51
|
Zhang Y, Gallant É, Park JD, Seyedsayamdost MR. The Small-Molecule Language of Dynamic Microbial Interactions. Annu Rev Microbiol 2022; 76:641-660. [PMID: 35679616 PMCID: PMC10171915 DOI: 10.1146/annurev-micro-042722-091052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Although microbes are routinely grown in monocultures in the laboratory, they are almost never encountered as single species in the wild. Our ability to detect and identify new microorganisms has advanced significantly in recent years, but our understanding of the mechanisms that mediate microbial interactions has lagged behind. What makes this task more challenging is that microbial alliances can be dynamic, consisting of multiple phases. The transitions between phases, and the interactions in general, are often mediated by a chemical language consisting of small molecules, also referred to as secondary metabolites or natural products. In this microbial lexicon, the molecules are like words and through their effects on recipient cells they convey meaning. The current review highlights three dynamic microbial interactions in which some of the words and their meanings have been characterized, especially those that mediate transitions in selected multiphasic associations. These systems provide insights into the principles that govern microbial symbioses and a playbook for interrogating similar associations in diverse ecological niches. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Yifan Zhang
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA; ,
| | - Étienne Gallant
- Department of Chemistry, Princeton University, Princeton, New Jersey, USA; ,
| | - Jong-Duk Park
- Department of Chemistry, Princeton University, Princeton, New Jersey, USA; ,
| | - Mohammad R Seyedsayamdost
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA; , .,Department of Chemistry, Princeton University, Princeton, New Jersey, USA; ,
| |
Collapse
|
52
|
Raju DV, Nagarajan A, Pandit S, Nag M, Lahiri D, Upadhye V. Effect of bacterial quorum sensing and mechanism of antimicrobial resistance. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
53
|
Barcoto MO, Rodrigues A. Lessons From Insect Fungiculture: From Microbial Ecology to Plastics Degradation. Front Microbiol 2022; 13:812143. [PMID: 35685924 PMCID: PMC9171207 DOI: 10.3389/fmicb.2022.812143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/15/2022] [Indexed: 11/13/2022] Open
Abstract
Anthropogenic activities have extensively transformed the biosphere by extracting and disposing of resources, crossing boundaries of planetary threat while causing a global crisis of waste overload. Despite fundamental differences regarding structure and recalcitrance, lignocellulose and plastic polymers share physical-chemical properties to some extent, that include carbon skeletons with similar chemical bonds, hydrophobic properties, amorphous and crystalline regions. Microbial strategies for metabolizing recalcitrant polymers have been selected and optimized through evolution, thus understanding natural processes for lignocellulose modification could aid the challenge of dealing with the recalcitrant human-made polymers spread worldwide. We propose to look for inspiration in the charismatic fungal-growing insects to understand multipartite degradation of plant polymers. Independently evolved in diverse insect lineages, fungiculture embraces passive or active fungal cultivation for food, protection, and structural purposes. We consider there is much to learn from these symbioses, in special from the community-level degradation of recalcitrant biomass and defensive metabolites. Microbial plant-degrading systems at the core of insect fungicultures could be promising candidates for degrading synthetic plastics. Here, we first compare the degradation of lignocellulose and plastic polymers, with emphasis in the overlapping microbial players and enzymatic activities between these processes. Second, we review the literature on diverse insect fungiculture systems, focusing on features that, while supporting insects' ecology and evolution, could also be applied in biotechnological processes. Third, taking lessons from these microbial communities, we suggest multidisciplinary strategies to identify microbial degraders, degrading enzymes and pathways, as well as microbial interactions and interdependencies. Spanning from multiomics to spectroscopy, microscopy, stable isotopes probing, enrichment microcosmos, and synthetic communities, these strategies would allow for a systemic understanding of the fungiculture ecology, driving to application possibilities. Detailing how the metabolic landscape is entangled to achieve ecological success could inspire sustainable efforts for mitigating the current environmental crisis.
Collapse
Affiliation(s)
- Mariana O. Barcoto
- Center for the Study of Social Insects, São Paulo State University (UNESP), Rio Claro, Brazil
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, Brazil
| | - Andre Rodrigues
- Center for the Study of Social Insects, São Paulo State University (UNESP), Rio Claro, Brazil
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, Brazil
| |
Collapse
|
54
|
Abstract
The diversity, ubiquity, and significance of microbial communities is clear. However, the predictable and reliable manipulation of microbiomes to impact human, environmental, and agricultural health remains a challenge.
Collapse
|
55
|
Commensal and Pathogenic Bacterial-Derived Extracellular Vesicles in Host-Bacterial and Interbacterial Dialogues: Two Sides of the Same Coin. J Immunol Res 2022; 2022:8092170. [PMID: 35224113 PMCID: PMC8872691 DOI: 10.1155/2022/8092170] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 01/17/2022] [Accepted: 02/01/2022] [Indexed: 12/11/2022] Open
Abstract
Extracellular vesicles (EVs) cause effective changes in various domains of life. These bioactive structures are essential to the bidirectional organ communication. Recently, increasing research attention has been paid to EVs derived from commensal and pathogenic bacteria in their potential role to affect human disease risk for cancers and a variety of metabolic, gastrointestinal, psychiatric, and mental disorders. The present review presents an overview of both the protective and harmful roles of commensal and pathogenic bacteria-derived EVs in host-bacterial and interbacterial interactions. Bacterial EVs could impact upon human health by regulating microbiota–host crosstalk intestinal homeostasis, even in distal organs. The importance of vesicles derived from bacteria has been also evaluated regarding epigenetic modifications and applications. Generally, the evaluation of bacterial EVs is important towards finding efficient strategies for the prevention and treatment of various human diseases and maintaining metabolic homeostasis.
Collapse
|
56
|
Vandermaesen J, Du S, Daly AJ, Baetens JM, Horemans B, De Baets B, Boon N, Springael D. Interspecies Interactions of the 2,6-Dichlorobenzamide Degrading Aminobacter sp. MSH1 with Resident Sand Filter Bacteria: Indications for Mutual Cooperative Interactions That Improve BAM Mineralization Activity. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:1352-1364. [PMID: 34982540 DOI: 10.1021/acs.est.1c06653] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Bioaugmentation often involves an invasion process requiring the establishment and activity of a foreign microbe in the resident community of the target environment. Interactions with resident micro-organisms, either antagonistic or cooperative, are believed to impact invasion. However, few studies have examined the variability of interactions between an invader and resident species of its target environment, and none of them considered a bioremediation context. Aminobacter sp. MSH1 mineralizing the groundwater micropollutant 2,6-dichlorobenzamide (BAM), is proposed for bioaugmentation of sand filters used in drinking water production to avert BAM contamination. We examined the nature of the interactions between MSH1 and 13 sand filter resident bacteria in dual and triple species assemblies in sand microcosms. The residents affected MSH1-mediated BAM mineralization without always impacting MSH1 cell densities, indicating effects on cell physiology rather than on cell number. Exploitative competition explained most of the effects (70%), but indications of interference competition were also found. Two residents improved BAM mineralization in dual species assemblies, apparently in a mutual cooperation, and overruled negative effects by others in triple species systems. The results suggest that sand filter communities contain species that increase MSH1 fitness. This opens doors for assisting bioaugmentation through co-inoculation with "helper" bacteria originating from and adapted to the target environment.
Collapse
Affiliation(s)
- Johanna Vandermaesen
- Division of Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20 Bus 2459, B-3001 Heverlee, Belgium
| | - Siyao Du
- Division of Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20 Bus 2459, B-3001 Heverlee, Belgium
| | - Aisling J Daly
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Jan M Baetens
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Benjamin Horemans
- Division of Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20 Bus 2459, B-3001 Heverlee, Belgium
| | - Bernard De Baets
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Dirk Springael
- Division of Soil and Water Management, KU Leuven, Kasteelpark Arenberg 20 Bus 2459, B-3001 Heverlee, Belgium
| |
Collapse
|
57
|
Brady C, Orsi M, Doonan JM, Denman S, Arnold D. Brenneria goodwinii growth in vitro is improved by competitive interactions with other bacterial species associated with Acute Oak Decline. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100102. [PMID: 35005660 PMCID: PMC8717232 DOI: 10.1016/j.crmicr.2021.100102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Mutually competitive interactions prevail in pairwise cultures of AOD bacteria. In vitro growth of brenneria goodwinii is improved by bacterial competition. Co-culturing of AOD bacteria indicates evolving improved fitness of B. goodwinii. B. goodwinii and R. victoriana can collaborate in vitro to outcompete G. quercinecans.
Brenneria goodwinii, Rahnella victoriana and Gibbsiella quercinecans are three bacterial species frequently isolated together from oak displaying symptoms of Acute Oak Decline (AOD), which include weeping patches on trunks. All three bacterial species play a role in lesion formation in the current episode of AOD in Britain, although B. goodwinii is the most dominant. The ongoing research into stem lesion formation characteristic of this polybacterial syndrome has been focussed primarily on the pathogenicity, identification and taxonomy of these bacteria. As all three species were newly classified within the past ten years, there are many unanswered questions regarding their ecology and interactions with each other. To determine the effect of bacterial interactions on fitness in vitro, we examined pairwise (diculture) and multispecies (triculture) interactions between B. goodwinii, R. victoriana and G. quercinecans in oak leaf media microcosms. Additionally, the effect of co-culturing on the evolution of these species was determined and the evolved B. goodwinii strains were examined further by whole genome sequencing. Our results indicate that B. goodwinii thrived in monoculture with significantly higher viable cell counts than the other two species. Additionally, B. goodwinii performed well in pairwise culture with mutually competitive interactions observed between B. goodwinii and R. victoriana, and between B. goodwinii and G. quercinecans. In the multispecies triculture, B. goodwinii and R. victoriana appeared to exhibit co-ordinated behaviour to outcompete G. quercinecans. After four weeks B. goodwinii grown in co-culture with the other two species developed greater evolved fitness than the strain grown in monoculture as reflected by the increased viable cell counts. The competitive interactions taking place between the threes species indicated evolving improved fitness of B. goodwinii in vitro, that gave it a growth advantage over both R. victoriana and G. quercinecans which showed no significant changes in fitness. Overall, B. goodwinii gains greater benefit in terms of fitness from in vitro competitive interaction with the other two species.
Collapse
Affiliation(s)
- Carrie Brady
- Centre for Research in Bioscience, Faculty of Health and Life Sciences, University of the West of England, Coldharbour Lane, Bristol BS16 1QY, United Kingdom
| | - Mario Orsi
- Centre for Research in Bioscience, Faculty of Health and Life Sciences, University of the West of England, Coldharbour Lane, Bristol BS16 1QY, United Kingdom
| | - James M Doonan
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958 Frederiksberg C, Denmark
| | - Sandra Denman
- Centre for Forestry and Climate Change, Farnham, United Kingdom
| | - Dawn Arnold
- Centre for Research in Bioscience, Faculty of Health and Life Sciences, University of the West of England, Coldharbour Lane, Bristol BS16 1QY, United Kingdom.,Harper Adams University, Newport, Shropshire TF10 8NB, United Kingdom
| |
Collapse
|
58
|
Spatial persistence of Escherichia coli O157:H7 flowing on micropatterned structures inspired by stomata and microgrooves of leafy greens. INNOV FOOD SCI EMERG 2022. [DOI: 10.1016/j.ifset.2021.102889] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
59
|
Singh R, Dutta A, Bose T, Mande SS. A compendium of predicted growths and derived symbiotic relationships between 803 gut microbes in 13 different diets. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100127. [PMID: 35909605 PMCID: PMC9325735 DOI: 10.1016/j.crmicr.2022.100127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 03/11/2022] [Accepted: 03/20/2022] [Indexed: 11/30/2022] Open
Abstract
Simulated growth of 803 gut microbes in mono- and co-cultures in 13 distinct diets. Inferred symbiotic relationships and metabolic co-operation among gut microbes. Diet-based variations in metabolic co-operation among gut microbes. Validation of in silico findings against existing literature evidence.
Gut health is intimately linked to dietary habits and the microbial community (microbiota) that flourishes within. The delicate dependency of the latter on nutritional availability is also strongly influenced by interactions (such as, parasitic or mutualistic) between the resident microbes, often affecting their growth rate and ability to produce key metabolites. Since, cultivating the entire repertoire of gut microbes is a challenging task, metabolic models (genome-based metabolic reconstructions) could be employed to predict their growth patterns and interactions. Here, we have used 803 gut microbial metabolic models from the Virtual Metabolic Human repository, and subsequently optimized and simulated them to grow on 13 dietary compositions. The presented pairwise interaction data (https://osf.io/ay8bq/) and the associated bacterial growth rates are expected to be useful for (a) deducing microbial association patterns, (b) diet-based inference of personalised gut profiles, and (c) as a steppingstone for studying multi-species metabolic interactions.
Collapse
|
60
|
Rahimi-Midani A, Lee SW, Choi TJ. Potential Solutions Using Bacteriophages against Antimicrobial Resistant Bacteria. Antibiotics (Basel) 2021; 10:antibiotics10121496. [PMID: 34943708 PMCID: PMC8698741 DOI: 10.3390/antibiotics10121496] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 01/01/2023] Open
Abstract
Bacteriophages are viruses that specifically infect a bacterial host. They play a great role in the modern biotechnology and antibiotic-resistant microbe era. Since the discovery of phages, their application as a control agent has faced challenges that made antibiotics a better fit for combating pathogenic bacteria. Recently, with the novel sequencing technologies providing new insight into the nature of bacteriophages, their application has a second chance to be used. However, novel challenges need to be addressed to provide proper strategies for their practical application. This review focuses on addressing these challenges by initially introducing the nature of bacteriophages and describing the phage-host-dependent strategies for phage application. We also describe the effect of the long-term application of phages in natural environments and other bacterial communities. Overall, this review gathered crucial information for the future application of phages. We predict the use of phages will not be the only control strategy against pathogenic bacteria. Therefore, more studies must be done for low-risk control methods against antimicrobial-resistant bacteria.
Collapse
Affiliation(s)
- Aryan Rahimi-Midani
- Department of Applied Bioscience, Dong-A University, Busan 49315, Korea; (A.R.-M.); (S.-W.L.)
- Department of Microbiology, Pukyong National University, Busan 48513, Korea
| | - Seon-Woo Lee
- Department of Applied Bioscience, Dong-A University, Busan 49315, Korea; (A.R.-M.); (S.-W.L.)
| | - Tae-Jin Choi
- Department of Microbiology, Pukyong National University, Busan 48513, Korea
- Correspondence:
| |
Collapse
|
61
|
Hajipour MJ, Saei AA, Walker ED, Conley B, Omidi Y, Lee K, Mahmoudi M. Nanotechnology for Targeted Detection and Removal of Bacteria: Opportunities and Challenges. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2100556. [PMID: 34558234 PMCID: PMC8564466 DOI: 10.1002/advs.202100556] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 08/06/2021] [Indexed: 05/04/2023]
Abstract
The emergence of nanotechnology has created unprecedented hopes for addressing several unmet industrial and clinical issues, including the growing threat so-termed "antibiotic resistance" in medicine. Over the last decade, nanotechnologies have demonstrated promising applications in the identification, discrimination, and removal of a wide range of pathogens. Here, recent insights into the field of bacterial nanotechnology are examined that can substantially improve the fundamental understanding of nanoparticle and bacteria interactions. A wide range of developed nanotechnology-based approaches for bacterial detection and removal together with biofilm eradication are summarized. The challenging effects of nanotechnologies on beneficial bacteria in the human body and environment and the mechanisms of bacterial resistance to nanotherapeutics are also reviewed.
Collapse
Affiliation(s)
- Mohammad J. Hajipour
- Department of Radiology and Precision Health ProgramMichigan State UniversityEast LansingMI48824USA
| | - Amir Ata Saei
- Division of Physiological Chemistry IDepartment of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholm171 65Sweden
| | - Edward D. Walker
- Department of EntomologyMichigan State UniversityEast LansingMI48824USA
- Department of Microbiology and Molecular GeneticsMichigan State UniversityEast LansingMI48824USA
| | - Brian Conley
- Department of Chemistry and Chemical BiologyRutgersThe State University of New JerseyPiscatawayNJ08854USA
| | - Yadollah Omidi
- Department of Pharmaceutical SciencesCollege of PharmacyNova Southeastern UniversityFort LauderdaleFL33328USA
| | - Ki‐Bum Lee
- Department of Chemistry and Chemical BiologyRutgersThe State University of New JerseyPiscatawayNJ08854USA
| | - Morteza Mahmoudi
- Department of Radiology and Precision Health ProgramMichigan State UniversityEast LansingMI48824USA
| |
Collapse
|
62
|
Biogeography of Bacterial Communities and Specialized Metabolism in Human Aerodigestive Tract Microbiomes. Microbiol Spectr 2021; 9:e0166921. [PMID: 34704787 PMCID: PMC8549736 DOI: 10.1128/spectrum.01669-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The aerodigestive tract (ADT) is the primary portal through which pathogens and other invading microbes enter the body. As the direct interface with the environment, we hypothesize that the ADT microbiota possess biosynthetic gene clusters (BGCs) for antibiotics and other specialized metabolites to compete with both endogenous and exogenous microbes. From 1,214 bacterial genomes, representing 136 genera and 387 species that colonize the ADT, we identified 3,895 BGCs. To determine the distribution of BGCs and bacteria in different ADT sites, we aligned 1,424 metagenomes, from nine different ADT sites, onto the predicted BGCs. We show that alpha diversity varies across the ADT and that each site is associated with distinct bacterial communities and BGCs. We identify specific BGC families enriched in the buccal mucosa, external naris, gingiva, and tongue dorsum despite these sites harboring closely related bacteria. We reveal BGC enrichment patterns indicative of the ecology at each site. For instance, aryl polyene and resorcinol BGCs are enriched in the gingiva and tongue, which are colonized by many anaerobes. In addition, we find that streptococci colonizing the tongue and cheek possess different ribosomally synthesized and posttranslationally modified peptide BGCs. Finally, we highlight bacterial genera with BGCs but are underexplored for specialized metabolism and demonstrate the bioactivity of Actinomyces against other bacteria, including human pathogens. Together, our results demonstrate that specialized metabolism in the ADT is extensive and that by exploring these microbiomes further, we will better understand the ecology and biogeography of this system and identify new bioactive natural products. IMPORTANCE Bacteria produce specialized metabolites to compete with other microbes. Though the biological activities of many specialized metabolites have been determined, our understanding of their ecology is limited, particularly within the human microbiome. As the aerodigestive tract (ADT) faces the external environment, bacteria colonizing this tract must compete both among themselves and with invading microbes, including human pathogens. We analyzed the genomes of ADT bacteria to identify biosynthetic gene clusters (BGCs) for specialized metabolites. We found that the majority of ADT BGCs are uncharacterized and the metabolites they encode are unknown. We mapped the distribution of BGCs across the ADT and determined that each site is associated with its own distinct bacterial community and BGCs. By further characterizing these BGCs, we will inform our understanding of ecology and biogeography across the ADT, and we may uncover new specialized metabolites, including antibiotics.
Collapse
|
63
|
Li S, Dong L, Lian WH, Lin ZL, Lu CY, Xu L, Li L, Hozzein WN, Li WJ. Exploring untapped potential of Streptomyces spp. in Gurbantunggut Desert by use of highly selective culture strategy. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 790:148235. [PMID: 34380255 DOI: 10.1016/j.scitotenv.2021.148235] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/28/2021] [Accepted: 05/28/2021] [Indexed: 06/13/2023]
Abstract
Streptomycetes have been, for over 70 years, one of the most abundant sources for the discovery of new antibiotics and clinic drugs. However, in recent decades, it has been more and more difficult to obtain new phylotypes of the genus Streptomyces by using conventional samples and culture strategies. In this study, we combined culture-dependent and culture-independent approaches to better explore the Streptomyces communities in desert sandy soils. Moreover, two different culture strategies termed Conventional Culture Procedure (CCP) and Streptomycetes Culture Procedure (SCP) were employed to evaluate the isolation efficiency of Streptomyces spp. with different intensities of selectivity. The 16S rRNA gene amplicon analysis revealed a very low abundance (0.04-0.37%, average 0.22%) of Streptomyces in all the desert samples, conversely the percentage of Streptomyces spp. obtained by the culture-dependent method was very high (5.20-39.57%, average 27.76%), especially in the rhizospheric sand soils (38.40-39.57%, average 38.99%). Meanwhile, a total of 1589 pure cultures were isolated successfully, dominated by Streptomyces (29.52%), Microvirga (8.06%) and Bacillus (7.68%). In addition, 400 potential new species were obtained, 48 of which belonged to the genus Streptomyces. More importantly, our study demonstrated the SCP strategy which had highly selectivity could greatly expand the number and phylotypes of Streptomyces spp. by almost 4-fold than CCP strategy. These results provide insights on the diversity investigation of desert Streptomyces, and it could be reference for researchers to bring more novel actinobacteria strains from the environment into culture.
Collapse
Affiliation(s)
- Shuai Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Lei Dong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China.
| | - Wen-Hui Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Zhi-Liang Lin
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Chun-Yan Lu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Lu Xu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Li Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
| | - Wael N Hozzein
- Zoology Department, College of Science, King Saud University, Riyadh 999088, Saudi Arabia; Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni-Suef 62511, Egypt
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China.
| |
Collapse
|
64
|
Lunjani N, Ahearn-Ford S, Dube FS, Hlela C, O'Mahony L. Mechanisms of microbe-immune system dialogue within the skin. Genes Immun 2021; 22:276-288. [PMID: 33993202 PMCID: PMC8497273 DOI: 10.1038/s41435-021-00133-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/09/2021] [Accepted: 04/26/2021] [Indexed: 02/01/2023]
Abstract
The prevalence and severity of dermatological conditions such as atopic dermatitis have increased dramatically during recent decades. Many of the factors associated with an altered risk of developing inflammatory skin disorders have also been shown to alter the composition and diversity of non-pathogenic microbial communities that inhabit the human host. While the most densely microbial populated organ is the gut, culture and non-culture-based technologies have revealed a dynamic community of bacteria, fungi, viruses and mites that exist on healthy human skin, which change during disease. In this review, we highlight some of the recent findings on the mechanisms through which microbes interact with each other on the skin and the signalling systems that mediate communication between the immune system and skin-associated microbes. In addition, we summarize the ongoing clinical studies that are targeting the microbiome in patients with skin disorders. While significant efforts are still required to decipher the mechanisms underpinning host-microbe communication relevant to skin health, it is likely that disease-related microbial communities, or Dermatypes, will help identify personalized treatments and appropriate microbial reconstitution strategies.
Collapse
Affiliation(s)
- Nonhlanhla Lunjani
- Department of Dermatology, University of Cape Town, Cape Town, South Africa
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | - Felix S Dube
- Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease & Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Carol Hlela
- Department of Dermatology, University of Cape Town, Cape Town, South Africa
| | - Liam O'Mahony
- APC Microbiome Ireland, University College Cork, Cork, Ireland.
- Department of Medicine, University College Cork, Cork, Ireland.
- School of Microbiology, University College Cork, Cork, Ireland.
| |
Collapse
|
65
|
Abstract
Microorganisms live in dense and diverse communities, with interactions between cells guiding community development and phenotype. The ability to perturb specific intercellular interactions in space and time provides a powerful route to determining the critical interactions and design rules for microbial communities. Approaches using optogenetic tools to modulate these interactions offer promise, as light can be exquisitely controlled in space and time. We report new plasmids for rapid integration of an optogenetic system into Saccharomyces cerevisiae to engineer light control of expression of a gene of interest. In a proof-of-principle study, we demonstrate the ability to control a model cooperative interaction, namely, the expression of the enzyme invertase (SUC2) which allows S. cerevisiae to hydrolyze sucrose and utilize it as a carbon source. We demonstrate that the strength of this cooperative interaction can be tuned in space and time by modulating light intensity and through spatial control of illumination. Spatial control of light allows cooperators and cheaters to be spatially segregated, and we show that the interplay between cooperative and inhibitory interactions in space can lead to pattern formation. Our strategy can be applied to achieve spatiotemporal control of expression of a gene of interest in S. cerevisiae to perturb both intercellular and interspecies interactions. IMPORTANCE Recent advances in microbial ecology have highlighted the importance of intercellular interactions in controlling the development, composition, and resilience of microbial communities. In order to better understand the role of these interactions in governing community development, it is critical to be able to alter them in a controlled manner. Optogenetically controlled interactions offer advantages over static perturbations or chemically controlled interactions, as light can be manipulated in space and time and does not require the addition of nutrients or antibiotics. Here, we report a system for rapidly achieving light control of a gene of interest in the important model organism Saccharomyces cerevisiae and demonstrate that by controlling expression of the enzyme invertase, we can control cooperative interactions. This approach will be useful for understanding intercellular and interspecies interactions in natural and synthetic microbial consortia containing S. cerevisiae and serves as a proof of principle for implementing this approach in other consortia.
Collapse
|
66
|
Sadeghi J, Chaganti SR, Shahraki AH, Heath DD. Microbial community and abiotic effects on aquatic bacterial communities in north temperate lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 781:146771. [PMID: 33812116 DOI: 10.1016/j.scitotenv.2021.146771] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 03/11/2021] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
The aquatic bacterial community (BC) plays a vital role in determining the nature and rate of ecosystem function. However, the biotic and abiotic factors influencing BC structure and function are largely unknown. Hence, the current study characterizes the impact of biotic and abiotic factors on aquatic bacterial biodiversity to determine whether the dominant effects are biotic or abiotic by partitioning their relative effects across temperate Canadian lakes. We collected water samples from sixty southern Ontario lakes and characterized their BC and microbial eukaryotic community (MEC) compositions using high throughput metabarcode sequencing of 16S and 18S rRNA gene fragments. The diversity and richness of aquatic BCs differed considerably among our study lakes, and those differences were explained by environmental, spatial, and biotic (MEC) factors (31%, 23%, and 23% of variance explained, respectively). The relatively large contribution from biotic and abiotic factors (54%), relative to spatial effects, shows deterministic processes prevail in shaping BC assembly in freshwater lakes. However, spatial effects also contributed significantly, highlighting the role of stochastic processes (ecological drift and coupled with limited dispersal) in shaping BC structure. Furthermore, our co-occurrence network analysis showed strong positive and negative interactions within and between the BCs and MECs, indicating mutualistic or antagonistic co-occurrence patterns relationships play important roles in driving the variation in BC composition among our sampled lakes. Considered together, our community analyses show that deterministic and stochastic processes combined contribute to determining the aquatic BC composition, and hence likely function as well, across a broad array of temperate freshwater lakes.
Collapse
Affiliation(s)
- Javad Sadeghi
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Canada
| | - Subba Rao Chaganti
- Cooperative Institute for Great Lakes Research, SEAS, University of Michigan, Ann Arbor, MI, USA.
| | | | - Daniel D Heath
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Canada; Department of Integrative Biology, University of Windsor, Windsor, ON, Canada.
| |
Collapse
|
67
|
Kern L, Abdeen SK, Kolodziejczyk AA, Elinav E. Commensal inter-bacterial interactions shaping the microbiota. Curr Opin Microbiol 2021; 63:158-171. [PMID: 34365152 DOI: 10.1016/j.mib.2021.07.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 12/14/2022]
Abstract
The gut microbiota, a complex ecosystem of microorganisms of different kingdoms, impacts host physiology and disease. Within this ecosystem, inter-bacterial interactions and their impacts on microbiota community structure and the eukaryotic host remain insufficiently explored. Microbiota-related inter-bacterial interactions range from symbiotic interactions, involving exchange of nutrients, enzymes, and genetic material; competition for nutrients and space, mediated by biophysical alterations and secretion of toxins and anti-microbials; to predation of overpopulating bacteria. Collectively, these understudied interactions hold important clues as to forces shaping microbiota diversity, niche formation, and responses to signals perceived from the host, incoming pathogens and the environment. In this review, we highlight the roles and mechanisms of selected inter-bacterial interactions in the microbiota, and their potential impacts on the host and pathogenic infection. We discuss challenges in mechanistically decoding these complex interactions, and prospects of harnessing them as future targets for rational microbiota modification in a variety of diseases.
Collapse
Affiliation(s)
- Lara Kern
- Immunology Department, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Suhaib K Abdeen
- Immunology Department, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | | | - Eran Elinav
- Immunology Department, Weizmann Institute of Science, Rehovot, 7610001, Israel; Cancer-Microbiota Division Deutsches Krebsforschungszentrum (DKFZ), Neuenheimer Feld 280, 69120 Heidelberg, Germany.
| |
Collapse
|
68
|
Tovi N, Orevi T, Grinberg M, Kashtan N, Hadar Y, Minz D. Pairwise Interactions of Three Related Pseudomonas Species in Plant Roots and Inert Surfaces. Front Microbiol 2021; 12:666522. [PMID: 34335497 PMCID: PMC8320352 DOI: 10.3389/fmicb.2021.666522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 06/07/2021] [Indexed: 11/13/2022] Open
Abstract
Bacteria are social organisms that interact extensively within and between species while responding to external stimuli from their environments. Designing synthetic microbial communities can enable efficient and beneficial microbiome implementation in many areas. However, in order to design an efficient community, one must consider the interactions between their members. Using a reductionist approach, we examined pairwise interactions of three related Pseudomonas species in various microenvironments including plant roots and inert surfaces. Our results show that the step between monoculture and co-culture is already very complex. Monoculture root colonization patterns demonstrate that each isolate occupied a particular location on wheat roots, such as root tip, distance from the tip, or scattered along the root. However, pairwise colonization outcomes on the root did not follow the bacterial behavior in monoculture, suggesting various interaction patterns. In addition, we show that interspecies interactions on a microscale on inert surface take part in co-culture colonization and that the interactions are affected by the presence of root extracts and depend on its source. The understanding of interrelationships on the root may contribute to future attempts to manipulate and improve bacterial colonization and to intervene with root microbiomes to construct and design effective synthetic microbial consortia.
Collapse
Affiliation(s)
- Nesli Tovi
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization - Volcani Center, Rishon LeZion, Israel.,Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Tomer Orevi
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Maor Grinberg
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Nadav Kashtan
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Yitzhak Hadar
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Dror Minz
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization - Volcani Center, Rishon LeZion, Israel
| |
Collapse
|
69
|
Jurėnas D, Payelleville A, Roghanian M, Turnbull KJ, Givaudan A, Brillard J, Hauryliuk V, Cascales E. Photorhabdus antibacterial Rhs polymorphic toxin inhibits translation through ADP-ribosylation of 23S ribosomal RNA. Nucleic Acids Res 2021; 49:8384-8395. [PMID: 34255843 PMCID: PMC8661411 DOI: 10.1093/nar/gkab608] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/10/2021] [Accepted: 07/01/2021] [Indexed: 11/18/2022] Open
Abstract
Bacteria have evolved sophisticated mechanisms to deliver potent toxins into bacterial competitors or into eukaryotic cells in order to destroy rivals and gain access to a specific niche or to hijack essential metabolic or signaling pathways in the host. Delivered effectors carry various activities such as nucleases, phospholipases, peptidoglycan hydrolases, enzymes that deplete the pools of NADH or ATP, compromise the cell division machinery, or the host cell cytoskeleton. Effectors categorized in the family of polymorphic toxins have a modular structure, in which the toxin domain is fused to additional elements acting as cargo to adapt the effector to a specific secretion machinery. Here we show that Photorhabdus laumondii, an entomopathogen species, delivers a polymorphic antibacterial toxin via a type VI secretion system. This toxin inhibits protein synthesis in a NAD+-dependent manner. Using a biotinylated derivative of NAD, we demonstrate that translation is inhibited through ADP-ribosylation of the ribosomal 23S RNA. Mapping of the modification further showed that the adduct locates on helix 44 of the thiostrepton loop located in the GTPase-associated center and decreases the GTPase activity of the EF-G elongation factor.
Collapse
Affiliation(s)
- Dukas Jurėnas
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - CNRS, UMR 7255, Marseille, France
| | - Amaury Payelleville
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - CNRS, UMR 7255, Marseille, France.,DGIMI, Univ Montpellier, INRAE, Montpellier, France
| | - Mohammad Roghanian
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden, Umeå University, 901 87 Umeå, Sweden
| | | | | | | | - Vasili Hauryliuk
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden, Umeå University, 901 87 Umeå, Sweden.,Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden.,University of Tartu, Institute of Technology, 50411 Tartu, Estonia
| | - Eric Cascales
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - CNRS, UMR 7255, Marseille, France
| |
Collapse
|
70
|
Microbiological Monitoring of the Environment Using the "Association Rules" Approach and Disinfection Procedure Evaluation in a Hospital Center in Morocco. JOURNAL OF ENVIRONMENTAL AND PUBLIC HEALTH 2021; 2021:7682042. [PMID: 34285698 PMCID: PMC8275422 DOI: 10.1155/2021/7682042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/12/2021] [Accepted: 06/23/2021] [Indexed: 11/18/2022]
Abstract
Background The hospital environment, especially surfaces and medical devices, is a source of contamination for patients. Objective This study carried out, to the best of our knowledge, for the first time at Taza Hospital in Morocco aimed to assess the microbiological quality of surfaces and medical devices in surgical departments and to evaluate the disinfection procedure in time and space. Methods Samples were taken by swabbing after cleaning the hospital surface or medical device, to isolate and identify germs which were inoculated on semiselective culture media then identified by standard biochemical and physiological tests, using the analytical profile index (API) galleries. Moreover, the association rules extraction model between sites on the one hand and germs on the other hand was used for sampling. Results The study showed that 83% of the samples have been contaminated after biocleaning. The most contaminated services have been men's and women's surgeries. 62% of isolated germs have been identified as Gram-positive bacteria, 29% as Gram-negative bacteria, and 9% as fungi. Concerning the association rules extraction model, a strong association between some contaminated sites and the presence of germ has been found, such as the association between wall and nightstand and door cuff, meaning that the wall and nightstand contamination is systematically linked to that of the door cuff. The disinfection procedure efficacy evaluation has enabled suggesting renewing it each 4 h. Conclusion Microbiological monitoring of surfaces is necessary at hospital level through the use of the association rule extraction model, which is very important to optimize the sampling, cleaning, and disinfection site scenarios of the most contaminated ones.
Collapse
|
71
|
Wai Chun CN, Tajarudin HA, Ismail N, Azahari B, Mohd Zaini Makhtar M. Elucidation of Mechanical, Physical, Chemical and Thermal Properties of Microbial Composite Films by Integrating Sodium Alginate with Bacillus subtilis sp. Polymers (Basel) 2021; 13:polym13132103. [PMID: 34206741 PMCID: PMC8271853 DOI: 10.3390/polym13132103] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 05/28/2021] [Accepted: 05/28/2021] [Indexed: 11/30/2022] Open
Abstract
Materials are the foundation in human development for improving human standards of life. This research aimed to develop microbial composite films by integrating sodium alginate with Bacillus subtilis. Sodium alginate film was fabricated as control. The microbial composite films were fabricated by integrating 0.1, 0.2, 0.3, 0.4, 0.5 and 0.6 g of Bacillus subtilis into the sodium alginate. Evaluations were performed on the mechanical, physical, chemical and thermal properties of the films. It was found that films reinforced with Bacillus subtilis significantly improved all the mentioned properties. Results show that 0.5 g microbial composite films had the highest tensile strength, breaking strain and toughness, which were 0.858 MPa, 87.406% and 0.045 MJ/m3, respectively. The thickness of the film was 1.057 mm. White light opacity, black light opacity and brightness values were 13.65%, 40.55% and 8.19%, respectively. It also had the highest conductivity, which was 37 mV, while its water absorption ability was 300.93%. Furthermore, it had a higher melting point of 218.94 °C and higher decomposition temperature of 252.69 °C. SEM also showed that it had filled cross-sectional structure and smoother surface compared to the sodium alginate film. Additionally, FTIR showed that 0.5 g microbial composite films possessed more functional groups at 800 and 662 cm−1 wavenumbers that referred to C–C, C–OH, C–H ring and side group vibrations and C–OH out-of-plane bending, respectively, which contributed to the stronger bonds in the microbial composite film. Initial conclusions depict the potential of Bacillus subtilis to be used as reinforcing material in the development of microbial composite films, which also have the prospect to be used in electronic applications. This is due to the conductivity of the films increasing as Bacillus subtilis cell mass increases.
Collapse
Affiliation(s)
- Charles Ng Wai Chun
- School of Industrial Technology, Bioprocess Technology Division, Universiti Sains Malaysia, Penang 11800, Malaysia; (C.N.W.C.); (M.M.Z.M.)
| | - Husnul Azan Tajarudin
- School of Industrial Technology, Bioprocess Technology Division, Universiti Sains Malaysia, Penang 11800, Malaysia; (C.N.W.C.); (M.M.Z.M.)
- Correspondence: (H.A.T.); (N.I.)
| | - Norli Ismail
- School of Industrial Technology, Environmental Division, Universiti Sains Malaysia, Penang 11800, Malaysia
- Correspondence: (H.A.T.); (N.I.)
| | - Baharin Azahari
- School of Industrial Technology, Bioresource, Paper and Coatings Division, Universiti Sains Malaysia, Penang11800, Malaysia;
| | - Muaz Mohd Zaini Makhtar
- School of Industrial Technology, Bioprocess Technology Division, Universiti Sains Malaysia, Penang 11800, Malaysia; (C.N.W.C.); (M.M.Z.M.)
| |
Collapse
|
72
|
Stavrou C, Veraitch O, Morris-Jones S, Walker SL. Leg ulceration due to cutaneous melioidosis in a returning traveller. BMJ Case Rep 2021; 14:e241490. [PMID: 34127500 PMCID: PMC8204165 DOI: 10.1136/bcr-2020-241490] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/01/2021] [Indexed: 12/04/2022] Open
Abstract
A 26-year-old man, returned to the UK having travelled extensively in Asia. He was referred with a 3-month history of distal leg ulceration following an insect bite while in Thailand. Despite multiple courses of oral antibiotics, he developed two adjacent ulcers. A wound swab isolated an organism identified as Burkholderia thailandensis The histology of the skin biopsy was non-specific. A diagnosis of cutaneous melioidosis was made, based on clinical and microbiological grounds. The ulcers re-epithelialised on completion of intravenous ceftazidime followed by 3 months of high dose co-trimoxazole and wound care. Many clinical microbiology laboratories have limited diagnostics for security-related organisms, with the result that B. pseudomallei, the causative bacterium of melioidosis, may be misidentified. This case highlights the importance of maintaining high levels of clinical suspicion and close microbiological liaison in individuals returning from South-East Asia and northern Australia with such symptoms.
Collapse
Affiliation(s)
- Christiana Stavrou
- Department of Dermatology, University College London Hospitals NHS Foundation Trust, London, UK
| | - Ophelia Veraitch
- Department of Dermatology, University College London Hospitals NHS Foundation Trust, London, UK
| | - Stephen Morris-Jones
- Clinical Microbiology, University College London Hospitals NHS Foundation Trust, London, UK
| | - Stephen L Walker
- Hospital for Tropical Diseases and Department of Dermatology, University College London Hospitals NHS Foundation Trust, London, UK
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Department of Clinical Research, London, UK
| |
Collapse
|
73
|
Ceballos-González CF, Bolívar-Monsalve EJ, Quevedo-Moreno DA, Lam-Aguilar LL, Borrayo-Montaño KI, Yee-de León JF, Zhang YS, Alvarez MM, Trujillo-de Santiago G. High-Throughput and Continuous Chaotic Bioprinting of Spatially Controlled Bacterial Microcosms. ACS Biomater Sci Eng 2021; 7:2408-2419. [PMID: 33979127 DOI: 10.1021/acsbiomaterials.0c01646] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Microorganisms do not work alone but instead function as collaborative microsocieties. The spatial distribution of different bacterial strains (micro-biogeography) in a shared volumetric space and their degree of intimacy greatly influences their societal behavior. Current microbiological techniques are commonly focused on the culture of well-mixed bacterial communities and fail to reproduce the micro-biogeography of polybacterial societies. Here, we bioprinted fine-scale bacterial microcosms using chaotic flows induced by a printhead containing a static mixer. This straightforward approach (i.e., continuous chaotic bacterial bioprinting) enables the fabrication of hydrogel constructs with intercalated layers of bacterial strains. These multilayered constructs are used to analyze how the spatial distributions of bacteria affect their social behavior. For example, we show that bacteria within these biological microsystems engage in either cooperation or competition, depending on the degree of shared interface. The extent of inhibition in predator-prey scenarios (i.e., probiotic-pathogen bacteria) increases when bacteria are in greater intimacy. Furthermore, two Escherichia coli strains exhibit competitive behavior in well-mixed microenvironments, whereas stable coexistence prevails for longer times in spatially structured communities. We anticipate that chaotic bioprinting will contribute to the development of a greater complexity of polybacterial microsystems, tissue-microbiota models, and biomanufactured materials.
Collapse
Affiliation(s)
| | | | - Diego Alonso Quevedo-Moreno
- Departamento de Ingeniería Mecatrónica y Eléctrica, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo Leon 64849, México
| | - Li Lu Lam-Aguilar
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey, Nuevo Leon 64849, México
| | | | | | - Yu Shrike Zhang
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge 02139, Massachusetts United States
| | - Mario Moisés Alvarez
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey, Nuevo Leon 64849, México.,Departamento de Bioingeniería, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo Leon 64849, México
| | - Grissel Trujillo-de Santiago
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey, Nuevo Leon 64849, México.,Departamento de Ingeniería Mecatrónica y Eléctrica, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey, Nuevo Leon 64849, México
| |
Collapse
|
74
|
Puschhof J, Pleguezuelos-Manzano C, Clevers H. Organoids and organs-on-chips: Insights into human gut-microbe interactions. Cell Host Microbe 2021; 29:867-878. [PMID: 34111395 DOI: 10.1016/j.chom.2021.04.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/04/2021] [Accepted: 04/05/2021] [Indexed: 12/22/2022]
Abstract
The important and diverse roles of the gut microbiota in human health and disease are increasingly recognized. The difficulty of inferring causation from metagenomic microbiome sequencing studies and from mouse-human interspecies differences has prompted the development of sophisticated in vitro models of human gut-microbe interactions. Here, we review recent advances in the co-culture of microbes with intestinal and colonic epithelia, comparing the rapidly developing fields of organoids and organs-on-chips with other standard models. We describe how specific individual processes by which microbes and epithelia interact can be recapitulated in vitro. Using examples of bacterial, viral, and parasitic infections, we highlight the advantages of each culture model and discuss current trends and future possibilities to build more complex co-cultures.
Collapse
Affiliation(s)
- Jens Puschhof
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Cayetano Pleguezuelos-Manzano
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands; The Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.
| |
Collapse
|
75
|
Ñahui Palomino RA, Vanpouille C, Costantini PE, Margolis L. Microbiota-host communications: Bacterial extracellular vesicles as a common language. PLoS Pathog 2021; 17:e1009508. [PMID: 33984071 PMCID: PMC8118305 DOI: 10.1371/journal.ppat.1009508] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Both gram-negative and gram-positive bacteria release extracellular vesicles (EVs) that contain components from their mother cells. Bacterial EVs are similar in size to mammalian-derived EVs and are thought to mediate bacteria–host communications by transporting diverse bioactive molecules including proteins, nucleic acids, lipids, and metabolites. Bacterial EVs have been implicated in bacteria–bacteria and bacteria–host interactions, promoting health or causing various pathologies. Although the science of bacterial EVs is less developed than that of eukaryotic EVs, the number of studies on bacterial EVs is continuously increasing. This review highlights the current state of knowledge in the rapidly evolving field of bacterial EV science, focusing on their discovery, isolation, biogenesis, and more specifically on their role in microbiota–host communications. Knowledge of these mechanisms may be translated into new therapeutics and diagnostics based on bacterial EVs.
Collapse
Affiliation(s)
- Rogers A. Ñahui Palomino
- Section on Intercellular Interaction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Christophe Vanpouille
- Section on Intercellular Interaction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Paolo E. Costantini
- Section on Intercellular Interaction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Leonid Margolis
- Section on Intercellular Interaction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
| |
Collapse
|
76
|
Saraiva JP, Worrich A, Karakoç C, Kallies R, Chatzinotas A, Centler F, Nunes da Rocha U. Mining Synergistic Microbial Interactions: A Roadmap on How to Integrate Multi-Omics Data. Microorganisms 2021; 9:microorganisms9040840. [PMID: 33920040 PMCID: PMC8070991 DOI: 10.3390/microorganisms9040840] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/13/2021] [Accepted: 04/08/2021] [Indexed: 11/24/2022] Open
Abstract
Mining interspecies interactions remain a challenge due to the complex nature of microbial communities and the need for computational power to handle big data. Our meta-analysis indicates that genetic potential alone does not resolve all issues involving mining of microbial interactions. Nevertheless, it can be used as the starting point to infer synergistic interspecies interactions and to limit the search space (i.e., number of species and metabolic reactions) to a manageable size. A reduced search space decreases the number of additional experiments necessary to validate the inferred putative interactions. As validation experiments, we examine how multi-omics and state of the art imaging techniques may further improve our understanding of species interactions’ role in ecosystem processes. Finally, we analyze pros and cons from the current methods to infer microbial interactions from genetic potential and propose a new theoretical framework based on: (i) genomic information of key members of a community; (ii) information of ecosystem processes involved with a specific hypothesis or research question; (iii) the ability to identify putative species’ contributions to ecosystem processes of interest; and, (iv) validation of putative microbial interactions through integration of other data sources.
Collapse
Affiliation(s)
- Joao Pedro Saraiva
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Anja Worrich
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Canan Karakoç
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Rene Kallies
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, 04103 Leipzig, Germany
| | - Florian Centler
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany; (J.P.S.); (A.W.); (C.K.); (R.K.); (A.C.); (F.C.)
- Correspondence:
| |
Collapse
|
77
|
Bacterial profiling of Haemonchus contortus gut microbiome infecting Dohne Merino sheep in South Africa. Sci Rep 2021; 11:5905. [PMID: 33723324 PMCID: PMC7961046 DOI: 10.1038/s41598-021-85282-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/26/2021] [Indexed: 11/09/2022] Open
Abstract
A metagenomic approach was used to study the gut microbiome of Haemonchus contortus field strains and that of its predilection site, the abomasum of Dohne Merino sheep. The abomasum contents and H. contortus were collected from 10 naturally infected Dohne Merino sheep. The H. contortus specimens were classified and sexually differentiated using morphometric characters and was further confirmed through molecular identification. We investigated differences and similarities between the bacterial composition of the adult male and female H. contortus gut microbiomes, which were both dominated by bacteria from the Escherichia, Shigella, Vibrio and Halomonas genera. Major abundance variations were identified between the shared adult male and female H. contortus microbiomes. The results also revealed that Succiniclasticum, Rikenellaceae RC9 gut group and Candidatus Saccharimonas were the predominant genera in the Dohne Merino abomasum. This study provides insight into the highly diverse bacterial composition of the H. contortus gut microbiome and the Dohne Merino abomasum which needs to be studied further to explore the complex interactions of different gastrointestinal nematode microbiomes with the host.
Collapse
|
78
|
Senne de Oliveira Lino F, Bajic D, Vila JCC, Sánchez A, Sommer MOA. Complex yeast-bacteria interactions affect the yield of industrial ethanol fermentation. Nat Commun 2021; 12:1498. [PMID: 33686084 PMCID: PMC7940389 DOI: 10.1038/s41467-021-21844-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 02/10/2021] [Indexed: 01/31/2023] Open
Abstract
Sugarcane ethanol fermentation represents a simple microbial community dominated by S. cerevisiae and co-occurring bacteria with a clearly defined functionality. In this study, we dissect the microbial interactions in sugarcane ethanol fermentation by combinatorically reconstituting every possible combination of species, comprising approximately 80% of the biodiversity in terms of relative abundance. Functional landscape analysis shows that higher-order interactions counterbalance the negative effect of pairwise interactions on ethanol yield. In addition, we find that Lactobacillus amylovorus improves the yeast growth rate and ethanol yield by cross-feeding acetaldehyde, as shown by flux balance analysis and laboratory experiments. Our results suggest that Lactobacillus amylovorus could be considered a beneficial bacterium with the potential to improve sugarcane ethanol fermentation yields by almost 3%. These data highlight the biotechnological importance of comprehensively studying microbial communities and could be extended to other microbial systems with relevance to human health and the environment.
Collapse
Affiliation(s)
| | - Djordje Bajic
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
| | - Jean Celestin Charles Vila
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
| | - Alvaro Sánchez
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
| | - Morten Otto Alexander Sommer
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
| |
Collapse
|
79
|
Gram-negative bacteria associated with a dominant arboreal ant species outcompete phyllosphere-associated bacteria species in a tropical canopy. Oecologia 2021; 195:959-970. [PMID: 33630170 DOI: 10.1007/s00442-021-04878-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 02/10/2021] [Indexed: 01/05/2023]
Abstract
Ants have efficient and well-studied social immunity mechanisms, which prevent the colony contamination. Little is known about how workers keep their outside territory clear of diseases. We investigated the interactions between Azteca chartifex ants, their associated bacteria and bacteria on the phyllosphere of Byrsonima sericea trees, comparing plants patrolled and not by the ants. The hypothesis is that bacteria associated with the worker's exoskeleton may outcompete the leaf bacteria. Culturable bacteria were isolated from ants, from the main and satellite nests, and from phyllosphere of B. sericea taken from trees that had A. chartifex nests and from trees without nests. The isolates were grouped by Gram guilds and identified at the genus level. There was a higher percentage of Gram-negative isolates in the ants and on the leaves patrolled by them. There was a higher growth rate of ant bacteria from the main nest compared to those found in ants from the satellite nests. The most representative genus among ant isolates was Enterobacter, also found on leaves patrolled by ants. Under favourable in vitro conditions, A. chartifex Gram-negative bacteria outcompete leaf bacteria by overgrowth, showing a greater competition capacity over the Gram-positive bacteria from leaves with no previous interaction with ants in the field. It was demonstrated that ants carry bacteria capable of outcompeting exogenous bacteria associated with their outside territory. The leaf microbiota of a patrolled tree could be shaped by the ant microbiota, suggesting that large ant colonies may have a key role in structuring canopy plant-microbe interactions.
Collapse
|
80
|
Petruschke H, Schori C, Canzler S, Riesbeck S, Poehlein A, Daniel R, Frei D, Segessemann T, Zimmerman J, Marinos G, Kaleta C, Jehmlich N, Ahrens CH, von Bergen M. Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome. MICROBIOME 2021; 9:55. [PMID: 33622394 PMCID: PMC7903761 DOI: 10.1186/s40168-020-00981-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/16/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND The intestinal microbiota plays a crucial role in protecting the host from pathogenic microbes, modulating immunity and regulating metabolic processes. We studied the simplified human intestinal microbiota (SIHUMIx) consisting of eight bacterial species with a particular focus on the discovery of novel small proteins with less than 100 amino acids (= sProteins), some of which may contribute to shape the simplified human intestinal microbiota. Although sProteins carry out a wide range of important functions, they are still often missed in genome annotations, and little is known about their structure and function in individual microbes and especially in microbial communities. RESULTS We created a multi-species integrated proteogenomics search database (iPtgxDB) to enable a comprehensive identification of novel sProteins. Six of the eight SIHUMIx species, for which no complete genomes were available, were sequenced and de novo assembled. Several proteomics approaches including two earlier optimized sProtein enrichment strategies were applied to specifically increase the chances for novel sProtein discovery. The search of tandem mass spectrometry (MS/MS) data against the multi-species iPtgxDB enabled the identification of 31 novel sProteins, of which the expression of 30 was supported by metatranscriptomics data. Using synthetic peptides, we were able to validate the expression of 25 novel sProteins. The comparison of sProtein expression in each single strain versus a multi-species community cultivation showed that six of these sProteins were only identified in the SIHUMIx community indicating a potentially important role of sProteins in the organization of microbial communities. Two of these novel sProteins have a potential antimicrobial function. Metabolic modelling revealed that a third sProtein is located in a genomic region encoding several enzymes relevant for the community metabolism within SIHUMIx. CONCLUSIONS We outline an integrated experimental and bioinformatics workflow for the discovery of novel sProteins in a simplified intestinal model system that can be generically applied to other microbial communities. The further analysis of novel sProteins uniquely expressed in the SIHUMIx multi-species community is expected to enable new insights into the role of sProteins on the functionality of bacterial communities such as those of the human intestinal tract. Video abstract.
Collapse
Affiliation(s)
- Hannes Petruschke
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany
| | - Christian Schori
- Agroscope, Molecular Diagnostics, Genomics & Bioinformatics and SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Sebastian Canzler
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany
| | - Sarah Riesbeck
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany
| | - Anja Poehlein
- Institute of Microbiology and Genetics, Department of Genomic and Applied Microbiology, Georg-August University of Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Institute of Microbiology and Genetics, Department of Genomic and Applied Microbiology, Georg-August University of Göttingen, Göttingen, Germany
| | - Daniel Frei
- Agroscope, Molecular Diagnostics, Genomics & Bioinformatics and SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Tina Segessemann
- Agroscope, Molecular Diagnostics, Genomics & Bioinformatics and SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Johannes Zimmerman
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Georgios Marinos
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany
| | - Christian H Ahrens
- Agroscope, Molecular Diagnostics, Genomics & Bioinformatics and SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland.
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany.
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Leipzig, Germany.
| |
Collapse
|
81
|
Arjes HA, Willis L, Gui H, Xiao Y, Peters J, Gross C, Huang KC. Three-dimensional biofilm colony growth supports a mutualism involving matrix and nutrient sharing. eLife 2021; 10:e64145. [PMID: 33594973 PMCID: PMC7925131 DOI: 10.7554/elife.64145] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 02/15/2021] [Indexed: 12/16/2022] Open
Abstract
Life in a three-dimensional biofilm is typical for many bacteria, yet little is known about how strains interact in this context. Here, we created essential gene CRISPR interference knockdown libraries in biofilm-forming Bacillus subtilis and measured competitive fitness during colony co-culture with wild type. Partial knockdown of some translation-related genes reduced growth rates and led to out-competition. Media composition led some knockdowns to compete differentially as biofilm versus non-biofilm colonies. Cells depleted for the alanine racemase AlrA died in monoculture but survived in a biofilm colony co-culture via nutrient sharing. Rescue was enhanced in biofilm colony co-culture with a matrix-deficient parent due to a mutualism involving nutrient and matrix sharing. We identified several examples of mutualism involving matrix sharing that occurred in three-dimensional biofilm colonies but not when cultured in two dimensions. Thus, growth in a three-dimensional colony can promote genetic diversity through sharing of secreted factors and may drive evolution of mutualistic behavior.
Collapse
Affiliation(s)
- Heidi A Arjes
- Department of Bioengineering, Stanford University School of MedicineStanfordUnited States
| | - Lisa Willis
- Department of Bioengineering, Stanford University School of MedicineStanfordUnited States
| | - Haiwen Gui
- Department of Bioengineering, Stanford University School of MedicineStanfordUnited States
| | - Yangbo Xiao
- Department of Bioengineering, Stanford University School of MedicineStanfordUnited States
| | - Jason Peters
- Department of Cell and Tissue Biology, University of California San FranciscoSan FranciscoUnited States
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-MadisonMadisonUnited States
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-MadisonMadisonUnited States
- Department of Bacteriology, University of Wisconsin-MadisonMadisonUnited States
- Department of Medical Microbiology and Immunology, University of Wisconsin-MadisonMadisonUnited States
| | - Carol Gross
- Department of Cell and Tissue Biology, University of California San FranciscoSan FranciscoUnited States
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University School of MedicineStanfordUnited States
- Department of Microbiology & Immunology, Stanford University School of MedicineStanfordUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| |
Collapse
|
82
|
Visualization of probiotics via epifluorescence microscopy and fluorescence in situ hybridization (FISH). J Microbiol Methods 2021; 182:106151. [PMID: 33592223 DOI: 10.1016/j.mimet.2021.106151] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 01/28/2021] [Accepted: 01/28/2021] [Indexed: 11/21/2022]
Abstract
Aerobic plate counts, the standard for bacterial enumeration in the probiotic industry, can be biased towards fast-growing organisms that replicate on synthetic media and can significantly underestimate total bacterial abundance. Culture-independent approaches such as fluorescence in situ hybridization (FISH) hold promise as a means to rapidly and accurately enumerate bacteria in probiotic products. In addition, FISH has the potential to more accurately represent bacterial growth dynamics in the environment in which products are applied without imposing additional growth constraints that are required for enumeration via plate counts. In this study, we designed and optimized three new FISH probes to visualize and quantify Bacillus amyloliquefaciens, Bacillus pumilus, and Bacillus licheniformis within probiotic products. Microscopy-based estimates were consistent or higher than label claims for Pediococcus acidilactici, Pediococcus pentosaceus, Lactobacillus plantarum, Bacillus subtilis, Bacillus amyloliquefaciens, Bacillus licheniformis and Bacillus pumilus in both a direct fed microbial (DFM) product as well as a crop microbial biostimulant (CMB) product. Quantification with FISH after a germination experiment revealed the potential for this approach to be used after application of the product.
Collapse
|
83
|
Cha S, Lim HG, Kwon S, Kim DH, Kang CW, Jung GY. Design of mutualistic microbial consortia for stable conversion of carbon monoxide to value-added chemicals. Metab Eng 2021; 64:146-153. [PMID: 33571657 DOI: 10.1016/j.ymben.2021.02.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 12/22/2020] [Accepted: 02/02/2021] [Indexed: 12/31/2022]
Abstract
Carbon monoxide (CO) is a promising carbon source for producing value-added biochemicals via microbial fermentation. However, its microbial conversion has been challenging because of difficulties in genetic engineering of CO-utilizing microorganisms and, more importantly, maintaining CO consumption which is negatively affected by the toxicity of CO and accumulated byproducts. To overcome these issues, we devised mutualistic microbial consortia, co-culturing Eubacterium limosum and genetically engineered Escherichia coli for the production of 3-hydroxypropionic acid (3-HP) and itaconic acid (ITA). During the co-culture, E. limosum assimilated CO and produced acetate, a toxic by-product, while E. coli utilized acetate as a sole carbon source. We found that this mutualistic interaction dramatically stabilized and improved CO consumption of E. limosum compared to monoculture. Consequently, the improved CO consumption allowed successful production of 3-HP and ITA from CO. This study is the first demonstration of value-added biochemical production from CO using a microbial consortium. Moreover, it suggests that synthetic mutualistic microbial consortium can serve as a powerful platform for the valorization of CO.
Collapse
Affiliation(s)
- Sanghak Cha
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-RoNam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Hyun Gyu Lim
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-RoNam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Seokmu Kwon
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-RoNam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Dong-Hwan Kim
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-RoNam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Chae Won Kang
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-RoNam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-RoNam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea; School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-RoNam-Gu, Pohang, Gyeongbuk, 37673, Republic of Korea.
| |
Collapse
|
84
|
Revilla L, Mayorgas A, Corraliza AM, Masamunt MC, Metwaly A, Haller D, Tristán E, Carrasco A, Esteve M, Panés J, Ricart E, Lozano JJ, Salas A. Multi-omic modelling of inflammatory bowel disease with regularized canonical correlation analysis. PLoS One 2021; 16:e0246367. [PMID: 33556098 PMCID: PMC7870068 DOI: 10.1371/journal.pone.0246367] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 01/18/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Personalized medicine requires finding relationships between variables that influence a patient's phenotype and predicting an outcome. Sparse generalized canonical correlation analysis identifies relationships between different groups of variables. This method requires establishing a model of the expected interaction between those variables. Describing these interactions is challenging when the relationship is unknown or when there is no pre-established hypothesis. Thus, our aim was to develop a method to find the relationships between microbiome and host transcriptome data and the relevant clinical variables in a complex disease, such as Crohn's disease. RESULTS We present here a method to identify interactions based on canonical correlation analysis. We show that the model is the most important factor to identify relationships between blocks using a dataset of Crohn's disease patients with longitudinal sampling. First the analysis was tested in two previously published datasets: a glioma and a Crohn's disease and ulcerative colitis dataset where we describe how to select the optimum parameters. Using such parameters, we analyzed our Crohn's disease data set. We selected the model with the highest inner average variance explained to identify relationships between transcriptome, gut microbiome and clinically relevant variables. Adding the clinically relevant variables improved the average variance explained by the model compared to multiple co-inertia analysis. CONCLUSIONS The methodology described herein provides a general framework for identifying interactions between sets of omic data and clinically relevant variables. Following this method, we found genes and microorganisms that were related to each other independently of the model, while others were specific to the model used. Thus, model selection proved crucial to finding the existing relationships in multi-omics datasets.
Collapse
Affiliation(s)
- Lluís Revilla
- Centro de Investigación Biomédica en Red de Enfermedades Hepática y Digestivas (CIBERehd), Barcelona, Spain
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, Barcelona, Spain
| | - Aida Mayorgas
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, Barcelona, Spain
| | - Ana M. Corraliza
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, Barcelona, Spain
| | - Maria C. Masamunt
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, Barcelona, Spain
| | - Amira Metwaly
- Chair of Nutrition and Immunology, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Dirk Haller
- Chair of Nutrition and Immunology, Technical University of Munich, Freising-Weihenstephan, Germany
- ZIEL Institute for Food and Health, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Eva Tristán
- Centro de Investigación Biomédica en Red de Enfermedades Hepática y Digestivas (CIBERehd), Barcelona, Spain
- Department of Gastroenterology, Hospital Universitari Mútua Terrassa, Barcelona, Spain
| | - Anna Carrasco
- Centro de Investigación Biomédica en Red de Enfermedades Hepática y Digestivas (CIBERehd), Barcelona, Spain
- Department of Gastroenterology, Hospital Universitari Mútua Terrassa, Barcelona, Spain
| | - Maria Esteve
- Centro de Investigación Biomédica en Red de Enfermedades Hepática y Digestivas (CIBERehd), Barcelona, Spain
- Department of Gastroenterology, Hospital Universitari Mútua Terrassa, Barcelona, Spain
| | - Julian Panés
- Centro de Investigación Biomédica en Red de Enfermedades Hepática y Digestivas (CIBERehd), Barcelona, Spain
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, Barcelona, Spain
| | - Elena Ricart
- Centro de Investigación Biomédica en Red de Enfermedades Hepática y Digestivas (CIBERehd), Barcelona, Spain
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, Barcelona, Spain
| | - Juan J. Lozano
- Centro de Investigación Biomédica en Red de Enfermedades Hepática y Digestivas (CIBERehd), Barcelona, Spain
| | - Azucena Salas
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, Barcelona, Spain
| |
Collapse
|
85
|
Del Valle I, Fulk EM, Kalvapalle P, Silberg JJ, Masiello CA, Stadler LB. Translating New Synthetic Biology Advances for Biosensing Into the Earth and Environmental Sciences. Front Microbiol 2021; 11:618373. [PMID: 33633695 PMCID: PMC7901896 DOI: 10.3389/fmicb.2020.618373] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/17/2020] [Indexed: 12/26/2022] Open
Abstract
The rapid diversification of synthetic biology tools holds promise in making some classically hard-to-solve environmental problems tractable. Here we review longstanding problems in the Earth and environmental sciences that could be addressed using engineered microbes as micron-scale sensors (biosensors). Biosensors can offer new perspectives on open questions, including understanding microbial behaviors in heterogeneous matrices like soils, sediments, and wastewater systems, tracking cryptic element cycling in the Earth system, and establishing the dynamics of microbe-microbe, microbe-plant, and microbe-material interactions. Before these new tools can reach their potential, however, a suite of biological parts and microbial chassis appropriate for environmental conditions must be developed by the synthetic biology community. This includes diversifying sensing modules to obtain information relevant to environmental questions, creating output signals that allow dynamic reporting from hard-to-image environmental materials, and tuning these sensors so that they reliably function long enough to be useful for environmental studies. Finally, ethical questions related to the use of synthetic biosensors in environmental applications are discussed.
Collapse
Affiliation(s)
- Ilenne Del Valle
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, TX, United States
| | - Emily M. Fulk
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, TX, United States
| | - Prashant Kalvapalle
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, TX, United States
| | - Jonathan J. Silberg
- Department of BioSciences, Rice University, Houston, TX, United States
- Department of Bioengineering, Rice University, Houston, TX, United States
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, United States
| | - Caroline A. Masiello
- Department of BioSciences, Rice University, Houston, TX, United States
- Department of Earth, Environmental and Planetary Sciences, Rice University, Houston, TX, United States
- Department of Chemistry, Rice University, Houston, TX, United States
| | - Lauren B. Stadler
- Department of Civil and Environmental Engineering, Rice University, Houston, TX, United States
| |
Collapse
|
86
|
Pedrozo HA, Dallagnol AM, Schvezov CE. Genetic algorithm applied to simultaneous parameter estimation in bacterial growth. J Bioinform Comput Biol 2021; 19:2050045. [PMID: 33504290 DOI: 10.1142/s0219720020500456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Several mathematical models have been developed to understand the interactions of microorganisms in foods and predict their growth. The resulting model equations for the growth of interacting cells include several parameters that must be determined for the specific conditions to be modeled. In this study, these parameters were determined by using inverse engineering and a multi-objective optimization procedure that allows fitting more than one experimental growth curve simultaneously. A genetic algorithm was applied to obtain the best parameter values of a model that permit the construction of the front of Pareto with 50 individuals or phenotypes. The method was applied to three experimental data sets of simultaneous growth of lactic acid bacteria (LAB) and Listeria monocytogenes (LM). Then, the proposed method was compared with a conventional mono-objective sequential fit. We concluded that the multi-objective fit by the genetic algorithm gives superior results with more parameter identifiability than the conventional sequential approach.
Collapse
Affiliation(s)
- Hector A Pedrozo
- Instituto de Materiales de Misiones (CONICET-UNaM), Felix de Azara 1552, 3300 Posadas, Argentina
| | - Andrea M Dallagnol
- Instituto de Materiales de Misiones (CONICET-UNaM), Felix de Azara 1552, 3300 Posadas, Argentina
| | - Carlos E Schvezov
- Instituto de Materiales de Misiones (CONICET-UNaM), Felix de Azara 1552, 3300 Posadas, Argentina
| |
Collapse
|
87
|
Jones ML, Rivett DW, Pascual-García A, Bell T. Relationships between community composition, productivity and invasion resistance in semi-natural bacterial microcosms. eLife 2021; 10:71811. [PMID: 34662276 PMCID: PMC8523168 DOI: 10.7554/elife.71811] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/19/2021] [Indexed: 01/03/2023] Open
Abstract
Common garden experiments that inoculate a standardised growth medium with synthetic microbial communities (i.e. constructed from individual isolates or using dilution cultures) suggest that the ability of the community to resist invasions by additional microbial taxa can be predicted by the overall community productivity (broadly defined as cumulative cell density and/or growth rate). However, to the best of our knowledge, no common garden study has yet investigated the relationship between microbial community composition and invasion resistance in microcosms whose compositional differences reflect natural, rather than laboratory-designed, variation. We conducted experimental invasions of two bacterial strains (Pseudomonas fluorescens and Pseudomonas putida) into laboratory microcosms inoculated with 680 different mixtures of bacteria derived from naturally occurring microbial communities collected in the field. Using 16S rRNA gene amplicon sequencing to characterise microcosm starting composition, and high-throughput assays of community phenotypes including productivity and invader survival, we determined that productivity is a key predictor of invasion resistance in natural microbial communities, substantially mediating the effect of composition on invasion resistance. The results suggest that similar general principles govern invasion in artificial and natural communities, and that factors affecting resident community productivity should be a focal point for future microbial invasion experiments.
Collapse
Affiliation(s)
- Matt Lloyd Jones
- Department of Life Sciences, Imperial College London, Silwood Park CampusAscotUnited Kingdom
| | - Damian William Rivett
- Department of Life Sciences, Imperial College London, Silwood Park CampusAscotUnited Kingdom
| | - Alberto Pascual-García
- Department of Life Sciences, Imperial College London, Silwood Park CampusAscotUnited Kingdom
| | - Thomas Bell
- Department of Life Sciences, Imperial College London, Silwood Park CampusAscotUnited Kingdom
| |
Collapse
|
88
|
Ross BN, Whiteley M. Ignoring social distancing: advances in understanding multi-species bacterial interactions. Fac Rev 2020; 9:23. [PMID: 33659955 PMCID: PMC7886066 DOI: 10.12703/r/9-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Almost every ecosystem on this planet is teeming with microbial communities made of diverse bacterial species. At a reductionist view, many of these bacteria form pairwise interactions, but, as the field of view expands, the neighboring organisms and the abiotic environment can play a crucial role in shaping the interactions between species. Over the years, a strong foundation of knowledge has been built on isolated pairwise interactions between bacteria, but now the field is advancing toward understanding how cohabitating bacteria and natural surroundings affect these interactions. Use of bottom-up approaches, piecing communities together, and top-down approaches that deconstruct communities are providing insight on how different species interact. In this review, we highlight how studies are incorporating more complex communities, mimicking the natural environment, and recurring findings such as the importance of cooperation for stability in harsh environments and the impact of bacteria-induced environmental pH shifts. Additionally, we will discuss how omics are being used as a top-down approach to identify previously unknown interspecies bacterial interactions and the challenges of these types of studies for microbial ecology.
Collapse
Affiliation(s)
- Brittany N Ross
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Emory-Children's Cystic Fibrosis Center, Atlanta, Georgia, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Marvin Whiteley
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Emory-Children's Cystic Fibrosis Center, Atlanta, Georgia, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
| |
Collapse
|
89
|
Rasmussen TS, Mentzel CMJ, Kot W, Castro-Mejía JL, Zuffa S, Swann JR, Hansen LH, Vogensen FK, Hansen AK, Nielsen DS. Faecal virome transplantation decreases symptoms of type 2 diabetes and obesity in a murine model. Gut 2020; 69:2122-2130. [PMID: 32165408 DOI: 10.1136/gutjnl-2019-320005] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 02/11/2020] [Accepted: 02/21/2020] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Development of obesity and type 2 diabetes (T2D) are associated with gut microbiota (GM) changes. The gut viral community is predominated by bacteriophages (phages), which are viruses that attack bacteria in a host-specific manner. The antagonistic behaviour of phages has the potential to alter the GM. As a proof-of-concept, we demonstrate the efficacy of faecal virome transplantation (FVT) from lean donors for shifting the phenotype of obese mice into closer resemblance of lean mice. DESIGN The FVT consisted of viromes with distinct profiles extracted from the caecal content of mice from different vendors that were fed a low-fat (LF) diet for 14 weeks. Male C57BL/6NTac mice were divided into five groups: LF (as diet control), high-fat (HF) diet, HF+ampicillin (Amp), HF+Amp+FVT and HF+FVT. At weeks 6 and 7 of the study, the HF+FVT and HF+Amp+FVT mice were treated with FVT by oral gavage. The Amp groups were treated with Amp 24 hours prior to first FVT treatment. RESULTS Six weeks after first FVT, the HF+FVT mice showed a significant decrease in weight gain compared with the HF group. Further, glucose tolerance was comparable between the LF and HF+FVT mice, while the other HF groups all had impaired glucose tolerance. These observations were supported by significant shifts in GM composition, blood plasma metabolome and expression levels of genes associated with obesity and T2D development. CONCLUSIONS Transfer of caecal viral communities from mice with a lean phenotype into mice with an obese phenotype led to reduced weight gain and normalised blood glucose parameters relative to lean mice. We hypothesise that this effect is mediated via FVT-induced GM changes.
Collapse
Affiliation(s)
| | | | - Witold Kot
- Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Simone Zuffa
- Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | | | | | | | - Axel Kornerup Hansen
- Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | |
Collapse
|
90
|
Gonzalo M, Deveau A, Aigle B. Inhibitions Dominate but Stimulations and Growth Rescues Are Not Rare Among Bacterial Isolates from Grains of Forest Soil. MICROBIAL ECOLOGY 2020; 80:872-884. [PMID: 32879989 DOI: 10.1007/s00248-020-01579-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 08/18/2020] [Indexed: 06/11/2023]
Abstract
Soil is a complex environment made of multiple microhabitats in which a wide variety of microorganisms co-exist and interact to form dynamic communities. While the abiotic factors that regulate the structure of these communities are now quite well documented, our knowledge of how bacteria interact with each other within these communities is still insufficient. Literature reveals so far contradictory results and is mainly focused on antagonistic interactions. To start filling this gap, we isolated 35 different bacterial isolates from grains of soil assuming that, at this scale, these bacteria would have been likely interacting in their natural habitat. We tested pairwise interactions between all isolates from each grain and scored positive and negative interactions. We compared the effects of simultaneous versus delayed co-inoculations, allowing or not to a strain to modify first its environment. One hundred fifty-seven interactions, either positive or negative, were recorded among the 525 possible one's. Members of the Bacillus subtilis, Pseudomonas and Streptomyces genera were responsible for most inhibitions, while positive interactions occurred between isolates of the Bacillales order and only in delayed inoculation conditions. Antagonist isolates had broad spectral abilities to acquire nutrients from organic and inorganic matter, while inhibited isolates tended to have little potentials. Despite an overall domination of antagonistic interactions (87%), a third of the isolates were able to stimulate or rescue the growth of other isolates, suggesting that cooperation between bacteria may be underestimated.
Collapse
Affiliation(s)
- Milena Gonzalo
- Université de Lorraine, INRAE, IAM, F-54000, Nancy, France
- Université de Lorraine, INRAE , DynAMic, F-54000, Nancy, France
| | - Aurélie Deveau
- Université de Lorraine, INRAE, IAM, F-54000, Nancy, France.
| | - Bertrand Aigle
- Université de Lorraine, INRAE , DynAMic, F-54000, Nancy, France.
| |
Collapse
|
91
|
Pacwa-Płociniczak M, Biniecka P, Bondarczuk K, Piotrowska-Seget Z. Metagenomic Functional Profiling Reveals Differences in Bacterial Composition and Function During Bioaugmentation of Aged Petroleum-Contaminated Soil. Front Microbiol 2020; 11:2106. [PMID: 32983067 PMCID: PMC7487420 DOI: 10.3389/fmicb.2020.02106] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/10/2020] [Indexed: 02/01/2023] Open
Abstract
Our objective was to study the bacterial community changes that determine enhanced removal of petroleum hydrocarbons from soils subjected to bioaugmentation with the hydrocarbon-degrading strains Rhodococcus erythropolis CD 130, CD 167, and their combination. To achieve this, a high-throughput sequencing of the 16S rRNA gene was performed. The changes in the bacterial community composition were most apparent the day after bacterial inoculation. These changes represented an increase in the percentage abundance of Rhodococcus and Pseudomonas genera. Surprisingly, members of the Rhodococcus genus were not present after day 91. At the end of the experiment, the bacterial communities from the CD 130, CD 167, and control soils had a similar structure. Nevertheless, the composition of the bacteria in the CD 130 + CD 167 soil was still distinct from the control. Metagenomic predictions from the 16S rRNA gene sequences showed that the introduction of bacteria had a significant influence on the predicted pathways (metabolism of xenobiotics, lipids, terpenoids, polyketides, and amino acids) on day one. On day 182, differences in the abundance of functional pathways were also detected in the CD 130 and CD 130 + CD 167 soils. Additionally, we observed that on day one, in all bioaugmented soils, the alkH gene was mainly contributed by the Rhodococcus and Mycobacterium genera, whereas in non-treated soil, this gene was contributed only by the Mycobacterium genus. Interestingly, from day 91, the Mycobacterium genus was the main contributor for the tested genes in all studied soils. Our results showed that hydrocarbon depletion from the analyzed soils resulted from the activity of the autochthonous bacteria. However, these changes in the composition and function of the indigenous bacterial community occurred under the influence of the introduced bacteria.
Collapse
Affiliation(s)
- Magdalena Pacwa-Płociniczak
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Paulina Biniecka
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Kinga Bondarczuk
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Białystok, Poland
| | - Zofia Piotrowska-Seget
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| |
Collapse
|
92
|
Rosca AS, Castro J, Sousa LGV, Cerca N. Gardnerella and vaginal health: the truth is out there. FEMS Microbiol Rev 2020; 44:73-105. [PMID: 31697363 DOI: 10.1093/femsre/fuz027] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 11/06/2019] [Indexed: 12/16/2022] Open
Abstract
The human vagina is a dynamic ecosystem in which homeostasis depends on mutually beneficial interactions between the host and their microorganisms. However, the vaginal ecosystem can be thrown off balance by a wide variety of factors. Bacterial vaginosis (BV) is the most common vaginal infection in women of childbearing age but its etiology is not yet fully understood, with different controversial theories being raised over the years. What is generally accepted is that BV is often characterized by a shift in the composition of the normal vaginal microbiota, from a Lactobacillus species dominated microbiota to a mixture of anaerobic and facultative anaerobic bacteria. During BV, a polymicrobial biofilm develops in the vaginal microenvironment, being mainly composed of Gardnerella species. The interactions between vaginal microorganisms are thought to play a pivotal role in the shift from health to disease and might also increase the risk of sexually transmitted infections acquisition. Here, we review the current knowledge regarding the specific interactions that occur in the vaginal niche and discuss mechanisms by which these interactions might be mediated. Furthermore, we discuss the importance of novel strategies to fight chronic vaginal infections.
Collapse
Affiliation(s)
- Aliona S Rosca
- Centre of Biological Engineering (CEB), Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Joana Castro
- Centre of Biological Engineering (CEB), Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Lúcia G V Sousa
- Centre of Biological Engineering (CEB), Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Nuno Cerca
- Centre of Biological Engineering (CEB), Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| |
Collapse
|
93
|
Terry JS, Anderson LBR, Scherman MS, McAlister CE, Perera R, Schountz T, Geiss BJ. Development of SARS-CoV-2 Nucleocapsid Specific Monoclonal Antibodies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.09.03.280370. [PMID: 32908982 PMCID: PMC7480041 DOI: 10.1101/2020.09.03.280370] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The global COVID-19 pandemic has caused massive disruptions in every society around the world. To help fight COVID-19, new molecular tools specifically targeting critical components of the causative agent of COVID-19, SARS-Coronavirus-2 (SARS-CoV-2), are desperately needed. The SARS-CoV-2 nucleocapsid protein is a major component of the viral replication processes, integral to viral particle assembly, and is a major diagnostic marker for infection and immune protection. Currently available antibody reagents targeting the nucleocapsid protein were primarily developed against the related SARS-CoV virus and are not specific to SARS-CoV-2 nucleocapsid protein. Therefore, in this work we developed and characterized a series of new mouse monoclonal antibodies against the SARS-CoV-2 nucleocapsid protein. The anti-nucleocapsid monoclonal antibodies were tested in ELISA, western blot, and immunofluorescence analyses. The variable regions from the heavy and light chains from five select clones were cloned and sequenced, and preliminary epitope mapping of the sequenced clones was performed. Overall, the new antibody reagents described here will be of significant value in the fight against COVID-19.
Collapse
Affiliation(s)
- James S. Terry
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Loran BR Anderson
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Michael S. Scherman
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Carley E. McAlister
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
- Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Rushika Perera
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
- Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Tony Schountz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
- Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Brian J. Geiss
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
- Arthropod-borne and Infectious Diseases Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
- School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado, USA
| |
Collapse
|
94
|
Moitinho MA, Souza DT, Chiaramonte JB, Bononi L, Melo IS, Taketani RG. The unexplored bacterial lifestyle on leaf surface. Braz J Microbiol 2020; 51:1233-1240. [PMID: 32363565 PMCID: PMC7455623 DOI: 10.1007/s42770-020-00287-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 04/25/2020] [Indexed: 01/19/2023] Open
Abstract
Social interactions impact microbial communities and these relationships are mediated by small molecules. The chemical ecology of bacteria on the phylloplane environment is still little explored. The harsh environmental conditions found on leaf surface require high metabolic performances of the bacteria in order to survive. That is interesting both for scientific fields of prospecting natural molecules and for the ecological studies. Important queries about the bacterial lifestyle on leaf surface remain not fully comprehended. Does the hostility of the environment increase the populations' cellular altruism by the production of molecules, which can benefit the whole community? Or does the reverse occur and the production of molecules related to competition between species is increased? Does the phylogenetic distance between the bacterial populations influence the chemical profile during social interactions? Do phylogenetically related bacteria tend to cooperate more than the distant ones? The phylloplane contains high levels of yet uncultivated microorganisms, and understanding the molecular basis of the social networks on this habitat is crucial to gain new insights on the ecology of the mysterious community members due to interspecies molecular dependence. Here, we review and discuss what is known about bacterial social interactions and their chemical lifestyle on leaf surface.
Collapse
Affiliation(s)
- Marta A Moitinho
- Laboratory of Environmental Microbiology, EMBRAPA Environment, Brazilian Agricultural Research Corporation, SP 340, Km 127.5, Jaguariúna, São Paulo, 13820-000, Brazil
- College of Agriculture Luiz de Queiroz, University of São Paulo, Av. Pádua Dias, 11, Piracicaba, São Paulo, 13418-900, Brazil
| | - Danilo T Souza
- Laboratory of Mass Spectrometry Applied Natural Products Chemistry; Department of Chemistry, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Av. Bandeirantes, 3900, Monte Alegre, Ribeirão Preto, São Paulo, 14040-901, Brazil
| | - Josiane B Chiaramonte
- Laboratory of Environmental Microbiology, EMBRAPA Environment, Brazilian Agricultural Research Corporation, SP 340, Km 127.5, Jaguariúna, São Paulo, 13820-000, Brazil
- College of Agriculture Luiz de Queiroz, University of São Paulo, Av. Pádua Dias, 11, Piracicaba, São Paulo, 13418-900, Brazil
| | - Laura Bononi
- Laboratory of Environmental Microbiology, EMBRAPA Environment, Brazilian Agricultural Research Corporation, SP 340, Km 127.5, Jaguariúna, São Paulo, 13820-000, Brazil
- College of Agriculture Luiz de Queiroz, University of São Paulo, Av. Pádua Dias, 11, Piracicaba, São Paulo, 13418-900, Brazil
| | - Itamar S Melo
- Laboratory of Environmental Microbiology, EMBRAPA Environment, Brazilian Agricultural Research Corporation, SP 340, Km 127.5, Jaguariúna, São Paulo, 13820-000, Brazil
| | - Rodrigo G Taketani
- College of Agriculture Luiz de Queiroz, University of São Paulo, Av. Pádua Dias, 11, Piracicaba, São Paulo, 13418-900, Brazil.
- CETEM, Centre for Mineral Technology, MCTIC Ministry of Science, Technology, Innovation and Communication, Av. Pedro Calmon, 900, Cidade Universitária, Ilha do Fundão, Rio de Janeiro, 21941-908, Brazil.
| |
Collapse
|
95
|
Strain Background, Species Frequency, and Environmental Conditions Are Important in Determining Pseudomonas aeruginosa and Staphylococcus aureus Population Dynamics and Species Coexistence. Appl Environ Microbiol 2020; 86:AEM.00962-20. [PMID: 32651205 DOI: 10.1128/aem.00962-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/04/2020] [Indexed: 01/09/2023] Open
Abstract
Bacterial communities in the environment and in infections are typically diverse, yet we know little about the factors that determine interspecies interactions. Here, we apply concepts from ecological theory to understand how biotic and abiotic factors affect interaction patterns between the two opportunistic human pathogens Pseudomonas aeruginosa and Staphylococcus aureus, which often cooccur in polymicrobial infections. Specifically, we conducted a series of short- and long-term competition experiments between P. aeruginosa PAO1 (as our reference strain) and three different S. aureus strains (Cowan I, 6850, and JE2) at three starting frequencies and under three environmental (culturing) conditions. We found that the competitive ability of P. aeruginosa strongly depended on the strain background of S. aureus, whereby P. aeruginosa dominated against Cowan I and 6850 but not against JE2. In the latter case, both species could end up as winners depending on conditions. Specifically, we observed strong frequency-dependent fitness patterns, including positive frequency dependence, where P. aeruginosa could dominate JE2 only when common (not when rare). Finally, changes in environmental (culturing) conditions fundamentally altered the competitive balance between the two species in a way that P. aeruginosa dominance increased when moving from shaken to static environments. Altogether, our results highlight that ecological details can have profound effects on the competitive dynamics between coinfecting pathogens and determine whether two species can coexist or invade each others' populations from a state of rare frequency. Moreover, our findings might parallel certain dynamics observed in chronic polymicrobial infections.IMPORTANCE Bacterial infections are frequently caused by more than one species, and such polymicrobial infections are often considered more virulent and more difficult to treat than the respective monospecies infections. Pseudomonas aeruginosa and Staphylococcus aureus are among the most important pathogens in polymicrobial infections, and their cooccurrence is linked to worse disease outcome. There is great interest in understanding how these two species interact and what the consequences for the host are. While previous studies have mainly looked at molecular mechanisms implicated in interactions between P. aeruginosa and S. aureus, here we show that ecological factors, such as strain background, species frequency, and environmental conditions, are important elements determining population dynamics and species coexistence patterns. We propose that the uncovered principles also play major roles in infections and, therefore, proclaim that an integrative approach combining molecular and ecological aspects is required to fully understand polymicrobial infections.
Collapse
|
96
|
Lisle JT. Nutrient Removal and Uptake by Native Planktonic and Biofilm Bacterial Communities in an Anaerobic Aquifer. Front Microbiol 2020; 11:1765. [PMID: 32849390 PMCID: PMC7403441 DOI: 10.3389/fmicb.2020.01765] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 07/06/2020] [Indexed: 11/29/2022] Open
Abstract
Managed aquifer recharge (MAR) offers a collection of water storage and storage options that have been used by resource managers to mitigate the reduced availability of fresh water. One of these technologies is aquifer storage and recovery (ASR), where surface water is treated then recharged into a storage zone within an existing aquifer for later recovery and discharge into a body of water. During the storage phase of ASR, nutrient concentrations in the recharge water have been shown to decrease due, presumably via the uptake by the native aquifer microbial community. In this study, the native microbial community in an anaerobic carbonate aquifer zone targeted for ASR storage was segregated into planktonic and biofilm communities then challenged with NO3-N, PO4-P, and acetate as dissolved organic carbon (DOC) to determine their respective removal and uptake rates. The planktonic community removed NO3-N at a rate of 0.059 mg L–1d–1, PO4-P at 5.73 × 10–8–1.03 × 10–7 mg L–1d–1 and DOC at 0.015–0.244 mg L–1d–1. The biofilm community was significantly more proficient, removing NO3-N at 0.116 mg L–1d–1 (1.6–9.0 μg m–2d–1), PO4-P at 4.20–5.91 × 10–5 mg L–1d–1 (2.47–9.88 ng m–2d–1) and DOC at 0.301–0.696 mg L–1d–1 (29.0–71.0 μg m–2d–1). Additionally, the PO4-P sorption rate onto the carbonate aquifer matrix ranged from 1.64 × 10–7 to 9.25 × 10–7 mg PO4-P m–2 day–1. These rates were applied to field data collected at an ASR facility in central Florida and from the same aquifer storage zone from which the biofilm communities were grown. With only 10% of the available surface area within the storage zone being colonized by biofilms, typical concentrations of NO3-N, PO4-P, and DOC in the recharged filtered surface waters would be reduced to below detection limits, and by 81.4 and 91.1%, respectively, during a 150 days storage period.
Collapse
Affiliation(s)
- John T Lisle
- St. Petersburg Coastal and Marine Science Center, United States Geological Survey, St. Petersburg, FL, United States
| |
Collapse
|
97
|
Pandit A, Adholeya A, Cahill D, Brau L, Kochar M. Microbial biofilms in nature: unlocking their potential for agricultural applications. J Appl Microbiol 2020; 129:199-211. [PMID: 32034822 DOI: 10.1111/jam.14609] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 01/23/2020] [Accepted: 02/05/2020] [Indexed: 12/17/2022]
Abstract
Soil environments are dynamic and the plant rhizosphere harbours a phenomenal diversity of micro-organisms which exchange signals and beneficial nutrients. Bipartite beneficial or symbiotic interactions with host roots, such as mycorrhizae and various bacteria, are relatively well characterized. In addition, a tripartite interaction also exists between plant roots, arbuscular mycorrhizal fungi (AMF) and associated bacteria. Bacterial biofilms exist as a sheet of bacterial cells in association with AMF structures, embedded within a self-produced exopolysaccharide matrix. Such biofilms may play important functional roles within these tripartite interactions. However, the details about such interactions in the rhizosphere and their relevant functional relationships have not been elucidated. This review explores the current understanding of naturally occurring microbial biofilms, and their interaction with biotic surfaces, especially AMF. The possible roles played by bacterial biofilms and the potential for their application for a more productive and sustainable agriculture is discussed in this review.
Collapse
Affiliation(s)
- A Pandit
- TERI Deakin Nanobiotechnology Centre, Sustainable Agriculture Division, The Energy and Resources Institute, TERI Gram, Gwal Pahari, Gurugram, Haryana, India
- School of Life and Environmental Sciences, Deakin University, Geelong, Vic, Australia
| | - A Adholeya
- TERI Deakin Nanobiotechnology Centre, Sustainable Agriculture Division, The Energy and Resources Institute, TERI Gram, Gwal Pahari, Gurugram, Haryana, India
| | - D Cahill
- School of Life and Environmental Sciences, Deakin University, Geelong, Vic, Australia
| | - L Brau
- School of Life and Environmental Sciences, Deakin University, Geelong, Vic, Australia
| | - M Kochar
- TERI Deakin Nanobiotechnology Centre, Sustainable Agriculture Division, The Energy and Resources Institute, TERI Gram, Gwal Pahari, Gurugram, Haryana, India
| |
Collapse
|
98
|
Kim N, Kim JJ, Kim I, Mannaa M, Park J, Kim J, Lee H, Lee S, Park D, Sul WJ, Seo Y. Type VI secretion systems of plant-pathogenic Burkholderia glumae BGR1 play a functionally distinct role in interspecies interactions and virulence. MOLECULAR PLANT PATHOLOGY 2020; 21:1055-1069. [PMID: 32643866 PMCID: PMC7368126 DOI: 10.1111/mpp.12966] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/28/2020] [Accepted: 05/31/2020] [Indexed: 05/02/2023]
Abstract
In the environment, bacteria show close association, such as interspecies interaction, with other bacteria as well as host organisms. The type VI secretion system (T6SS) in gram-negative bacteria is involved in bacterial competition or virulence. The plant pathogen Burkholderia glumae BGR1, causing bacterial panicle blight in rice, has four T6SS gene clusters. The presence of at least one T6SS gene cluster in an organism indicates its distinct role, like in the bacterial and eukaryotic cell targeting system. In this study, deletion mutants targeting four tssD genes, which encode the main component of T6SS needle formation, were constructed to functionally dissect the four T6SSs in B. glumae BGR1. We found that both T6SS group_4 and group_5, belonging to the eukaryotic targeting system, act independently as bacterial virulence factors toward host plants. In contrast, T6SS group_1 is involved in bacterial competition by exerting antibacterial effects. The ΔtssD1 mutant lost the antibacterial effect of T6SS group_1. The ΔtssD1 mutant showed similar virulence as the wild-type BGR1 in rice because the ΔtssD1 mutant, like the wild-type BGR1, still has key virulence factors such as toxin production towards rice. However, metagenomic analysis showed different bacterial communities in rice infected with the ΔtssD1 mutant compared to wild-type BGR1. In particular, the T6SS group_1 controls endophytic plant-associated bacteria such as Luteibacter and Dyella in rice plants and may have an advantage in competing with endophytic plant-associated bacteria for settlement inside rice plants in the environment. Thus, B. glumae BGR1 causes disease using T6SSs with functionally distinct roles.
Collapse
Affiliation(s)
- Namgyu Kim
- Department of Integrated Biological SciencePusan National UniversityBusanKorea
| | - Jin Ju Kim
- Department of Systems BiotechnologyChung‐Ang UniversityAnseongKorea
| | - Inyoung Kim
- Department of Integrated Biological SciencePusan National UniversityBusanKorea
| | - Mohamed Mannaa
- Department of Integrated Biological SciencePusan National UniversityBusanKorea
| | - Jungwook Park
- Department of Integrated Biological SciencePusan National UniversityBusanKorea
| | - Juyun Kim
- Department of Integrated Biological SciencePusan National UniversityBusanKorea
| | - Hyun‐Hee Lee
- Department of Integrated Biological SciencePusan National UniversityBusanKorea
| | | | | | - Woo Jun Sul
- Department of Systems BiotechnologyChung‐Ang UniversityAnseongKorea
| | - Young‐Su Seo
- Department of Integrated Biological SciencePusan National UniversityBusanKorea
| |
Collapse
|
99
|
Stewart JD, Shakya KM, Bilinski T, Wilson JW, Ravi S, Choi CS. Variation of near surface atmosphere microbial communities at an urban and a suburban site in Philadelphia, PA, USA. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 724:138353. [PMID: 32408469 DOI: 10.1016/j.scitotenv.2020.138353] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/28/2020] [Accepted: 03/30/2020] [Indexed: 06/11/2023]
Abstract
Microorganisms are abundant in the near surface atmosphere and make up a significant fraction of organic aerosols with implications on both human health and ecosystem services. Despite their importance, studies investigating biogeographical patterns of the atmospheric microbiome between urban and suburban areas are limited. Urban and suburban locations (including their microbial communities) vary considerably depending on climate, topography, industrial activities, demographics and other socio-economic factors. Hence, we need more location-specific data to make informed decision affecting air quality, human health, and the implication of a changing climate and policy decisions. The objective of this study was to describe how the atmospheric microbiome varies in composition and function between urban and suburban sites. We used high-throughput sequencing to analyze microbial communities collected at different times from PM2.5 samples collected by active sampling method (using a pump and an impactor) and dust settling of TSP collected by passive sampling method (no pump and no impactor) from an urban and suburban site. We found diverse communities unique in composition at both sites with equivalent functional potential. Taxonomic composition varied significantly with Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Other phyla in greater relative abundance at the urban site. In contrast, Cyanobacteria, Tenericutes, Fusobacteria, and Deinococcus, were enriched at the suburban site. Community diversity also demonstrated a high degree of temporal variation within site. We identified over one-third of the communities as potentially pathogenic taxa (urban: 47.52% ± 14.40%, suburban: 34.53% ± 14.60%) and determined the majority of organisms come from animal-associated host or are environmental non-specific. Potentially pathogenic taxa and source environments were similar between active- and passive- sampling method results. Our research is novel it adds to the underrepresented set of studies on atmospheric microbial structure and function across land types and is the first to compare suburban and urban atmospheric communities.
Collapse
Affiliation(s)
- J D Stewart
- Department of Geography & the Environment, Villanova University, PA, USA
| | - K M Shakya
- Department of Geography & the Environment, Villanova University, PA, USA.
| | - T Bilinski
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - J W Wilson
- Department of Biology, Villanova University, PA, USA
| | - S Ravi
- Department of Earth & Environmental Science, Temple University, PA, USA
| | - Chong Seok Choi
- Department of Earth & Environmental Science, Temple University, PA, USA
| |
Collapse
|
100
|
Chávez-Madero C, de León-Derby MD, Samandari M, Ceballos-González CF, Bolívar-Monsalve EJ, Mendoza-Buenrostro C, Holmberg S, Garza-Flores NA, Almajhadi MA, González-Gamboa I, Yee-de León JF, Martínez-Chapa SO, Rodríguez CA, Wickramasinghe HK, Madou M, Dean D, Khademhosseini A, Zhang YS, Alvarez MM, Trujillo-de Santiago G. Using chaotic advection for facile high-throughput fabrication of ordered multilayer micro- and nanostructures: continuous chaotic printing. Biofabrication 2020; 12:035023. [PMID: 32224513 DOI: 10.1088/1758-5090/ab84cc] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
This paper introduces the concept of continuous chaotic printing, i.e. the use of chaotic flows for deterministic and continuous extrusion of fibers with internal multilayered micro- or nanostructures. Two free-flowing materials are coextruded through a printhead containing a miniaturized Kenics static mixer (KSM) composed of multiple helicoidal elements. This produces a fiber with a well-defined internal multilayer microarchitecture at high-throughput (>1.0 m min-1). The number of mixing elements and the printhead diameter determine the number and thickness of the internal lamellae, which are generated according to successive bifurcations that yield a vast amount of inter-material surface area (∼102 cm2 cm-3) at high resolution (∼10 µm). This creates structures with extremely high surface area to volume ratio (SAV). Comparison of experimental and computational results demonstrates that continuous chaotic 3D printing is a robust process with predictable output. In an exciting new development, we demonstrate a method for scaling down these microstructures by 3 orders of magnitude, to the nanoscale level (∼150 nm), by feeding the output of a continuous chaotic 3D printhead into an electrospinner. The simplicity and high resolution of continuous chaotic printing strongly supports its potential use in novel applications, including-but not limited to-bioprinting of multi-scale layered biological structures such as bacterial communities, living tissues composed of organized multiple mammalian cell types, and fabrication of smart multi-material and multilayered constructs for biomedical applications.
Collapse
Affiliation(s)
- Carolina Chávez-Madero
- Centro de Biotecnología-FEMSA, Tecnologico de Monterrey, Monterrey 64849, NL, México. Departamento de Ingeniería Mecatrónica y Eléctrica, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Monterrey 64849, NL, México. Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge 02139, MA, United States of America. These authors contributed equally to this work
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|