
|
17
|
Araos R, Montgomery V, Ugalde JA, Snyder GM, D’Agata EMC. Microbial Disruption Indices to Detect Colonization With Multidrug-Resistant Organisms. Infect Control Hosp Epidemiol 2017; 38:1312-1318. [PMID: 28899445 PMCID: PMC6262892 DOI: 10.1017/ice.2017.190] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
OBJECTIVE To characterize the microbial disruption indices of hospitalized patients to predict colonization with multidrug-resistant organisms (MDROs). DESIGN A cross-sectional survey of the fecal microbiome was conducted in a tertiary referral, acute-care hospital in Boston, Massachusetts. PARTICIPANTS The study population consisted of adult patients hospitalized in general medical/surgical wards. METHODS Rectal swabs were obtained from patients within 48 hours of hospital admission and screened for MDRO colonization using conventional culture techniques. The V4 region of the 16S rRNA gene was sequenced to assess the fecal microbiome. Microbial diversity and composition, as well as the functional potential of the microbial communities present in fecal samples, were compared between patients with and without MDRO colonization. RESULTS A total of 44 patients were included in the study, of whom 11 (25%) were colonized with at least 1 MDRO. Reduced microbial diversity and high abundance of metabolic pathways associated with multidrug-resistance mechanisms characterized the fecal microbiome of patients colonized with MDRO at hospital admission. CONCLUSIONS Our data suggest that microbial disruption indices may be key to predicting MDRO colonization and could provide novel infection control approaches. Infect Control Hosp Epidemiol 2017;38:1312-1318.
Collapse
Affiliation(s)
- Rafael Araos
- Genomics and Resistant Microbes (GeRM) Group, Facultad de Medicina Clinica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Veronica Montgomery
- Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia
| | - Juan A. Ugalde
- Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Graham M. Snyder
- Department of Medicine, Division of Infectious Diseases, Beth Israel Deaconess Medical Center, Boston, MA
| | | |
Collapse
|
18
|
Fujio-Vejar S, Vasquez Y, Morales P, Magne F, Vera-Wolf P, Ugalde JA, Navarrete P, Gotteland M. The Gut Microbiota of Healthy Chilean Subjects Reveals a High Abundance of the Phylum Verrucomicrobia. Front Microbiol 2017; 8:1221. [PMID: 28713349 PMCID: PMC5491548 DOI: 10.3389/fmicb.2017.01221] [Citation(s) in RCA: 165] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 06/16/2017] [Indexed: 12/31/2022] Open
Abstract
The gut microbiota is currently recognized as an important factor regulating the homeostasis of the gastrointestinal tract and influencing the energetic metabolism of the host as well as its immune and central nervous systems. Determining the gut microbiota composition of healthy subjects is therefore necessary to establish a baseline allowing the detection of microbiota alterations in pathologic conditions. Accordingly, the aim of this study was to characterize the gut microbiota of healthy Chilean subjects using 16S rRNA gene sequencing. Fecal samples were collected from 41 young, asymptomatic, normal weight volunteers (age: 25 ± 4 years; ♀:48.8%; BMI: 22.5 ± 1.6 kg/m2) with low levels of plasma (IL6 and hsCRP) and colonic (fecal calprotectin) inflammatory markers. The V3-V4 region of the 16S rRNA gene of bacterial DNA was amplified and sequenced using MiSeq Illumina system. 109,180 ± 13,148 sequences/sample were obtained, with an α-diversity of 3.86 ± 0.37. The dominant phyla were Firmicutes (43.6 ± 9.2%) and Bacteroidetes (41.6 ± 13.1%), followed by Verrucomicrobia (8.5 ± 10.4%), Proteobacteria (2.8 ± 4.8%), Actinobacteria (1.8 ± 3.9%) and Euryarchaeota (1.4 ± 2.7%). The core microbiota representing the genera present in all the subjects included Bacteroides, Prevotella, Parabacteroides (phylum Bacteroidetes), Phascolarctobacterium, Faecalibacterium, Ruminococcus, Lachnospira, Oscillospira, Blautia, Dorea, Roseburia, Coprococcus, Clostridium, Streptococcus (phylum Firmicutes), Akkermansia (phylum Verrucomicrobia), and Collinsella (phylum Actinobacteria). Butyrate-producing genera including Faecalibacterium, Roseburia, Coprococcus, and Oscillospira were detected. The family Methanobacteriaceae was reported in 83% of the subjects and Desulfovibrio, the most representative sulfate-reducing genus, in 76%. The microbiota of the Chilean individuals significantly differed from those of Papua New Guinea and the Matses ethnic group and was closer to that of the Argentinians and sub-populations from the United States. Interestingly, the microbiota of the Chilean subjects stands out for its richness in Verrucomicrobia; the mucus-degrading bacterium Akkermansia muciniphila is the only identified member of this phylum. This is an important finding considering that this microorganism has been recently proposed as a hallmark of healthy gut due to its anti-inflammatory and immunostimulant properties and its ability to improve gut barrier function, insulin sensitivity and endotoxinemia. These results constitute an important baseline that will facilitate the characterization of dysbiosis in the main diseases affecting the Chilean population.
Collapse
Affiliation(s)
- Sayaka Fujio-Vejar
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology, University of ChileSantiago, Chile.,Department of Nutrition, Faculty of Medicine, University of ChileSantiago, Chile
| | - Yessenia Vasquez
- Centro de Genética y Genómica, Facultad de Medicina, Clínica Alemana Universidad del DesarrolloSantiago, Chile
| | - Pamela Morales
- Department of Nutrition, Faculty of Medicine, University of ChileSantiago, Chile
| | - Fabien Magne
- Microbiology and Mycology Program, Institute of Biomedical Sciences, Faculty of Medicine, University of ChileSantiago, Chile
| | - Patricia Vera-Wolf
- Centro de Genética y Genómica, Facultad de Medicina, Clínica Alemana Universidad del DesarrolloSantiago, Chile
| | - Juan A Ugalde
- Centro de Genética y Genómica, Facultad de Medicina, Clínica Alemana Universidad del DesarrolloSantiago, Chile
| | - Paola Navarrete
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology, University of ChileSantiago, Chile
| | - Martin Gotteland
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology, University of ChileSantiago, Chile.,Department of Nutrition, Faculty of Medicine, University of ChileSantiago, Chile
| |
Collapse
|
19
|
Millán-Aguiñaga N, Chavarria KL, Ugalde JA, Letzel AC, Rouse GW, Jensen PR. Phylogenomic Insight into Salinispora (Bacteria, Actinobacteria) Species Designations. Sci Rep 2017; 7:3564. [PMID: 28620214 PMCID: PMC5472633 DOI: 10.1038/s41598-017-02845-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 04/18/2017] [Indexed: 11/12/2022] Open
Abstract
Bacteria represent the most genetically diverse kingdom of life. While great progress has been made in describing this diversity, it remains difficult to identify the phylogenetic and ecological characteristics that delineate groups of bacteria that possess species-like properties. One major challenge associated with species delineations is that not all shared genes have the same evolutionary history, and thus the choice of loci can have a major impact on phylogenetic reconstruction. Sequencing the genomes of large numbers of closely related strains provides new opportunities to distinguish ancestral from acquired alleles and assess the effects of recombination on phylogenetic inference. Here we analyzed the genomes of 119 strains of the marine actinomycete genus Salinispora, which is currently comprised of three named species that share 99% 16S rRNA gene sequence identity. While 63% of the core genome showed evidence of recombination, this had no effect on species-level phylogenomic resolution. Recombination did however blur intra-species relationships and biogeographic resolution. The genome-wide average nucleotide identity provided a new perspective on Salinispora diversity, revealing as many as seven new species. Patterns of orthologous group distributions reveal a genetic basis to delineation the candidate taxa and insight into the levels of genetic cohesion associated with bacterial species.
Collapse
Affiliation(s)
- Natalie Millán-Aguiñaga
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States.,Universidad Autónoma de Baja California. Facultad de Ciencias Marinas, Ensenada, Baja California, Mexico
| | - Krystle L Chavarria
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States
| | - Juan A Ugalde
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States.,Centro de Bioinformática y Biología Integrativa, Facultad de Ciencias Biológicas, Universidad Andrés Bella, Santiago, Chile
| | - Anne-Catrin Letzel
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States
| | - Greg W Rouse
- Marine Biology Research Division Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States. .,Marine Biology Research Division Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States.
| |
Collapse
|
20
|
Undabarrena A, Ugalde JA, Seeger M, Cámara B. -Genomic data mining of the marine actinobacteria Streptomyces sp. H-KF8 unveils insights into multi-stress related genes and metabolic pathways involved in antimicrobial synthesis. PeerJ 2017; 5:e2912. [PMID: 28229018 PMCID: PMC5312570 DOI: 10.7717/peerj.2912] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 12/14/2016] [Indexed: 12/25/2022] Open
Abstract
Streptomyces sp. H-KF8 is an actinobacterial strain isolated from marine sediments of a Chilean Patagonian fjord. Morphological characterization together with antibacterial activity was assessed in various culture media, revealing a carbon-source dependent activity mainly against Gram-positive bacteria (S. aureus and L. monocytogenes). Genome mining of this antibacterial-producing bacterium revealed the presence of 26 biosynthetic gene clusters (BGCs) for secondary metabolites, where among them, 81% have low similarities with known BGCs. In addition, a genomic search in Streptomyces sp. H-KF8 unveiled the presence of a wide variety of genetic determinants related to heavy metal resistance (49 genes), oxidative stress (69 genes) and antibiotic resistance (97 genes). This study revealed that the marine-derived Streptomyces sp. H-KF8 bacterium has the capability to tolerate a diverse set of heavy metals such as copper, cobalt, mercury, chromate and nickel; as well as the highly toxic tellurite, a feature first time described for Streptomyces. In addition, Streptomyces sp. H-KF8 possesses a major resistance towards oxidative stress, in comparison to the soil reference strain Streptomyces violaceoruber A3(2). Moreover, Streptomyces sp. H-KF8 showed resistance to 88% of the antibiotics tested, indicating overall, a strong response to several abiotic stressors. The combination of these biological traits confirms the metabolic versatility of Streptomyces sp. H-KF8, a genetically well-prepared microorganism with the ability to confront the dynamics of the fjord-unique marine environment.
Collapse
Affiliation(s)
- Agustina Undabarrena
- Departmento de Química & Centro de Biotecnología, Universidad Técnica Federico Santa María , Valparaiso , Chile
| | - Juan A Ugalde
- Centro de Genética y Genómica, Facultad de Medicina Clinica Alemana, Universidad del Desarrollo , Santiago , Chile
| | - Michael Seeger
- Departmento de Química & Centro de Biotecnología, Universidad Técnica Federico Santa María , Valparaiso , Chile
| | - Beatriz Cámara
- Departmento de Química & Centro de Biotecnología, Universidad Técnica Federico Santa María , Valparaiso , Chile
| |
Collapse
|
21
|
Asenjo F, Olmos A, Henríquez-Piskulich P, Polanco V, Aldea P, Ugalde JA, Trombert AN. Genome sequencing and analysis of the first complete genome of Lactobacillus kunkeei strain MP2, an Apis mellifera gut isolate. PeerJ 2016; 4:e1950. [PMID: 27114887 PMCID: PMC4841242 DOI: 10.7717/peerj.1950] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 03/29/2016] [Indexed: 01/23/2023] Open
Abstract
Background. The honey bee (Apis mellifera) is the most important pollinator in agriculture worldwide. However, the number of honey bees has fallen significantly since 2006, becoming a huge ecological problem nowadays. The principal cause is CCD, or Colony Collapse Disorder, characterized by the seemingly spontaneous abandonment of hives by their workers. One of the characteristics of CCD in honey bees is the alteration of the bacterial communities in their gastrointestinal tract, mainly due to the decrease of Firmicutes populations, such as the Lactobacilli. At this time, the causes of these alterations remain unknown. We recently isolated a strain of Lactobacillus kunkeei (L. kunkeei strain MP2) from the gut of Chilean honey bees. L. kunkeei, is one of the most commonly isolated bacterium from the honey bee gut and is highly versatile in different ecological niches. In this study, we aimed to elucidate in detail, the L. kunkeei genetic background and perform a comparative genome analysis with other Lactobacillus species. Methods. L. kunkeei MP2 was originally isolated from the guts of Chilean A. mellifera individuals. Genome sequencing was done using Pacific Biosciences single-molecule real-time sequencing technology. De novo assembly was performed using Celera assembler. The genome was annotated using Prokka, and functional information was added using the EggNOG 3.1 database. In addition, genomic islands were predicted using IslandViewer, and pro-phage sequences using PHAST. Comparisons between L. kunkeei MP2 with other L. kunkeei, and Lactobacillus strains were done using Roary. Results. The complete genome of L. kunkeei MP2 comprises one circular chromosome of 1,614,522 nt. with a GC content of 36,9%. Pangenome analysis with 16 L. kunkeei strains, identified 113 unique genes, most of them related to phage insertions. A large and unique region of L. kunkeei MP2 genome contains several genes that encode for phage structural protein and replication components. Comparative analysis of MP2 with other Lactobacillus species, identified several unique genes of L. kunkeei MP2 related with metabolism, biofilm generation, survival under stress conditions, and mobile genetic elements (MGEs). Discussion. The presence of multiple mobile genetic elements, including phage sequences, suggest a high degree of genetic variability in L. kunkeei. Its versatility and ability to survive in different ecological niches (bee guts, flowers, fruits among others) could be given by its genetic capacity to change and adapt to different environments. L. kunkeei could be a new source of Lactobacillus with beneficial properties. Indeed, L. kunkeei MP2 could play an important role in honey bee nutrition through the synthesis of components as isoprenoids.
Collapse
Affiliation(s)
- Freddy Asenjo
- Centro de Genética y Genómica, Facultad de Medicina, Clinica Alemana Universidad del Desarrollo , Santiago , Chile
| | - Alejandro Olmos
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor , Santiago , Chile
| | | | - Victor Polanco
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile; Centro de Estudios Apícolas CEAPI Mayor, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Patricia Aldea
- Centro de Estudios Apícolas CEAPI Mayor, Facultad de Ciencias, Universidad Mayor , Santiago , Chile
| | - Juan A Ugalde
- Centro de Genética y Genómica, Facultad de Medicina, Clinica Alemana Universidad del Desarrollo , Santiago , Chile
| | - Annette N Trombert
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor , Santiago , Chile
| |
Collapse
|
22
|
Morales P, Fujio S, Navarrete P, Ugalde JA, Magne F, Carrasco-Pozo C, Tralma K, Quezada M, Hurtado C, Covarrubias N, Brignardello J, Henriquez D, Gotteland M. Impact of Dietary Lipids on Colonic Function and Microbiota: An Experimental Approach Involving Orlistat-Induced Fat Malabsorption in Human Volunteers. Clin Transl Gastroenterol 2016; 7:e161. [PMID: 27054579 PMCID: PMC4855161 DOI: 10.1038/ctg.2016.20] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 03/07/2016] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES: High-fat diets alter gut microbiota and barrier function, inducing metabolic endotoxemia and low-grade inflammation. Whether these effects are due to the high dietary lipid content or to the concomitant decrease of carbohydrate intake is unclear. The aim of this study was to determine whether higher amounts of dietary fat reaching the colon (through orlistat administration) affect the colonic ecosystem in healthy volunteers and the effect of the prebiotic oligofructose (OF) in this model. METHODS: Forty-one healthy young subjects were distributed among four groups: Control (C), Prebiotic (P), Orlistat (O), and Orlistat/Prebiotic (OP). They consumed a fat-standardized diet (60 g/day) during Week-1 (baseline) and after 1 week of washout, Week-3. During Week-3, they also received their respective treatment (Orlistat: 2 × 120 mg/day, OF: 16 g/day, and maltodextrin as placebo). A 72-h stool collection was carried out at the end of Week-1 (T0) and Week-3 (T1). Fecal fat, calprotectin, and short-chain fatty acids (SCFAs) as well as the antioxidant activity of fecal waters (ferric-reducing antioxidant power), fecal microbiota composition (by deep sequencing), and gut permeability (Sucralose/Lactulose/Mannitol test) were determined at these times. RESULTS: Fecal fat excretion was higher in the O (P=0.0050) and OP (P=0.0069) groups. This event was accompanied, in the O group, by an increased calprotectin content (P=0.047) and a decreased fecal antioxidant activity (P=0.047). However, these alterations did not alter gut barrier function and the changes observed in the composition of the fecal microbiota only affected bacterial populations with low relative abundance (<0.01%); in consequences, fecal SCFA remained mainly unchanged. Part of the colonic alterations induced by orlistat were prevented by OF administration. CONCLUSIONS: In the context of an equilibrated diet, the acute exposition of the colonic ecosystem to high amounts of dietary lipids is associated with an incremented excretion of fecal calprotectin and pro-oxidant activity of the colonic content, in the absence of significant changes in the microbiota.
Collapse
Affiliation(s)
- Pamela Morales
- Department of Nutrition, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Sayaka Fujio
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago, Chile
| | - Paola Navarrete
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago, Chile
| | - Juan A Ugalde
- Center for Genomics and Bioinformatics, Faculty of Sciences, Universidad Mayor, Santiago, Chile
| | - Fabien Magne
- Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | | | - Karina Tralma
- Department of Nutrition, Faculty of Medicine, University of Chile, Santiago, Chile
| | - MariaPaz Quezada
- Department of Nutrition, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Carmen Hurtado
- Gastroentenrology Section, University of Chile Clinical Hospital, University of Chile, Santiago, Chile
| | - Natalia Covarrubias
- Gastroentenrology Section, University of Chile Clinical Hospital, University of Chile, Santiago, Chile
| | - Jerusa Brignardello
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago, Chile
| | - Daniela Henriquez
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago, Chile
| | - Martin Gotteland
- Department of Nutrition, Faculty of Medicine, University of Chile, Santiago, Chile.,Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago, Chile
| |
Collapse
|
23
|
Tang X, Li J, Millán-Aguiñaga N, Zhang JJ, O’Neill EC, Ugalde JA, Jensen PR, Mantovani SM, Moore BS. Identification of Thiotetronic Acid Antibiotic Biosynthetic Pathways by Target-directed Genome Mining. ACS Chem Biol 2015; 10:2841-2849. [PMID: 26458099 DOI: 10.1021/acschembio.5b00658] [Citation(s) in RCA: 177] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent genome sequencing efforts have led to the rapid accumulation of uncharacterized or "orphaned" secondary metabolic biosynthesis gene clusters (BGCs) in public databases. This increase in DNA-sequenced big data has given rise to significant challenges in the applied field of natural product genome mining, including (i) how to prioritize the characterization of orphan BGCs and (ii) how to rapidly connect genes to biosynthesized small molecules. Here, we show that by correlating putative antibiotic resistance genes that encode target-modified proteins with orphan BGCs, we predict the biological function of pathway specific small molecules before they have been revealed in a process we call target-directed genome mining. By querying the pan-genome of 86 Salinispora bacterial genomes for duplicated house-keeping genes colocalized with natural product BGCs, we prioritized an orphan polyketide synthase-nonribosomal peptide synthetase hybrid BGC (tlm) with a putative fatty acid synthase resistance gene. We employed a new synthetic double-stranded DNA-mediated cloning strategy based on transformation-associated recombination to efficiently capture tlm and the related ttm BGCs directly from genomic DNA and to heterologously express them in Streptomyces hosts. We show the production of a group of unusual thiotetronic acid natural products, including the well-known fatty acid synthase inhibitor thiolactomycin that was first described over 30 years ago, yet never at the genetic level in regards to biosynthesis and autoresistance. This finding not only validates the target-directed genome mining strategy for the discovery of antibiotic producing gene clusters without a priori knowledge of the molecule synthesized but also paves the way for the investigation of novel enzymology involved in thiotetronic acid natural product biosynthesis.
Collapse
Affiliation(s)
- Xiaoyu Tang
- Scripps
Institution of Oceanography, University of California, San Diego, La Jolla, California, United States
| | - Jie Li
- Scripps
Institution of Oceanography, University of California, San Diego, La Jolla, California, United States
| | - Natalie Millán-Aguiñaga
- Scripps
Institution of Oceanography, University of California, San Diego, La Jolla, California, United States
| | - Jia Jia Zhang
- Scripps
Institution of Oceanography, University of California, San Diego, La Jolla, California, United States
| | - Ellis C. O’Neill
- Scripps
Institution of Oceanography, University of California, San Diego, La Jolla, California, United States
| | - Juan A. Ugalde
- Centro
de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Campus Huechuraba, Camino a la Pirámide 5750, Santiago, Chile
| | - Paul R. Jensen
- Scripps
Institution of Oceanography, University of California, San Diego, La Jolla, California, United States
| | - Simone M. Mantovani
- Scripps
Institution of Oceanography, University of California, San Diego, La Jolla, California, United States
| | - Bradley S. Moore
- Scripps
Institution of Oceanography, University of California, San Diego, La Jolla, California, United States
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, United States
| |
Collapse
|
24
|
Martin LJ, Adams RI, Bateman A, Bik HM, Hawks J, Hird SM, Hughes D, Kembel SW, Kinney K, Kolokotronis SO, Levy G, McClain C, Meadow JF, Medina RF, Mhuireach G, Moreau CS, Munshi-South J, Nichols LM, Palmer C, Popova L, Schal C, Täubel M, Trautwein M, Ugalde JA, Dunn RR. Evolution of the indoor biome. Trends Ecol Evol 2015; 30:223-32. [DOI: 10.1016/j.tree.2015.02.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 02/08/2015] [Accepted: 02/09/2015] [Indexed: 11/15/2022]
|
25
|
Plominsky AM, Delherbe N, Ugalde JA, Allen EE, Blanchet M, Ikeda P, Santibañez F, Hanselmann K, Ulloa O, De la Iglesia R, von Dassow P, Astorga M, Gálvez MJ, González ML, Henríquez-Castillo C, Vaulot D, Lopes do Santos A, van den Engh G, Gimpel C, Bertoglio F, Delgado Y, Docmac F, Elizondo-Patrone C, Narváez S, Sorroche F, Rojas-Herrera M, Trefault N. Metagenome sequencing of the microbial community of a solar saltern crystallizer pond at cáhuil lagoon, chile. Genome Announc 2014; 2:e01172-14. [PMID: 25395641 PMCID: PMC4241667 DOI: 10.1128/genomea.01172-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 10/06/2014] [Indexed: 11/22/2022]
Abstract
Cáhuil Lagoon in central Chile harbors distinct microbial communities in various solar salterns that are arranged as interconnected ponds with increasing salt concentrations. Here, we report the metagenome of the 3.0- to 0.2-µm fraction of the microbial community present in a crystallizer pond with 34% salinity.
Collapse
Affiliation(s)
- Alvaro M Plominsky
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Nathalie Delherbe
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Juan A Ugalde
- Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | | | - Marine Blanchet
- Biogeochemistry and Microbiology, Université Pierre et Marie Curie, Paris, France
| | - Priscila Ikeda
- Oceanographic Institute, University of Sao Paulo, São Paulo, Brazil
| | | | - Kurt Hanselmann
- Department of Earth Sciences, Climate Geology, Geomicrobiology, ETH Zürich, Zürich, Switzerland
| | | | - Rodrigo De la Iglesia
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Peter von Dassow
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Marcia Astorga
- Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile
| | - María Jesús Gálvez
- Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile
| | | | | | | | | | | | - Carla Gimpel
- Departamento Científico, Instituto Antártico Chileno, Punta Arenas, Chile
| | - Florencia Bertoglio
- Centro Universitario Regional Este, Universidad de la República, Rocha, Uruguay
| | - Yolaine Delgado
- Departamento de Microbiología, Universidad de La Habana, La Habana, Cuba
| | - Felipe Docmac
- Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | | | - Silvia Narváez
- Instituto de Investigaciones Marinas, INVEMAR, Santa Marta, Colombia
| | - Fernando Sorroche
- Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Córdoba, Argentina
| | | | | |
Collapse
|
26
|
Malfatti F, Turk V, Tinta T, Mozetič P, Manganelli M, Samo TJ, Ugalde JA, Kovač N, Stefanelli M, Antonioli M, Fonda-Umani S, Del Negro P, Cataletto B, Hozić A, Ivošević Denardis N, Zutić V, Svetličić V, Mišić Radić T, Radić T, Fuks D, Azam F. Microbial mechanisms coupling carbon and phosphorus cycles in phosphorus-limited northern Adriatic Sea. Sci Total Environ 2014; 470-471:1173-1183. [PMID: 24246940 DOI: 10.1016/j.scitotenv.2013.10.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Revised: 10/11/2013] [Accepted: 10/13/2013] [Indexed: 06/02/2023]
Abstract
The coastal northern Adriatic Sea receives pulsed inputs of riverine nutrients, causing phytoplankton blooms and seasonally sustained dissolved organic carbon (DOC) accumulation-hypothesized to cause episodes of massive mucilage. The underlying mechanisms regulating P and C cycles and their coupling are unclear. Extensive biogeochemical parameters, processes and community composition were measured in a 64-day mesocosms deployed off Piran, Slovenia. We followed the temporal trends of C and P fluxes in P-enriched (P+) and unenriched (P-) mesocosms. An intense diatom bloom developed then crashed; however, substantial primary production was maintained throughout, supported by tightly coupled P regeneration by bacteria and phytoplankton. Results provide novel insights on post-bloom C and P dynamics and mechanisms. 1) Post-bloom DOC accumulation to 186 μM remained elevated despite high bacterial carbon demand. Presumably, a large part of DOC accumulated due to the bacterial ectohydrolytic processing of primary productivity that adventitiously generated slow-to-degrade DOC; 2) bacteria heavily colonized post-bloom diatom aggregates, rendering them microscale hotspots of P regeneration due to locally intense bacterial ectohydrolase activities; 3) Pi turnover was rapid thus suggesting high P flux through the DOP pool (dissolved organic phosphorus) turnover; 4) Alpha- and Gamma-proteobacteria dominated the bacterial communities despite great differences of C and P pools and fluxes in both mesocosms. However, minor taxa showed dramatic changes in community compositions. Major OTUs were presumably generalists adapted to diverse productivity regimes.We suggest that variation in bacterial ectohydrolase activities on aggregates, regulating the rates of POM→DOM transition as well as dissolved polymer hydrolysis, could become a bottleneck in P regeneration. This could be another regulatory step, in addition to APase, in the microbial regulation of P cycle and the coupling between C and P cycles.
Collapse
Affiliation(s)
- F Malfatti
- Scripps Institution of Oceanography, University California San Diego, 92037 La Jolla, USA
| | - V Turk
- National Institute of Biology, Marine Station Piran, 66330 Piran, Slovenia
| | - T Tinta
- National Institute of Biology, Marine Station Piran, 66330 Piran, Slovenia
| | - P Mozetič
- National Institute of Biology, Marine Station Piran, 66330 Piran, Slovenia
| | - M Manganelli
- Istituto Superiore per la Prevenzione e la Sicurezza del Lavoro (ISPESL), DIPIA, 00040 Monteporzio Catone, Roma, Italy; Istituto Superiore di Sanità, Dept. of Environment and Primary Prevention, Roma, Italy
| | - T J Samo
- Scripps Institution of Oceanography, University California San Diego, 92037 La Jolla, USA
| | - J A Ugalde
- Scripps Institution of Oceanography, University California San Diego, 92037 La Jolla, USA
| | - N Kovač
- National Institute of Biology, Marine Station Piran, 66330 Piran, Slovenia
| | - M Stefanelli
- Istituto Superiore per la Prevenzione e la Sicurezza del Lavoro (ISPESL), DIPIA, 00040 Monteporzio Catone, Roma, Italy; Istituto Superiore di Sanità, Dept. of Environment and Primary Prevention, Roma, Italy
| | - M Antonioli
- Universita' degli Studi di Trieste, Dipartimento di Biologia, 34127 Trieste, Italy
| | - S Fonda-Umani
- Universita' degli Studi di Trieste, Dipartimento di Biologia, 34127 Trieste, Italy
| | - P Del Negro
- Istituto Nazionale di Oceanografia e Geofisica Sperimentale, Sezione Bio, 34151 Santa Croce, Trieste, Italy
| | - B Cataletto
- Istituto Nazionale di Oceanografia e Geofisica Sperimentale, Sezione Bio, 34151 Santa Croce, Trieste, Italy
| | - A Hozić
- Ruđer Bošković Institute, Division for Marine and Environmental Research, 10000 Zagreb, Croatia
| | - N Ivošević Denardis
- Ruđer Bošković Institute, Division for Marine and Environmental Research, 10000 Zagreb, Croatia
| | - V Zutić
- Ruđer Bošković Institute, Division for Marine and Environmental Research, 10000 Zagreb, Croatia
| | - V Svetličić
- Ruđer Bošković Institute, Division for Marine and Environmental Research, 10000 Zagreb, Croatia
| | - T Mišić Radić
- Ruđer Bošković Institute, Division for Marine and Environmental Research, 10000 Zagreb, Croatia
| | - T Radić
- Institute for Adriatic Crops and Karst Reclamation, Split, Croatia
| | - D Fuks
- Ruđer Bošković Institute, Center for Marine Research, Rovinj, Croatia
| | - F Azam
- Scripps Institution of Oceanography, University California San Diego, 92037 La Jolla, USA
| |
Collapse
|
27
|
Ugalde JA, Gallardo MJ, Belmar C, Muñoz P, Ruiz-Tagle N, Ferrada-Fuentes S, Espinoza C, Allen EE, Gallardo VA. Microbial life in a fjord: metagenomic analysis of a microbial mat in Chilean patagonia. PLoS One 2013; 8:e71952. [PMID: 24015199 PMCID: PMC3756073 DOI: 10.1371/journal.pone.0071952] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 07/05/2013] [Indexed: 01/09/2023] Open
Abstract
The current study describes the taxonomic and functional composition of metagenomic sequences obtained from a filamentous microbial mat isolated from the Comau fjord, located in the northernmost part of the Chilean Patagonia. The taxonomic composition of the microbial community showed a high proportion of members of the Gammaproteobacteria, including a high number of sequences that were recruited to the genomes of Moritella marina MP-1 and Colwelliapsycherythraea 34H, suggesting the presence of populations related to these two psychrophilic bacterial species. Functional analysis of the community indicated a high proportion of genes coding for the transport and metabolism of amino acids, as well as in energy production. Among the energy production functions, we found protein-coding genes for sulfate and nitrate reduction, both processes associated with Gammaproteobacteria-related sequences. This report provides the first examination of the taxonomic composition and genetic diversity associated with these conspicuous microbial mat communities and provides a framework for future microbial studies in the Comau fjord.
Collapse
Affiliation(s)
- Juan A Ugalde
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Podell S, Ugalde JA, Narasingarao P, Banfield JF, Heidelberg KB, Allen EE. Assembly-driven community genomics of a hypersaline microbial ecosystem. PLoS One 2013; 8:e61692. [PMID: 23637883 PMCID: PMC3630111 DOI: 10.1371/journal.pone.0061692] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 03/13/2013] [Indexed: 01/10/2023] Open
Abstract
Microbial populations inhabiting a natural hypersaline lake ecosystem in Lake Tyrrell, Victoria, Australia, have been characterized using deep metagenomic sampling, iterative de novo assembly, and multidimensional phylogenetic binning. Composite genomes representing habitat-specific microbial populations were reconstructed for eleven different archaea and one bacterium, comprising between 0.6 and 14.1% of the planktonic community. Eight of the eleven archaeal genomes were from microbial species without previously cultured representatives. These new genomes provide habitat-specific reference sequences enabling detailed, lineage-specific compartmentalization of predicted functional capabilities and cellular properties associated with both dominant and less abundant community members, including organisms previously known only by their 16S rRNA sequences. Together, these data provide a comprehensive, culture-independent genomic blueprint for ecosystem-wide analysis of protein functions, population structure, and lifestyles of co-existing, co-evolving microbial groups within the same natural habitat. The “assembly-driven” community genomic approach demonstrated in this study advances our ability to push beyond single gene investigations, and promotes genome-scale reconstructions as a tangible goal in the quest to define the metabolic, ecological, and evolutionary dynamics that underpin environmental microbial diversity.
Collapse
Affiliation(s)
- Sheila Podell
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Juan A. Ugalde
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Priya Narasingarao
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Jillian F. Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, California, United States of America
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, United States of America
| | - Karla B. Heidelberg
- Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
| | - Eric E. Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
| |
Collapse
|
29
|
Ugalde JA, Podell S, Narasingarao P, Allen EE. Xenorhodopsins, an enigmatic new class of microbial rhodopsins horizontally transferred between archaea and bacteria. Biol Direct 2011; 6:52. [PMID: 21985229 PMCID: PMC3198991 DOI: 10.1186/1745-6150-6-52] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Accepted: 10/10/2011] [Indexed: 02/26/2023] Open
Abstract
Based on unique, coherent properties of phylogenetic analysis, key amino acid substitutions and structural modeling, we have identified a new class of unusual microbial rhodopsins related to the Anabaena sensory rhodopsin (ASR) protein, including multiple homologs not previously recognized. We propose the name xenorhodopsin for this class, reflecting a taxonomically diverse membership spanning five different Bacterial phyla as well as the Euryarchaeotal class Nanohaloarchaea. The patchy phylogenetic distribution of xenorhodopsin homologs is consistent with historical dissemination through horizontal gene transfer. Shared characteristics of xenorhodopsin-containing microbes include the absence of flagellar motility and isolation from high light habitats.
Collapse
Affiliation(s)
- Juan A Ugalde
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093-0202, USA
| | | | | | | |
Collapse
|
30
|
Narasingarao P, Podell S, Ugalde JA, Brochier-Armanet C, Emerson JB, Brocks JJ, Heidelberg KB, Banfield JF, Allen EE. De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities. ISME J 2011; 6:81-93. [PMID: 21716304 DOI: 10.1038/ismej.2011.78] [Citation(s) in RCA: 227] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This study describes reconstruction of two highly unusual archaeal genomes by de novo metagenomic assembly of multiple, deeply sequenced libraries from surface waters of Lake Tyrrell (LT), a hypersaline lake in NW Victoria, Australia. Lineage-specific probes were designed using the assembled genomes to visualize these novel archaea, which were highly abundant in the 0.1-0.8 μm size fraction of lake water samples. Gene content and inferred metabolic capabilities were highly dissimilar to all previously identified hypersaline microbial species. Distinctive characteristics included unique amino acid composition, absence of Gvp gas vesicle proteins, atypical archaeal metabolic pathways and unusually small cell size (approximately 0.6 μm diameter). Multi-locus phylogenetic analyses demonstrated that these organisms belong to a new major euryarchaeal lineage, distantly related to halophilic archaea of class Halobacteria. Consistent with these findings, we propose creation of a new archaeal class, provisionally named 'Nanohaloarchaea'. In addition to their high abundance in LT surface waters, we report the prevalence of Nanohaloarchaea in other hypersaline environments worldwide. The simultaneous discovery and genome sequencing of a novel yet ubiquitous lineage of uncultivated microorganisms demonstrates that even historically well-characterized environments can reveal unexpected diversity when analyzed by metagenomics, and advances our understanding of the ecology of hypersaline environments and the evolutionary history of the archaea.
Collapse
Affiliation(s)
- Priya Narasingarao
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Abstract
Recreating ancestral proteins in the laboratory increasingly is being used to study the evolutionary history of protein function. More efficient gene synthesis techniques and the decreasing costs of commercial oligosynthesis are making this approach both simpler and less expensive to perform. Developments in ancestral reconstruction methods, particularly more realistic likelihood models of molecular evolution, allow for the accurate reconstruction of more ancient proteins than previously possible. This chapter reviews phylogenetic methods of ancestral inference, strategies for investigating alternative reconstructions, gene synthesis, and design, and an application of these methods to the reconstruction of an ancestor in the green fluorescent protein family.
Collapse
Affiliation(s)
- Belinda S W Chang
- Department of Zoology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| | | | | |
Collapse
|
32
|
Abstract
In proteins homologous to the green fluorescent protein (GFP), formation of red fluorescence requires three autocatalytic steps, whereas only two are needed for green fluorescence. Multiple red/green color diversification events in the GFP superfamily may reflect convergent evolution of the more complex three-step pathway. In the great star coral Montastraea cavernosa, a recreated common ancestor of green and red proteins turned out to be green, indicating that in this case red proteins evolved their color independently from most other homologous red proteins. Furthermore, red color appears to have evolved gradually by small incremental transitions.
Collapse
Affiliation(s)
- Juan A Ugalde
- Whitney Laboratory, University of Florida, Gainesville, FL, USA
| | | | | |
Collapse
|
33
|
Shagin DA, Barsova EV, Yanushevich YG, Fradkov AF, Lukyanov KA, Labas YA, Semenova TN, Ugalde JA, Meyers A, Nunez JM, Widder EA, Lukyanov SA, Matz MV. GFP-like proteins as ubiquitous metazoan superfamily: evolution of functional features and structural complexity. Mol Biol Evol 2004; 21:841-50. [PMID: 14963095 DOI: 10.1093/molbev/msh079] [Citation(s) in RCA: 295] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Homologs of the green fluorescent protein (GFP), including the recently described GFP-like domains of certain extracellular matrix proteins in Bilaterian organisms, are remarkably similar at the protein structure level, yet they often perform totally unrelated functions, thereby warranting recognition as a superfamily. Here we describe diverse GFP-like proteins from previously undersampled and completely new sources, including hydromedusae and planktonic Copepoda. In hydromedusae, yellow and nonfluorescent purple proteins were found in addition to greens. Notably, the new yellow protein seems to follow exactly the same structural solution to achieving the yellow color of fluorescence as YFP, an engineered yellow-emitting mutant variant of GFP. The addition of these new sequences made it possible to resolve deep-level phylogenetic relationships within the superfamily. Fluorescence (most likely green) must have already existed in the common ancestor of Cnidaria and Bilateria, and therefore GFP-like proteins may be responsible for fluorescence and/or coloration in virtually any animal. At least 15 color diversification events can be inferred following the maximum parsimony principle in Cnidaria. Origination of red fluorescence and nonfluorescent purple-blue colors on several independent occasions provides a remarkable example of convergent evolution of complex features at the molecular level.
Collapse
|
34
|
Zeledón R, Ugalde JA, Paniagua LA. Entomological and ecological aspects of six sylvatic species of triatomines (Hemiptera, Reduviidae) from the collection of the National Biodiversity Institute of Costa Rica, Central America. Mem Inst Oswaldo Cruz 2001; 96:757-64. [PMID: 11562697 DOI: 10.1590/s0074-02762001000600002] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
A total of 797 specimens of wild adult triatomines, belonging to six species from the entomological collections of the Costa Rican National Biodiversity Institute, was studied from the standpoint of their relative abundance, as reflected by light traps, distribution in the country, seasonal variations and climatic and altitudinal preferences. Triatoma dimidiata was the most abundant species (32.9% of the total specimens), with a very extensive distribution in different ecological zones, being more common between 100 to 400 m above sea level mainly at the end of the dry season. T. dispar was the third in frequency (21.5%), with narrower distribution, more abundant between 600 to 800 m and scarce during the dry season. Panstrongylus geniculatus and P. rufotuberculatus, second and fourth in frequency (22.1% and 15.1%, respectively), were widely distributed on both the Pacific and Caribbean basins, the former being more common between 80 to 270 m all year round and the latter below 800 m mainly during the first semester. Eratyrus cuspidatus which represented only 4.9% of the insects, was also present on both basins mainly below 200 m with a tendency to be scarce during certain months of the year, and was found in all types of ecological zones. Finally, Rhodnius pallescens, the least abundant species (3.6%) was restricted to very humid areas below 20 m, on the north side and Caribbean basin. With the exception of R. pallescens, males were more commonly found than females. Some epidemiological implications related to the six species are discussed.
Collapse
Affiliation(s)
- R Zeledón
- Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica.
| | | | | |
Collapse
|