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Taguer M, Xiao J, Crawford R, Shi H, Cheng MP, Citron M, Hannigan GD, Kasper SH. Spatial recovery of the murine gut microbiota after antibiotics perturbation. mBio 2024; 15:e0070724. [PMID: 38832780 PMCID: PMC11253616 DOI: 10.1128/mbio.00707-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 03/31/2024] [Indexed: 06/05/2024] Open
Abstract
Bacterial communities are highly complex, with interaction networks dictating ecosystem function. Bacterial interactions are constrained by the spatial organization of these microbial communities, yet studying the spatial organization of microbial communities at the single-cell level has been technically challenging. Here, we use the recently developed high-phylogenetic-resolution microbiota mapping by fluorescence in situ hybridization technology to image the gut microbiota at the species and single-cell level. We simultaneously image 63 different bacterial species to spatially characterize the perturbation and recovery of the gut microbiota to ampicillin and vancomycin in the cecum and distal colon of mice. To decipher the biology in this complex imaging data, we developed an analytical framework to characterize the spatial changes of the gut microbiota to a perturbation. The three-tiered analytical approach includes image-level diversity, pairwise colocalization analysis, and hypothesis-driven neighborhood analysis. Through this workflow, we identify biogeographic and antibiotic-based differences in the spatial organization of the gut microbiota. We demonstrate that the cecal microbiota has increased micrometer-scale diversity than the colon at baseline and recovers better from perturbation. Also, we identify potential foundation and keystone species that have high baseline neighborhood richness and that are associated with recovery from antibiotics. Through this workflow, we add a spatial layer to the characterization of bacterial communities and progress toward a better understanding of bacterial interactions leading to improved microbiome modulation strategies. IMPORTANCE Antibiotics have broad off-target effects on the gut microbiome. When the microbial community is unable to recover from antibiotics, it can lead to increased susceptibility to gastrointestinal infections and increased risk of immunological and metabolic diseases. In this study, we work to better understand how the gut microbiota recovers from antibiotics by employing a recent technology to image the entire bacterial community at once. Through this approach, we characterize the spatial changes in the gut microbiota after treatment with model antibiotics in both the cecum and colon of mice. We find antibiotic- and biogeographic-dependent spatial changes between bacterial species and that many of these spatial colocalizations do not recover to baseline levels even 35 days after antibiotic administration.
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Affiliation(s)
- M. Taguer
- Discovery Immunology, MRL, Merck & Co., Inc., Cambridge, Massachusetts, USA
| | - J. Xiao
- Infectious Diseases and Vaccine Research, MRL, Merck & Co., Inc., West Point, Pennsylvania, USA
| | - R. Crawford
- Informatics Technology, MRL, Merck & Co., Inc., West Point, Pennsylvania, USA
| | - H. Shi
- Kanvas Biosciences, Inc., Monmouth Junction, New Jersey, USA
| | - M. P. Cheng
- Kanvas Biosciences, Inc., Monmouth Junction, New Jersey, USA
| | - M. Citron
- Infectious Diseases and Vaccine Research, MRL, Merck & Co., Inc., West Point, Pennsylvania, USA
| | - G. D. Hannigan
- Informatics Technology, MRL, Merck & Co., Inc., Cambridge, Massachusetts, USA
| | - S. H. Kasper
- Discovery Immunology, MRL, Merck & Co., Inc., Cambridge, Massachusetts, USA
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Johnston J, Vilardi K, Cotto I, Sudarshan A, Bian K, Klaus S, Bachmann M, Parsons M, Wilson C, Bott C, Pinto A. Metatranscriptomic Analysis Reveals Synergistic Activities of Comammox and Anammox Bacteria in Full-Scale Attached Growth Nitrogen Removal System. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024. [PMID: 39001848 DOI: 10.1021/acs.est.4c04375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/15/2024]
Abstract
Leveraging comammox Nitrospira and anammox bacteria for shortcut nitrogen removal can drastically lower the carbon footprint of wastewater treatment facilities by decreasing aeration energy, carbon, alkalinity, and tank volume requirements while also potentially reducing nitrous oxide emissions. However, their co-occurrence as dominant nitrifying bacteria is rarely reported in full-scale wastewater treatment. As a result, there is a poor understanding of how operational parameters, in particular, dissolved oxygen, impact their activity and synergistic behavior. Here, we report the impact of dissolved oxygen concentration (DO = 2, 4, 6 mg/L) on the microbial community's transcriptomic expression in a full-scale integrated fixed film activated sludge (IFAS) municipal wastewater treatment facility where nitrogen removal is predominantly performed by comammox Nitrospira and anammox bacterial populations. 16S rRNA transcript compositions revealed anammox bacteria and Nitrospira were significantly more active in IFAS biofilms compared to suspended sludge biomass. In IFAS biofilms, anammox bacteria significantly increased hzo expression at lower dissolved oxygen concentrations and this increase was highly correlated with the amoA expression levels of comammox bacteria. Interestingly, the genes involved in nitrite oxidation by comammox bacteria were significantly more upregulated, relative to the genes involved in ammonia oxidation with decreasing dissolved oxygen concentrations. Ultimately, our findings suggest that comammox Nitrospira supplies anammox bacteria with nitrite via ammonia oxidation and that this synergistic behavior is dependent on dissolved oxygen concentrations.
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Affiliation(s)
- Juliet Johnston
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Katherine Vilardi
- Department of Civil and Environmental Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Irmarie Cotto
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Ashwin Sudarshan
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Kaiqin Bian
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Stephanie Klaus
- Hampton Roads Sanitation District, Virginia Beach, Virginia 23455, United States
| | - Megan Bachmann
- Hampton Roads Sanitation District, Virginia Beach, Virginia 23455, United States
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Mike Parsons
- Hampton Roads Sanitation District, Virginia Beach, Virginia 23455, United States
| | - Christopher Wilson
- Hampton Roads Sanitation District, Virginia Beach, Virginia 23455, United States
| | - Charles Bott
- Hampton Roads Sanitation District, Virginia Beach, Virginia 23455, United States
| | - Ameet Pinto
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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3
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Long AE, Pitta D, Hennessy M, Indugu N, Vecchiarelli B, Luethy D, Aceto H, Hurcombe S. Assessment of fecal bacterial viability and diversity in fresh and frozen fecal microbiota transplant (FMT) product in horses. BMC Vet Res 2024; 20:306. [PMID: 38987780 PMCID: PMC11234551 DOI: 10.1186/s12917-024-04166-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 07/01/2024] [Indexed: 07/12/2024] Open
Abstract
BACKGROUND Currently, lack of standardization for fecal microbiota transplantation (FMT) in equine practice has resulted in highly variable techniques, and there is no data on the bacterial metabolic activity or viability of the administered product. The objectives of this study were to compare the total and potentially metabolically active bacterial populations in equine FMT, and assess the effect of different frozen storage times, buffers, and temperatures on an equine FMT product. Fresh feces collected from three healthy adult horses was subjected to different storage methods. This included different preservation solutions (saline plus glycerol or saline only), temperature (-20 °C or -80 °C), and time (fresh, 30, 60, or 90 days). Samples underwent DNA extraction to assess total bacterial populations (both live and dead combined) and RNA extraction followed by reverse transcription to cDNA as a proxy to assess viable bacteria, then 16s rRNA gene amplicon sequencing using the V1-V2 region. RESULTS The largest difference in population indices and taxonomic composition at the genus level was seen when evaluating the results of DNA-based (total) and cDNA-based (potentially metabolically active) extraction method. At the community level, alpha diversity (observed species, Shannon diversity) was significantly decreased in frozen samples for DNA-based analysis (P < 0.05), with less difference seen for cDNA-based sequencing. Using DNA-based analysis, length of storage had a significant impact (P < 0.05) on the bacterial community profiles. For potentially metabolically active populations, storage overall had less of an effect on the bacterial community composition, with a significant effect of buffer (P < 0.05). Individual horse had the most significant effect within both DNA and cDNA bacterial communities. CONCLUSIONS Frozen storage of equine FMT material can preserve potentially metabolically active bacteria of the equine fecal microbiome, with saline plus glycerol preservation more effective than saline alone. Larger studies are needed to determine if these findings apply to other individual horses. The ability to freeze FMT material for use in equine patients could allow for easier clinical use of fecal transplant in horses with disturbances in their intestinal microbiome.
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Affiliation(s)
- Alicia E Long
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania, Kennett Square, PA, USA.
| | - Dipti Pitta
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania, Kennett Square, PA, USA
| | - Meagan Hennessy
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania, Kennett Square, PA, USA
| | - Nagaraju Indugu
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania, Kennett Square, PA, USA
| | - Bonnie Vecchiarelli
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania, Kennett Square, PA, USA
| | - Daniela Luethy
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania, Kennett Square, PA, USA
| | - Helen Aceto
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania, Kennett Square, PA, USA
| | - Samuel Hurcombe
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania, Kennett Square, PA, USA
- Veterinary Innovative Partners, New York, NY, USA
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4
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Lewis JD, Salipante SJ. Development of advanced control material for reverse transcription-mediated bacterial nucleic acid amplification tests. J Clin Microbiol 2024; 62:e0024324. [PMID: 38629844 PMCID: PMC11237385 DOI: 10.1128/jcm.00243-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 03/28/2024] [Indexed: 05/09/2024] Open
Abstract
Detection of bacterial RNA by nucleic acid amplification tests (NAATs), such as reverse transcription PCR (RT-PCR) and reverse transcription loop-mediated isothermal amplification (RT-LAMP), offers distinct advantages over DNA-based methods. However, such assays also present challenges in ascertaining positive and internal control material that can reliably monitor success over all phases of testing (bacterial lysis, nucleic acid recovery, reverse transcription, amplification, and signal detection): since they are unable to distinguish between amplification of bacterial RNA transcripts and the DNA templates that encode them, using intact organisms as controls can inform cell lysis but not successful detection of RNA. We developed a control strategy for RNA-based bacterial NAATs that allows ready discrimination of RNA from DNA templates using self-splicing bacterial introns, such that those nucleic acids ultimately encode different sequences. We engineered two vectors encoding synthetic transgenes based on this principle, one that is active in the Gram-negative bacterium Escherichia coli and one that functions in both E. coli and the Gram-positive organism Staphylococcus aureus. We subsequently designed RT-LAMP assays that either target RNA and DNA from transgenic organisms or target RNA exclusively and demonstrated the specificity of amplification using purified nucleic acids. Using multiplex fluorescent RT-LAMP of heat-lysed specimens, we showed the practicality of deploying such transgenic organisms as an internal control to ascertain sample integrity and assay performance during clinical diagnostic testing. Our approach has broad utility for RNA-based bacterial NAATs, especially point-of-care assays and other applications where nucleic acids are nonspecifically liberated for testing.
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Affiliation(s)
- Janessa D. Lewis
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Stephen J. Salipante
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
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5
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YAMANE M, SAKAI S, HIRAI M, TAKAYAMA M, SASAYAMA K, DOUCHI K, KAWABATA S, IKEDA S, SUGAWARA M. Lot-to-lot variation in the microbiota during the brewing process of kimoto-type Japanese rice wine. BIOSCIENCE OF MICROBIOTA, FOOD AND HEALTH 2024; 43:250-259. [PMID: 38966055 PMCID: PMC11220333 DOI: 10.12938/bmfh.2023-092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/10/2024] [Indexed: 07/06/2024]
Abstract
Kimoto-type Japanese rice wine (sake) has a wide variety of flavors, as the predominant microbes, including lactic acid bacteria (LAB) and nitrate-reducing bacteria, that spontaneously proliferate in the fermentation starter vary depending on the brewery. In this study, we traced the microbiota in four lots of starters manufactured in a newly established brewery and evaluated the lot-to-lot variation and characteristics of the microbiota in the brewery. The results of a 16S ribosomal RNA amplicon analysis showed that the starters brewed in the second brewing year had a more diverse microbiota than those in the first brewing year. Among the LAB predominated at the middle production stage, lactococci, including Leuconostoc spp., were detected in all the lots, while lactobacilli predominated for the first time in the second year. These results suggest that repeated brewing increased microbial diversity and altered the microbial transition pattern in the kimoto-style fermentation starters. Phylogenetic analyses for the LAB isolates from each starter identified Leuconostoc suionicum, Leuconostoc citreum, and Leuconostoc mesenteroides as predominant lactococci as well as a unique lactobacillus in place of Latilactobacillus sakei. We also found that a rice koji-derived Staphylococcus gallinarum with nitrate-reducing activity was generally predominant during the early production stage, suggesting that there was a case in which staphylococci played a role in nitrite production in the starters. These findings are expected to contribute to the understanding of the diversity of microbiota in kimoto-type sake brewing and enable control of the microbiota for consistent sake quality.
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Affiliation(s)
- Momoka YAMANE
- Department of Life and Food Sciences, Obihiro University of
Agriculture and Veterinary Medicine, West 2-11, Inada-cho, Obihiro, Hokkaido 080-8555,
Japan
- Kamikawa Taisetsu Sake Brewery Co., Ltd., Kamikawa-cho,
Hokkaido 078-1761, Japan
| | - Shuntaro SAKAI
- Department of Life and Food Sciences, Obihiro University of
Agriculture and Veterinary Medicine, West 2-11, Inada-cho, Obihiro, Hokkaido 080-8555,
Japan
| | - Miho HIRAI
- Department of Life and Food Sciences, Obihiro University of
Agriculture and Veterinary Medicine, West 2-11, Inada-cho, Obihiro, Hokkaido 080-8555,
Japan
| | - Mizuki TAKAYAMA
- Department of Life and Food Sciences, Obihiro University of
Agriculture and Veterinary Medicine, West 2-11, Inada-cho, Obihiro, Hokkaido 080-8555,
Japan
| | - Kohya SASAYAMA
- Department of Life and Food Sciences, Obihiro University of
Agriculture and Veterinary Medicine, West 2-11, Inada-cho, Obihiro, Hokkaido 080-8555,
Japan
| | - Kazutoshi DOUCHI
- Department of Life and Food Sciences, Obihiro University of
Agriculture and Veterinary Medicine, West 2-11, Inada-cho, Obihiro, Hokkaido 080-8555,
Japan
| | - Shinji KAWABATA
- Department of Life and Food Sciences, Obihiro University of
Agriculture and Veterinary Medicine, West 2-11, Inada-cho, Obihiro, Hokkaido 080-8555,
Japan
- Kamikawa Taisetsu Sake Brewery Co., Ltd., Kamikawa-cho,
Hokkaido 078-1761, Japan
| | - Shinya IKEDA
- Vegetable Crops Research Unit, USDA-ARS, Department of Food
Science, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Masayuki SUGAWARA
- Department of Life and Food Sciences, Obihiro University of
Agriculture and Veterinary Medicine, West 2-11, Inada-cho, Obihiro, Hokkaido 080-8555,
Japan
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6
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Siponen S, Jayaprakash B, Hokajärvi AM, Gomez-Alvarez V, Inkinen J, Ryzhikov I, Räsänen P, Ikonen J, Pursiainen A, Kauppinen A, Kolehmainen M, Paananen J, Torvinen E, Miettinen IT, Pitkänen T. Composition of active bacterial communities and presence of opportunistic pathogens in disinfected and non-disinfected drinking water distribution systems in Finland. WATER RESEARCH 2024; 248:120858. [PMID: 37988808 PMCID: PMC10840642 DOI: 10.1016/j.watres.2023.120858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/02/2023] [Accepted: 11/10/2023] [Indexed: 11/23/2023]
Abstract
Many factors, including microbiome structure and activity in the drinking water distribution system (DWDS), affect the colonization potential of opportunistic pathogens. The present study aims to describe the dynamics of active bacterial communities in DWDS and identify the factors that shape the community structures and activity in the selected DWDSs. Large-volume drinking water and hot water, biofilm, and water meter deposit samples were collected from five DWDSs. Total nucleic acids were extracted, and RNA was further purified and transcribed into its cDNA from a total of 181 water and biofilm samples originating from the DWDS of two surface water supplies (disinfected with UV and chlorine), two artificially recharged groundwater supplies (non-disinfected), and a groundwater supply (disinfected with UV and chlorine). In chlorinated DWDSs, concentrations of <0.02-0.97 mg/l free chlorine were measured. Bacterial communities in the RNA and DNA fractions were analysed using Illumina MiSeq sequencing with primer pair 341F-785R targeted to the 16S rRNA gene. The sequence libraries were analysed using QIIME pipeline, Program R, and MicrobiomeAnalyst. Not all bacterial cells were active based on their 16S rRNA content, and species richness was lower in the RNA fraction (Chao1 mean value 490) than in the DNA fraction (710). Species richness was higher in the two DWDSs distributing non-disinfected artificial groundwater (Chao1 mean values of 990 and 1 000) as compared to the two disinfected DWDSs using surface water (Chao1 mean values 190 and 460) and disinfected DWDS using ground water as source water (170). The difference in community structures between non-disinfected and disinfected water was clear in the beta-diversity analysis. Distance from the waterworks also affected the beta diversity of community structures, especially in disinfected distribution systems. The two most abundant bacteria in the active part of the community (RNA) and total bacterial community (DNA) belonged to the classes Alphaproteobacteria (RNA 28 %, DNA 44 %) and Gammaproteobacteria (RNA 32 %, DNA 30 %). The third most abundant and active bacteria class was Vampirovibrionia (RNA 15 %), whereas in the total community it was Paceibacteria (DNA 11 %). Class Nitrospiria was more abundant and active in both cold and hot water in DWDS that used chloramine disinfection compared to non-chlorinated or chlorine-using DWDSs. Thirty-eight operational taxonomic units (OTU) of Legionella, 30 of Mycobacterium, and 10 of Pseudomonas were detected among the sequences. The (RT)-qPCR confirmed the presence of opportunistic pathogens in the DWDSs studied as Legionella spp. was detected in 85 % (mean value 4.5 × 104 gene copies/100 ml), Mycobacterium spp. in 95 % (mean value 8.3 × 106 gene copies/100 ml), and Pseudomonas spp. in 78 % (mean value 1.6 × 105 gene copies/100 ml) of the water and biofilm samples. Sampling point inside the system (distance from the waterworks and cold/hot system) affected the active bacterial community composition. Chloramine as a chlorination method resulted in a recognizable community composition, with high abundance of bacteria that benefit from the excess presence of nitrogen. The results presented here confirm that each DWDS is unique and that opportunistic pathogens are present even in conditions when water quality is considered excellent.
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Affiliation(s)
- Sallamaari Siponen
- Finnish Institute for Health and Welfare, Department of Health Security, P.O. Box 95, 70701 Kuopio, Finland; University of Eastern Finland, Department of Environmental and Biological Sciences, P.O. Box 1627, 70211 Kuopio, Finland.
| | | | - Anna-Maria Hokajärvi
- Finnish Institute for Health and Welfare, Department of Health Security, P.O. Box 95, 70701 Kuopio, Finland
| | - Vicente Gomez-Alvarez
- U.S. Environmental Protection Agency, Office of Research and Development, 26W. Martin Luther King Dr., Cincinnati, OH 45268, United States
| | - Jenni Inkinen
- University of Eastern Finland, Institute of Biomedicine, P.O. Box 1627, 70211 Kuopio, Finland
| | - Ivan Ryzhikov
- University of Eastern Finland, Department of Environmental and Biological Sciences, P.O. Box 1627, 70211 Kuopio, Finland
| | - Pia Räsänen
- Finnish Institute for Health and Welfare, Department of Health Security, P.O. Box 95, 70701 Kuopio, Finland
| | - Jenni Ikonen
- Finnish Institute for Health and Welfare, Department of Health Security, P.O. Box 95, 70701 Kuopio, Finland
| | - Anna Pursiainen
- Finnish Institute for Health and Welfare, Department of Health Security, P.O. Box 95, 70701 Kuopio, Finland
| | - Ari Kauppinen
- Finnish Institute for Health and Welfare, Department of Health Security, P.O. Box 95, 70701 Kuopio, Finland
| | - Mikko Kolehmainen
- University of Eastern Finland, Department of Environmental and Biological Sciences, P.O. Box 1627, 70211 Kuopio, Finland
| | - Jussi Paananen
- University of Eastern Finland, Institute of Biomedicine, P.O. Box 1627, 70211 Kuopio, Finland
| | - Eila Torvinen
- University of Eastern Finland, Department of Environmental and Biological Sciences, P.O. Box 1627, 70211 Kuopio, Finland
| | - Ilkka T Miettinen
- Finnish Institute for Health and Welfare, Department of Health Security, P.O. Box 95, 70701 Kuopio, Finland
| | - Tarja Pitkänen
- Finnish Institute for Health and Welfare, Department of Health Security, P.O. Box 95, 70701 Kuopio, Finland; University of Helsinki, Faculty of Veterinary Medicine, Department of Food Hygiene and Environmental Health, P.O. Box 66, 00014 Helsinki, Finland
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7
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Shi Q, Chen Z, Yan H, Xu M, Cao KF, Mao Y, Chen X, Hu HY. Identification of significant live bacterial community shifts in different reclaimed waters during ozone and chlorine disinfection. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 896:165199. [PMID: 37391159 DOI: 10.1016/j.scitotenv.2023.165199] [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: 03/11/2023] [Revised: 06/12/2023] [Accepted: 06/27/2023] [Indexed: 07/02/2023]
Abstract
Ozone and chlorine are the most widely used disinfectants for water and wastewater disinfection. They play important role in microbial inactivation but could also pose a considerable selection effect on the microbial community of reclaimed water. Classical culture-based methods that rely on the assessment of conventional bacterial indicators (e.g., coliform bacteria) could hardly reflect the survival of disinfection residual bacteria (DRB) and hidden microbial risks in disinfected effluents. Hence, this study investigated the shifts of live bacterial community during ozone and chlorine disinfection in three reclaimed waters (i.e., two secondary effluents and one tertiary effluent), adopting Illumina Miseq sequencing technology in combination with a viability assay, propidium monoazide (PMA) pretreatment. Notably, statistical analyses of Wilcoxon rank-sum test confirmed the existance of distinct differences in bacterial community structure between samples with or without PMA pretreatment. On the phylum level, Proteobacteria commonly dominated in three undisinfected reclaimed waters, while ozone and chlorine disinfection posed varied effects on its relative abundance among different influents. On the genus level, ozone and chlorine disinfection significantly changed the bacterial composition and dominant species in reclaimed waters. Specifically, the typical DRB identified in ozone disinfected effluents were Pseudomonas, Nitrospira and Dechloromonas, while for chlorine disinfected effluents, Pseudomonas, Legionella, Clostridium, Mycobacterium and Romboutsia were recognized as typical DRB, which call for much attention. The Alpha and Beta diversity analysis results also suggested that different influent compositions greatly affected the bacterial community structure during disinfection processes. Since the experiments in present study were conducted in a short period and the dataset was relatively limited, prolonged experiment under different operational conditions are needed in future to illustrate the potential long-term effects of disinfection on the microbial community structure. The findings of this study could provide insights into microbial safety concern and control after disinfection for sustainable water reclamation and reuse.
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Affiliation(s)
- Qi Shi
- Environmental Simulation and Pollution Control State Key Joint Laboratory, State Environmental Protection Key Laboratory of Microorganism Application and Risk Control (SMARC), School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Zhuo Chen
- Environmental Simulation and Pollution Control State Key Joint Laboratory, State Environmental Protection Key Laboratory of Microorganism Application and Risk Control (SMARC), School of Environment, Tsinghua University, Beijing 100084, PR China; State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China; Beijing Laboratory for Environmental Frontier Technologies, Beijing 100084, PR China.
| | - Han Yan
- Environmental Simulation and Pollution Control State Key Joint Laboratory, State Environmental Protection Key Laboratory of Microorganism Application and Risk Control (SMARC), School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Meiying Xu
- State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Ke-Fan Cao
- Environmental Simulation and Pollution Control State Key Joint Laboratory, State Environmental Protection Key Laboratory of Microorganism Application and Risk Control (SMARC), School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Yu Mao
- Environmental Simulation and Pollution Control State Key Joint Laboratory, State Environmental Protection Key Laboratory of Microorganism Application and Risk Control (SMARC), School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Xiaowen Chen
- Environmental Simulation and Pollution Control State Key Joint Laboratory, State Environmental Protection Key Laboratory of Microorganism Application and Risk Control (SMARC), School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Hong-Ying Hu
- Environmental Simulation and Pollution Control State Key Joint Laboratory, State Environmental Protection Key Laboratory of Microorganism Application and Risk Control (SMARC), School of Environment, Tsinghua University, Beijing 100084, PR China; Beijing Laboratory for Environmental Frontier Technologies, Beijing 100084, PR China; Research Institute for Environmental Innovation (Suzhou), Tsinghua, Jiangsu, Suzhou, 215163, PR China
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8
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McQuillan JS, Alrefaey A, Turner AD, Morrell N, Stoner O, Brown R, Kay S, Cooke S, Bage T. Quantitative Polymerase Chain Reaction for the estimation of toxigenic microalgae abundance in shellfish production waters. HARMFUL ALGAE 2023; 128:102497. [PMID: 37714581 DOI: 10.1016/j.hal.2023.102497] [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: 06/19/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 09/17/2023]
Abstract
Certain species of marine microalgae produce potent biotoxins that pose a risk to human health if contaminated seafood is consumed, particularly filter feeding bivalve shellfish. In regions where this is likely to occur water and seafood produce are regularly monitored for the presence of harmful algal cells and their associated toxins, but the current approach is flawed by a lengthy delay before results are available to local authorities. Quantitative Polymerase Chain Reaction (qPCR) can be used to measure phytoplankton DNA sequences in a shorter timeframe, however it is not currently used in official testing practices. In this study, samples were collected almost weekly over six months from three sites within a known HAB hotspot, St Austell Bay in Cornwall, England. The abundance of algal cells in water was measured using microscopy and qPCR, and lipophilic toxins were quantified in mussel flesh using LC-MS/MS, focusing on the okadaic acid group. An increase in algal cell abundance occurred alongside an increase in the concentration of okadaic acid group toxins in mussel tissue at all three study sites, during September and October 2021. This event corresponded to an increase in the measured levels of Dinophysis accuminata DNA, measured using qPCR. In the following spring, the qPCR detected an increase in D. accuminata DNA levels in water samples, which was not detected by microscopy. Harmful algal species belonging to Alexandrium spp. and Pseudo-nitzschia spp. were also measured using qPCR, finding a similar increase in abundance in Autumn and Spring. The results are discussed with consideration of the potential merits and limitations of the qPCR technique versus conventional microscopy analysis, and its potential future role in phytoplankton surveillance under the Official Controls Regulations pertaining to shellfish.
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Affiliation(s)
- Jonathan S McQuillan
- Ocean Technology and Engineering, National Oceanography Centre, European Way, Southampton, SO14 3ZH, United Kingdom.
| | - Ahmed Alrefaey
- Ocean Technology and Engineering, National Oceanography Centre, European Way, Southampton, SO14 3ZH, United Kingdom
| | - Andrew D Turner
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, The Nothe, Weymouth, Dorset, DT4 8UB, United Kingdom
| | - Nadine Morrell
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, The Nothe, Weymouth, Dorset, DT4 8UB, United Kingdom
| | - Oliver Stoner
- School of Mathematics and Statistics, University of Glasgow, Glasgow, G12 8TA, United Kingdom
| | - Ross Brown
- Faculty of Health and Life Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, Devon, EX4 4QD, United Kingdom
| | - Suzanne Kay
- Faculty of Health and Life Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, Devon, EX4 4QD, United Kingdom
| | - Simon Cooke
- Cornwall Port Health Authority (Cornwall Council), The Docks, Falmouth, TR11 4NR, United Kingdom
| | - Timothy Bage
- Cornwall Port Health Authority (Cornwall Council), The Docks, Falmouth, TR11 4NR, United Kingdom
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9
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Buelow E, Dauga C, Carrion C, Mathé-Hubert H, Achaibou S, Gaschet M, Jové T, Chesneau O, Kennedy SP, Ploy MC, Da Re S, Dagot C. Hospital and urban wastewaters shape the matrix and active resistome of environmental biofilms. WATER RESEARCH 2023; 244:120408. [PMID: 37678036 DOI: 10.1016/j.watres.2023.120408] [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: 03/12/2023] [Revised: 07/22/2023] [Accepted: 07/24/2023] [Indexed: 09/09/2023]
Abstract
Understanding the dynamics of antibiotic resistance gene (ARG) transfer and dissemination in natural environments remains challenging. Biofilms play a crucial role in bacterial survival and antimicrobial resistance (AMR) dissemination in natural environments, particularly in aquatic systems. This study focused on hospital and urban wastewater (WW) biofilms to investigate the potential for ARG dissemination through mobile genetic elements (MGEs). The analysis included assessing the biofilm extracellular polymeric substances (EPS), microbiota composition as well as metatranscriptomic profiling of the resistome and mobilome. We produced both in vitro and in situ biofilms and performed phenotypic and genomic analyses. In the in vitro setup, untreated urban and hospital WW was used to establish biofilm reactors, with ciprofloxacin added as a selective agent at minimal selective concentration. In the in situ setup, biofilms were developed directly in hospital and urban WW pipes. We first showed that a) the composition of EPS differed depending on the growth environment (in situ and in vitro) and the sampling origin (hospital vs urban WW) and that b) ciprofloxacin impacted the composition of the EPS. The metatranscriptomic approach showed that a) expression of several ARGs and MGEs increased upon adding ciprofloxacin for biofilms from hospital WW only and b) that the abundance and type of plasmids that carried individual or multiple ARGs varied depending on the WW origins of the biofilms. When the same plasmids were present in both, urban and hospital WW biofilms, they carried different ARGs. We showed that hospital and urban wastewaters shaped the structure and active resistome of environmental biofilms, and we confirmed that hospital WW is an important hot spot for the dissemination and selection of antimicrobial resistance. Our study provides a comprehensive assessment of WW biofilms as crucial hotspots for ARG transfer. Hospital WW biofilms exhibited distinct characteristics, including higher eDNA abundance and expression levels of ARGs and MGEs, highlighting their role in antimicrobial resistance dissemination. These findings emphasize the importance of understanding the structural, ecological, functional, and genetic organization of biofilms in anthropized environments and their contribution to antibiotic resistance dynamics.
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Affiliation(s)
- Elena Buelow
- INSERM, CHU Limoges, RESINFIT, U1092, Univ. Limoges, F-87000, Limoges, France; CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, Univ. Grenoble Alpes, 38000, Grenoble, France.
| | - Catherine Dauga
- Institut Pasteur, Département Biologie Computationnelle, Université Paris Cité, F-75015, Paris, France; Biomics Pole, CITECH, Institut Pasteur, F-75015, Paris, France
| | - Claire Carrion
- CNRS, INSERM, CHU Limoges, BISCEm, UAR 2015, US 42, Univ. Limoges, F-87000, Limoges, France
| | - Hugo Mathé-Hubert
- CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, Univ. Grenoble Alpes, 38000, Grenoble, France
| | - Sophia Achaibou
- Biomics Pole, CITECH, Institut Pasteur, F-75015, Paris, France
| | - Margaux Gaschet
- INSERM, CHU Limoges, RESINFIT, U1092, Univ. Limoges, F-87000, Limoges, France
| | - Thomas Jové
- INSERM, CHU Limoges, RESINFIT, U1092, Univ. Limoges, F-87000, Limoges, France
| | - Olivier Chesneau
- Collection de l'Institut Pasteur (CIP), Microbiology Department, Institut Pasteur, Paris, 75015, France
| | - Sean P Kennedy
- Institut Pasteur, Département Biologie Computationnelle, Université Paris Cité, F-75015, Paris, France
| | - Marie-Cecile Ploy
- INSERM, CHU Limoges, RESINFIT, U1092, Univ. Limoges, F-87000, Limoges, France
| | - Sandra Da Re
- INSERM, CHU Limoges, RESINFIT, U1092, Univ. Limoges, F-87000, Limoges, France
| | - Christophe Dagot
- INSERM, CHU Limoges, RESINFIT, U1092, Univ. Limoges, F-87000, Limoges, France
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10
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Green SJ, Torok T, Allen JE, Eloe-Fadrosh E, Jackson SA, Jiang SC, Levine SS, Levy S, Schriml LM, Thomas WK, Wood JM, Tighe SW. Metagenomic Methods for Addressing NASA's Planetary Protection Policy Requirements on Future Missions: A Workshop Report. ASTROBIOLOGY 2023; 23:897-907. [PMID: 37102710 PMCID: PMC10457625 DOI: 10.1089/ast.2022.0044] [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: 04/10/2022] [Accepted: 01/23/2023] [Indexed: 06/19/2023]
Abstract
Molecular biology methods and technologies have advanced substantially over the past decade. These new molecular methods should be incorporated among the standard tools of planetary protection (PP) and could be validated for incorporation by 2026. To address the feasibility of applying modern molecular techniques to such an application, NASA conducted a technology workshop with private industry partners, academics, and government agency stakeholders, along with NASA staff and contractors. The technical discussions and presentations of the Multi-Mission Metagenomics Technology Development Workshop focused on modernizing and supplementing the current PP assays. The goals of the workshop were to assess the state of metagenomics and other advanced molecular techniques in the context of providing a validated framework to supplement the bacterial endospore-based NASA Standard Assay and to identify knowledge and technology gaps. In particular, workshop participants were tasked with discussing metagenomics as a stand-alone technology to provide rapid and comprehensive analysis of total nucleic acids and viable microorganisms on spacecraft surfaces, thereby allowing for the development of tailored and cost-effective microbial reduction plans for each hardware item on a spacecraft. Workshop participants recommended metagenomics approaches as the only data source that can adequately feed into quantitative microbial risk assessment models for evaluating the risk of forward (exploring extraterrestrial planet) and back (Earth harmful biological) contamination. Participants were unanimous that a metagenomics workflow, in tandem with rapid targeted quantitative (digital) PCR, represents a revolutionary advance over existing methods for the assessment of microbial bioburden on spacecraft surfaces. The workshop highlighted low biomass sampling, reagent contamination, and inconsistent bioinformatics data analysis as key areas for technology development. Finally, it was concluded that implementing metagenomics as an additional workflow for addressing concerns of NASA's robotic mission will represent a dramatic improvement in technology advancement for PP and will benefit future missions where mission success is affected by backward and forward contamination.
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Affiliation(s)
- Stefan J. Green
- Genomics and Microbiome Core Facility, Rush University Medical Center, Chicago, Illinois, USA
| | - Tamas Torok
- Ecology Department, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | - Emiley Eloe-Fadrosh
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Scott A. Jackson
- National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Sunny C. Jiang
- Department of Civil and Environmental Engineering, University of California, Irvine, California, USA
| | - Stuart S. Levine
- MIT BioMicro Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Lynn M. Schriml
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - W. Kelley Thomas
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire, USA
| | - Jason M. Wood
- Research Informatics Core, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Scott W. Tighe
- Vermont Integrative Genomics, University of Vermont, Burlington, Vermont, USA
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11
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Hugon AM, Golos TG. Non-human primate models for understanding the impact of the microbiome on pregnancy and the female reproductive tract†. Biol Reprod 2023; 109:1-16. [PMID: 37040316 PMCID: PMC10344604 DOI: 10.1093/biolre/ioad042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 04/06/2023] [Accepted: 04/06/2023] [Indexed: 04/12/2023] Open
Abstract
The microbiome has been shown, or implicated to be involved, in multiple facets of human health and disease, including not only gastrointestinal health but also metabolism, immunity, and neurology. Although the predominant focus of microbiome research has been on the gut, other microbial communities such as the vaginal or cervical microbiome are likely involved in physiological homeostasis. Emerging studies also aim to understand the role of different microbial niches, such as the endometrial or placental microbial communities, on the physiology and pathophysiology of reproduction, including their impact on reproductive success and the etiology of adverse pregnancy outcomes (APOs). The study of the microbiome during pregnancy, specifically how changes in maternal microbial communities can lead to dysfunction and disease, can advance the understanding of reproductive health and the etiology of APOs. In this review, we will discuss the current state of non-human primate (NHP) reproductive microbiome research, highlight the progress with NHP models of reproduction, and the diagnostic potential of microbial alterations in a clinical setting to promote pregnancy health. NHP reproductive biology studies have the potential to expand the knowledge and understanding of female reproductive tract microbial communities and host-microbe or microbe-microbe interactions associated with reproductive health through sequencing and analysis. Furthermore, in this review, we aim to demonstrate that macaques are uniquely suited as high-fidelity models of human female reproductive pathology.
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Affiliation(s)
- Anna Marie Hugon
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Thaddeus G Golos
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI, USA
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI, USA
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12
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Pavić D, Grbin D, Blagajac A, Ćurko J, Fiket Ž, Bielen A. Impact of nutrients and trace elements on freshwater microbial communities in Croatia: identifying bacterial bioindicator taxa. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023:10.1007/s11356-023-28179-4. [PMID: 37328727 DOI: 10.1007/s11356-023-28179-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 06/05/2023] [Indexed: 06/18/2023]
Abstract
Since aquatic microbial communities promptly respond to environmental changes, it is now evident that they can complement traditional taxa such as fish, macroinvertebrates and algae as bioindicators of water quality. The aim of this study was to correlate the physico-chemical parameters of water with the microbial community structure and the occurrence of putative bioindicator taxa. Thirty-five water samples were collected throughout Croatia and their physico-chemical parameters, including the concentration of trace elements using the high-resolution inductively coupled plasma mass spectrometry (HR-ICP-MS), and the composition of the microbial communities by high-throughput sequencing of the 16S rRNA marker gene, were analysed in parallel. Partial least squares regression (PLS-R) modelling revealed that a number of microbial taxa were positively correlated with some of the water parameters. For example, some taxa from the phylum Proteobacteria were positively correlated with the ion content of the water (e.g. Erythrobacter, Rhodobacteraceae, Alteromonadaceae), while some Firmicutes taxa, such as the well-known faecal indicators Enterococcus and Clostridium, were correlated with nutrient content (ammonium and total phosphorus). Among the trace elements, uranium was positively correlated with a highest number of microbial taxa. The results obtained will aid in development of protocols for eDNA-based biological assessment of water quality.
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Affiliation(s)
- Dora Pavić
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Dorotea Grbin
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Amalija Blagajac
- Department of Food Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Josip Ćurko
- Department of Food Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Željka Fiket
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Zagreb, Croatia
| | - Ana Bielen
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia.
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13
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Viitanen SJ, Tuomisto L, Salonen N, Eskola K, Kegler K. Escherichia coli-associated follicular cystitis in dogs: Clinical and pathologic characterization. J Vet Intern Med 2023; 37:1059-1066. [PMID: 37154220 PMCID: PMC10229364 DOI: 10.1111/jvim.16719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 04/07/2023] [Indexed: 05/10/2023] Open
Abstract
BACKGROUND Follicular cystitis is an uncommon inflammatory change in the urinary bladder wall characterized by the formation of tertiary lymphoid structures (TLSs) in the submucosa. OBJECTIVES To characterize clinical and pathologic features of follicular cystitis in dogs and to explore in situ distribution and possible role of Escherichia coli as an associated cause. ANIMALS Eight dogs diagnosed with follicular cystitis and 2 control dogs. METHODS Retrospective descriptive study. Dogs diagnosed with follicular cystitis (macroscopic follicular lesions in the urinary bladder mucosa and histopathologic detection of TLSs in bladder wall biopsies) were identified from medical records. Paraffin embedded bladder wall biopsies were subject to in situ hybridization for E. coli 16SrRNA identification. RESULTS Follicular cystitis was diagnosed in large breed (median weight 24.9 kg, interquartile range [IQR] 18.8-35.4 kg) female dogs with a history of chronic recurrent urinary tract infections (UTIs; median duration of clinical signs 7 months, IQR 3-17 months; median number of previous UTIs 5, IQR 4-6). Positive E. coli 16SrRNA signal was detected within developing, immature and mature TLSs in 7/8 dogs, through submucosal stroma in 8/8 dogs and within the urothelium in 3/8 dogs. CONCLUSIONS AND CLINICAL IMPORTANCE Chronic inflammation associated with an intramural E. coli infection in the urinary bladder wall represents a possible triggering factor for the development of follicular cystitis.
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Affiliation(s)
- Sanna J Viitanen
- Department of Equine and Small Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Laura Tuomisto
- Department of Veterinary Biosciences, Pathology and Parasitology Unit, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Nina Salonen
- Department of Equine and Small Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Katariina Eskola
- Department of Equine and Small Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Kristel Kegler
- Department of Veterinary Biosciences, Pathology and Parasitology Unit, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
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14
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Shekarriz E, Chen J, Xu Z, Liu H. Disentangling the Functional Role of Fungi in Cold Seep Sediment. Microbiol Spectr 2023; 11:e0197822. [PMID: 36912690 PMCID: PMC10100914 DOI: 10.1128/spectrum.01978-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 12/22/2022] [Indexed: 03/14/2023] Open
Abstract
Cold seeps are biological oases of the deep sea fueled by methane, sulfates, nitrates, and other inorganic sources of energy. Chemolithoautotrophic bacteria and archaea dominate seep sediment, and their diversity and biogeochemical functions are well established. Fungi are likewise diverse, metabolically versatile, and known for their ability to capture and oxidize methane. Still, no study has ever explored the functional role of the mycobiota in the cold seep biome. To assess the complex role of fungi and fill in the gaps, we performed network analysis on 147 samples to disentangle fungal-prokaryotic interactions (fungal 18S and prokaryotic 16S) in the Haima cold seep region. We demonstrated that fungi are central species with high connectivity at the epicenter of prokaryotic networks, reduce their random-attack vulnerability by 60%, and enhance information transfer efficiency by 15%. We then scavenged a global metagenomic and metatranscriptomic data set from 10 cold seep regions for fungal genes of interest (hydrophobins, cytochrome P450s, and ligninolytic family of enzymes); this is the first study to report active transcription of 2,500+ fungal genes in the cold seep sediment. The genera Fusarium and Moniliella were of notable importance and directly correlated with high methane abundance in the sulfate-methane transition zone (SMTZ), likely due to their ability to degrade and solubilize methane and oils. Overall, our results highlight the essential yet overlooked contribution of fungi to cold seep biological networks and the role of fungi in regulating cold seep biogeochemistry. IMPORTANCE The challenges we face when analyzing eukaryotic metagenomic and metatranscriptomic data sets have hindered our understanding of cold seep fungi and microbial eukaryotes. This fact does not make the mycobiota any less critical in mediating cold seep biogeochemistry. On the contrary, many fungal genera can oxidize and solubilize methane, produce methane, and play a unique role in nutrient recycling via saprotrophic enzymatic activity. In this study, we used network analysis to uncover key fungal-prokaryotic interactions that can mediate methane biogeochemistry and metagenomics and metatranscriptomics to report that fungi are transcriptionally active in the cold seep sediment. With concerns over rising methane levels and cold seeps being a pivotal source of global methane input, our holistic understanding of methane biogeochemistry with all domains of life is essential. We ultimately encourage scientists to utilize state-of-the-art tools and multifaceted approaches to uncover the role of microeukaryotic organisms in understudied systems.
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Affiliation(s)
- Erfan Shekarriz
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
| | - Jiawei Chen
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
| | - Zhimeng Xu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
| | - Hongbin Liu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, China
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15
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Lousada MB, Edelkamp J, Lachnit T, Fehrholz M, Jimenez F, Paus R. Laser capture microdissection as a method for investigating the human hair follicle microbiome reveals region-specific differences in the bacteriome profile. BMC Res Notes 2023; 16:29. [PMID: 36879274 PMCID: PMC9987047 DOI: 10.1186/s13104-023-06302-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 02/20/2023] [Indexed: 03/08/2023] Open
Abstract
OBJECTIVE Human hair follicles (HFs) are populated by a rich and diverse microbiome, traditionally evaluated by methods that inadvertently sample the skin microbiome and/or miss microbiota located in deeper HF regions. Thereby, these methods capture the human HF microbiome in a skewed and incomplete manner. This pilot study aimed to use laser-capture microdissection of human scalp HFs, coupled with 16S rRNA gene sequencing to sample the HF microbiome and overcome these methodological limitations. RESULTS HFs were laser-capture microdissected (LCM) into three anatomically distinct regions. All main known core HF bacterial colonisers, including Cutibacterium, Corynebacterium and Staphylococcus, were identified, in all three HF regions. Interestingly, region-specific variations in α-diversity and microbial abundance of the core microbiome genera and Reyranella were identified, suggestive of variations in microbiologically relevant microenvironment characteristics. This pilot study therefore shows that LCM-coupled with metagenomics is a powerful tool for analysing the microbiome of defined biological niches. Refining and complementing this method with broader metagenomic techniques will facilitate the mapping of dysbiotic events associated with HF diseases and targeted therapeutic interventions.
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Affiliation(s)
- Marta B Lousada
- Monasterium Laboratory, Skin&Hair Research, Muenster, Germany. .,Zoological Institute, Christian-Albrechts University Kiel, Kiel, Germany.
| | - J Edelkamp
- Monasterium Laboratory, Skin&Hair Research, Muenster, Germany
| | - T Lachnit
- Zoological Institute, Christian-Albrechts University Kiel, Kiel, Germany
| | - M Fehrholz
- Monasterium Laboratory, Skin&Hair Research, Muenster, Germany
| | - F Jimenez
- Mediteknia Skin & Hair Lab, Las Palmas de Gran Canaria, Spain.,Medical Pathology Group, IUIBS, Universidad de Las Palmas de Gran Canaria, Las Palmas, Spain
| | - R Paus
- Monasterium Laboratory, Skin&Hair Research, Muenster, Germany.,Dr Phillip Frost Department of Dermatology & Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, USA.,CUTANEON Skin & Hair Innovations, Hamburg, Germany
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16
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Rovira P, Brugnini G, Rodriguez J, Cabrera MC, Saadoun A, de Souza G, Luzardo S, Rufo C. Microbiological Changes during Long-Storage of Beef Meat under Different Temperature and Vacuum-Packaging Conditions. Foods 2023; 12:foods12040694. [PMID: 36832769 PMCID: PMC9955083 DOI: 10.3390/foods12040694] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/26/2023] [Accepted: 01/30/2023] [Indexed: 02/09/2023] Open
Abstract
We evaluated a combination of two temperatures and two packaging materials for long-term storage of vacuum-packaged (VP) beef striploins. Microbial populations and microbiome composition were monitored during refrigerated storage (120 days between 0-1.5 °C) and refrigerated-then-frozen storage (28 days between 0-1.5 °C then 92 days at -20 °C) under low-O2 permeability VP and high-O2 permeability VP with an antimicrobial (VPAM). Pseudomonas (PSE) and Enterobacteriaceae (EB) counts in VPAM samples were significantly higher (p < 0.05) than in VP samples at 28, 45, 90, and 120 days of storage. Microbiome data showed that bacteria of the genera Serratia and Brochothrix were more abundant in VPAM samples at 120 days, while lactic acid bacteria (LAB) dominated in VP samples. Frozen temperatures inhibited microbial growth and maintained a relatively stable microbiome. Refrigerated and frozen VPAM samples showed the greatest difference in the predicted metabolic functions at the end of storage driven by the microbiome composition, dominated by PSE and LAB, respectively. Although no signs of visible meat deterioration were observed in any sample, this study suggests that VP meat refrigerated and then frozen achieved better microbiological indicators at the end of the storage period.
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Affiliation(s)
- Pablo Rovira
- Sistema Ganadero Extensivo y Arroz-Ganadería, Instituto Nacional de Investigación Agropecuaria (INIA), Ruta 8 km 281, Treinta y Tres 33000, Uruguay
| | - Giannina Brugnini
- Instituto Polo Tecnológico de Pando, Facultad de Química, Universidad de la República, By Pass de Pando y Ruta 8, Pando 91000, Uruguay
| | - Jesica Rodriguez
- Instituto Polo Tecnológico de Pando, Facultad de Química, Universidad de la República, By Pass de Pando y Ruta 8, Pando 91000, Uruguay
| | - María C. Cabrera
- Facultad de Agronomía Udelar, Avenida Garzón 861, Montevideo 12900, Uruguay
- Facultad de Ciencias, Udelar, Calle Iguá 4225, Montevideo 11400, Uruguay
| | - Ali Saadoun
- Facultad de Agronomía Udelar, Avenida Garzón 861, Montevideo 12900, Uruguay
- Facultad de Ciencias, Udelar, Calle Iguá 4225, Montevideo 11400, Uruguay
| | - Guillermo de Souza
- Sistema Ganadero Extensivo y Agroalimentos, Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental INIA Tacuarembó, Ruta 5 km 386, Tacuarembó 45000, Uruguay
| | - Santiago Luzardo
- Sistema Ganadero Extensivo y Agroalimentos, Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental INIA Tacuarembó, Ruta 5 km 386, Tacuarembó 45000, Uruguay
- Correspondence: (S.L.); (C.R.)
| | - Caterina Rufo
- Instituto Polo Tecnológico de Pando, Facultad de Química, Universidad de la República, By Pass de Pando y Ruta 8, Pando 91000, Uruguay
- Correspondence: (S.L.); (C.R.)
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17
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Messman RD, Lemley CO. Bovine neonatal microbiome origins: a review of proposed microbial community presence from conception to colostrum. Transl Anim Sci 2023; 7:txad057. [PMID: 37334245 PMCID: PMC10276551 DOI: 10.1093/tas/txad057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/24/2023] [Indexed: 06/20/2023] Open
Abstract
In recent years, there has been an influx of research evaluating the roles of the reproductive tract microbiota in modulating reproductive performance. These efforts have resulted in a breadth of research exploring the bovine reproductive tract microbiota. The female reproductive tract microbiota has been characterized during the estrus cycle, at timed artificial insemination, during gestation, and postpartum. Additionally, there are recently published studies investigating in-utero inoculation of the bovine fetus. However, critical review of the literature to understand how the microbial shifts during a dam's lifecycle could impact neonatal outcomes is limited. This review demonstrates a consistency at the phyla level throughout both the maternal, paternal, and neonatal microbiomes. Moreover, this review challenges the current gestational inoculation hypothesis and suggests instead a maturation of the resident uterine microbiota throughout gestation to parturition. Recent literature is indicative of microbial composition influencing metabolomic parameters that have developmental programming effects in feed utilization and metabolic performance later in life. Thus, this review enumerates the potential origins of neonatal microbial inoculation from conception, through gestation, parturition, and colostrum consumption while introducing clear paucities where future research is needed to better understand the ramifications of the reproductive microbiome on neonates.
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Affiliation(s)
- Riley D Messman
- Department of Animal and Dairy Sciences, Mississippi State University, Mississippi State, MS 39762, USA
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18
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Ismail AA, Al-Hajji L, Azad I, Al-Yaqoot A, Habibi N, Alseidi M, Ahmed S. Self-cleaning application of mesoporous ZnO, TiO2 and Fe2O3 films with the accommodation of silver nanoparticles for antibacterial activity. J Taiwan Inst Chem Eng 2023. [DOI: 10.1016/j.jtice.2022.104627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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19
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Coker J, Zhalnina K, Marotz C, Thiruppathy D, Tjuanta M, D’Elia G, Hailu R, Mahosky T, Rowan M, Northen TR, Zengler K. A Reproducible and Tunable Synthetic Soil Microbial Community Provides New Insights into Microbial Ecology. mSystems 2022; 7:e0095122. [PMID: 36472419 PMCID: PMC9765266 DOI: 10.1128/msystems.00951-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 10/26/2022] [Indexed: 12/12/2022] Open
Abstract
Microbial soil communities form commensal relationships with plants to promote the growth of both parties. The optimization of plant-microbe interactions to advance sustainable agriculture is an important field in agricultural research. However, investigation in this field is hindered by a lack of model microbial community systems and efficient approaches for building these communities. Two key challenges in developing standardized model communities are maintaining community diversity over time and storing/resuscitating these communities after cryopreservation, especially considering the different growth rates of organisms. Here, a model synthetic community (SynCom) of 16 soil microorganisms commonly found in the rhizosphere of diverse plant species, isolated from soil surrounding a single switchgrass plant, has been developed and optimized for in vitro experiments. The model soil community grows reproducibly between replicates and experiments, with a high community α-diversity being achieved through growth in low-nutrient media and through the adjustment of the starting composition ratios for the growth of individual organisms. The community can additionally be cryopreserved with glycerol, allowing for easy replication and dissemination of this in vitro system. Furthermore, the SynCom also grows reproducibly in fabricated ecosystem devices (EcoFABs), demonstrating the application of this community to an existing in vitro plant-microbe system. EcoFABs allow reproducible research in model plant systems, offering the precise control of environmental conditions and the easy measurement of plant microbe metrics. Our results demonstrate the generation of a stable and diverse microbial SynCom for the rhizosphere that can be used with EcoFAB devices and can be shared between research groups for maximum reproducibility. IMPORTANCE Microbes associate with plants in distinct soil communities to the benefit of both the soil microbes and the plants. Interactions between plants and these microbes can improve plant growth and health and are therefore a field of study in sustainable agricultural research. In this study, a model community of 16 soil bacteria has been developed to further the reproducible study of plant-soil microbe interactions. The preservation of the microbial community has been optimized for dissemination to other research settings. Overall, this work will advance soil microbe research through the optimization of a robust, reproducible model community.
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Affiliation(s)
- Joanna Coker
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Kateryna Zhalnina
- Environmental Genomics and Systems Biology Division, Berkeley Lab, Berkeley, California, USA
| | - Clarisse Marotz
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Deepan Thiruppathy
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Megan Tjuanta
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Gavin D’Elia
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Rodas Hailu
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Talon Mahosky
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Meagan Rowan
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Trent R. Northen
- Environmental Genomics and Systems Biology Division, Berkeley Lab, Berkeley, California, USA
- The DOE Joint Genome Institute, Berkeley Lab, Berkeley, California, USA
| | - Karsten Zengler
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
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20
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Nasal microbiome disruption and recovery after mupirocin treatment in Staphylococcus aureus carriers and noncarriers. Sci Rep 2022; 12:19738. [PMID: 36396730 PMCID: PMC9671894 DOI: 10.1038/s41598-022-21453-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 09/27/2022] [Indexed: 11/18/2022] Open
Abstract
Nasal decolonization procedures against the opportunistic pathogen Staphylococcus aureus rely on topical antimicrobial drug usage, whose impact on the nasal microbiota is poorly understood. We examined this impact in healthy S. aureus carriers and noncarriers. This is a prospective interventional cohort study of 8 S. aureus carriers and 8 noncarriers treated with nasal mupirocin and chlorhexidine baths. Sequential nasal swabs were taken over 6 months. S. aureus was detected by quantitative culture and genotyped using spa typing. RNA-based 16S species-level metabarcoding was used to assess the living microbial diversity. The species Dolosigranulum pigrum, Moraxella nonliquefaciens and Corynebacterium propinquum correlated negatively with S. aureus carriage. Mupirocin treatment effectively eliminated S. aureus, D. pigrum and M. nonliquefaciens, but not corynebacteria. S. aureus recolonization in carriers occurred more rapidly than recolonization by the dominant species in noncarriers (median 3 vs. 6 months, respectively). Most recolonizing S. aureus isolates had the same spa type as the initial isolate. The impact of mupirocin-chlorhexidine treatment on the nasal microbiota was still detectable after 6 months. S. aureus recolonization predated microbiota recovery, emphasizing the strong adaptation of this pathogen to the nasal niche and the transient efficacy of the decolonization procedure.
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21
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Yap M, O’Sullivan O, O’Toole PW, Cotter PD. Development of sequencing-based methodologies to distinguish viable from non-viable cells in a bovine milk matrix: A pilot study. Front Microbiol 2022; 13:1036643. [PMID: 36466696 PMCID: PMC9713316 DOI: 10.3389/fmicb.2022.1036643] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 10/28/2022] [Indexed: 04/22/2024] Open
Abstract
Although high-throughput DNA sequencing-based methods have been of great value for determining the composition of microbial communities in various environments, there is the potential for inaccuracies arising from the sequencing of DNA from dead microorganisms. In this pilot study, we compared different sequencing-based methods to assess their relative accuracy with respect to distinguishing between viable and non-viable cells, using a live and heat-inactivated model community spiked into bovine milk. The methods used were shotgun metagenomics with and without propidium monoazide (PMA) treatment, RNA-based 16S rRNA sequencing and metatranscriptomics. The results showed that methods were generally accurate, though significant differences were found depending on the library types and sequencing technologies. Different molecular targets were the basis for variations in the results generated using different library types, while differences in the derived composition data from Oxford Nanopore Technologies-and Illumina-based sequencing likely reflect a combination of different sequencing depths, error rates and bioinformatics pipelines. Although PMA was successfully applied in this study, further optimisation is required before it can be applied in a more universal context for complex microbiomes. Overall, these methods show promise and represent another important step towards the ultimate establishment of approaches that can be applied to accurately identify live microorganisms in milk and other food niches.
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Affiliation(s)
- Min Yap
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Orla O’Sullivan
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Paul W. O’Toole
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- APC Microbiome Ireland, Cork, Ireland
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22
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Srinivas M, O’Sullivan O, Cotter PD, van Sinderen D, Kenny JG. The Application of Metagenomics to Study Microbial Communities and Develop Desirable Traits in Fermented Foods. Foods 2022; 11:3297. [PMCID: PMC9601669 DOI: 10.3390/foods11203297] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The microbial communities present within fermented foods are diverse and dynamic, producing a variety of metabolites responsible for the fermentation processes, imparting characteristic organoleptic qualities and health-promoting traits, and maintaining microbiological safety of fermented foods. In this context, it is crucial to study these microbial communities to characterise fermented foods and the production processes involved. High Throughput Sequencing (HTS)-based methods such as metagenomics enable microbial community studies through amplicon and shotgun sequencing approaches. As the field constantly develops, sequencing technologies are becoming more accessible, affordable and accurate with a further shift from short read to long read sequencing being observed. Metagenomics is enjoying wide-spread application in fermented food studies and in recent years is also being employed in concert with synthetic biology techniques to help tackle problems with the large amounts of waste generated in the food sector. This review presents an introduction to current sequencing technologies and the benefits of their application in fermented foods.
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Affiliation(s)
- Meghana Srinivas
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, P61 C996 Cork, Ireland
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- School of Microbiology, University College Cork, T12 CY82 Cork, Ireland
| | - Orla O’Sullivan
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, P61 C996 Cork, Ireland
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- VistaMilk SFI Research Centre, Fermoy, P61 C996 Cork, Ireland
| | - Paul D. Cotter
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, P61 C996 Cork, Ireland
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- VistaMilk SFI Research Centre, Fermoy, P61 C996 Cork, Ireland
| | - Douwe van Sinderen
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- School of Microbiology, University College Cork, T12 CY82 Cork, Ireland
| | - John G. Kenny
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, P61 C996 Cork, Ireland
- APC Microbiome Ireland, University College Cork, T12 CY82 Cork, Ireland
- VistaMilk SFI Research Centre, Fermoy, P61 C996 Cork, Ireland
- Correspondence:
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23
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Woodruff KL, Hummel GL, Austin KJ, Lake SL, Cunningham-Hollinger HC. Calf rumen microbiome from birth to weaning and shared microbial properties to the maternal rumen microbiome. J Anim Sci 2022; 100:skac264. [PMID: 35986918 PMCID: PMC9576027 DOI: 10.1093/jas/skac264] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/18/2022] [Indexed: 07/25/2023] Open
Abstract
Optimization of host performance in cattle may be achieved through programming of the rumen microbiome. Thus, understanding maternal influences on the development of the calf rumen microbiome is critical. We hypothesized that there exists a shared microbial profile between the cow and calf rumen microbiomes from birth through weaning. Specifically, our objective was to relate the calf's meconium and rumen fluid microbiomes in early life to that of the cow rumen fluid prior to parturition and at weaning. Rumen fluid was collected from multiparous Angus crossbred cows (n = 10) prior to parturition and at weaning. Immediately following the parturition, meconium and rumen fluid were collected from the calf. Rumen fluid was collected again from the calf on day 2, day 28, and at weaning. The rumen fluid microbial profile and subsequent volatile fatty acid (VFA) profile were characterized using 16S rRNA sequencing and gas liquid chromatography, respectively. Microbial data was analyzed using QIIME2 and the GLM procedure of SAS was used to analyze the VFA profile. Alpha diversity was similar in the early gut microbiome (meconium, rumen fluid at birth and day 2; q ≥ 0.12) and between the cow and calf at weaning (q ≥ 0.06). Microbial composition, determined by beta diversity, differed in the early rumen microbiome (rumen fluid at birth, day 2, and day 28; q ≤ 0.04), and VFA profiles complimented these results. There were similarities in composition between meconium, rumen fluid at birth, and rumen fluid from the cow at weaning (q ≥ 0.09). These data indicate successive development of the rumen microbiome and stabilization over time. Similarities between meconium and rumen fluid at birth potentially indicates in utero colonization of the calf gastrointestinal tract. Similarities in composition between the early calf rumen microbiome and the cow at weaning prompt an interesting comparison and area for future consideration in terms of identifying at what stage of gestation might colonization begin. Overall, this study provides insight into similarities between the cow and calf microbiomes and may be helpful in developing hypotheses for the pathway of colonization and programming potential in the early gut.
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Affiliation(s)
- Kelly L Woodruff
- University of Wyoming, Department of Animal Science, Laramie, WY 82071, USA
| | | | - Kathleen J Austin
- University of Wyoming, Department of Animal Science, Laramie, WY 82071, USA
| | - Scott L Lake
- University of Wyoming, Laramie Research and Extension Center, Laramie, WY 82070, USA
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24
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Trinh KTL, Lee NY. Recent Methods for the Viability Assessment of Bacterial Pathogens: Advances, Challenges, and Future Perspectives. Pathogens 2022; 11:pathogens11091057. [PMID: 36145489 PMCID: PMC9500772 DOI: 10.3390/pathogens11091057] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 11/28/2022] Open
Abstract
Viability assessment is a critical step in evaluating bacterial pathogens to determine infectious risks to public health. Based on three accepted viable criteria (culturability, metabolic activity, and membrane integrity), current viability assessments are categorized into three main strategies. The first strategy relies on the culturability of bacteria. The major limitation of this strategy is that it cannot detect viable but nonculturable (VBNC) bacteria. As the second strategy, based on the metabolic activity of bacteria, VBNC bacteria can be detected. However, VBNC bacteria sometimes can enter a dormant state that allows them to silence reproduction and metabolism; therefore, they cannot be detected based on culturability and metabolic activity. In order to overcome this drawback, viability assessments based on membrane integrity (third strategy) have been developed. However, these techniques generally require multiple steps, bulky machines, and laboratory technicians to conduct the tests, making them less attractive and popular applications. With significant advances in microfluidic technology, these limitations of current technologies for viability assessment can be improved. This review summarized and discussed the advances, challenges, and future perspectives of current methods for the viability assessment of bacterial pathogens.
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Affiliation(s)
- Kieu The Loan Trinh
- Department of Industrial Environmental Engineering, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Korea
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Korea
- Correspondence:
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25
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How to Verify Non-Presence-The Challenge of Axenic Algae Cultivation. Cells 2022; 11:cells11162594. [PMID: 36010670 PMCID: PMC9406910 DOI: 10.3390/cells11162594] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/12/2022] [Accepted: 08/15/2022] [Indexed: 01/04/2023] Open
Abstract
Many phycological applications require the growth and maintenance of pure algae cultures. In some research areas, such as biochemistry and physiology, axenic growth is essential to avoid misinterpretations caused by contaminants. Nonetheless, axenicity-defined as the state of only a single strain being present, free of any other organism-needs to be verified. We compare the available methods to assess axenicity. We first purified unialgal Limnospira fusiformis cultures with an established series of axenicity treatments, and by including two additional treatment steps. The presumable axenic cultures were then tested for their axenic state by applying conventional tests on LB (lysogeny broth) agar-plates, 16S rRNA gene amplicon sequencing, flow-cytometry and epifluorescence microscopy. Only the plate tests indicated axenic conditions. We found a linear relationship between total cell counts of contaminants achieved by flow cytometry and epifluorescence microscopy, with flow cytometry counts being consistently higher. In addition, 16S rRNA gene amplicon sequencing demonstrated its superiority by not only being an efficient tool for axenicity testing, but also for identification of persistent contaminants. Although classic plate tests are still commonly used to verify axenicity, we found the LB-agar-plate technique to be inappropriate. Cultivation-independent methods are highly recommended to test for axenic conditions. A combination of flow-cytometry and 16S rRNA gene amplicon sequencing complement each other and will yield the most reliable result.
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26
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Huang J, Liang Z, Liu Y, Zhou J, He F. Development of an MSPQC Nucleic Acid Sensor Based on CRISPR/Cas9 for the Detection of Mycobacterium tuberculosis. Anal Chem 2022; 94:11409-11415. [PMID: 35930710 DOI: 10.1021/acs.analchem.2c02538] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Accurate and rapid detection of nucleic acid plays a vital role in the clinical treatment of tuberculosis caused by Mycobacterium tuberculosis (M.TB). However, false-negative and false-positive results caused by base mismatches could affect the detection accuracy. Inspired by the unique property of CRISPR/Cas9, we proposed a new MSPQC M.TB sensor based on the CRISPR/Cas9 system, which can distinguish single-base mismatches in 10 bases from the protospacer adjacent motif (PAM) region. In the proposed sensor, single-stranded DNA on Au interdigital electrodes was used as a capture probe for the target and an initiator for hybridization chain reaction (HCR). HCR was used to generate long double-stranded DNA (dsDNA), which could span the Au interdigital electrodes. CRISPR/Cas9 was used as recognition components to recognize capture/target dsDNA. When the target existed, the capture probe hybridized with the target to form dsDNA, which could be recognized and cut by CRISPR/Cas9. Thus, the DNA connection between electrodes was cut off and resulted in the MSPQC response. When no target existed, the capture probe remained single-stranded and could not be recognized and cut by CRISPR/Cas9. Therefore, DNA connection between electrodes was reserved. Moreover, silver staining technology was utilized to improve the sensitivity of detection. M.TB was detected by the proposed sensor using specific sequence fragments of 16S rRNA of M.TB as the target. The detection time was down to 2.3 h. The limit of detection (LOD) was 30 CFU/mL.
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Affiliation(s)
- Ji Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Zi Liang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Yu Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
| | - Jiandang Zhou
- Department of Clinical Laboratory, The Third Xiangya Hospital, Xiangya Medical College of Central South University, Changsha 410208, P. R. China
| | - Fengjiao He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
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27
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Lu Q, Mao J, Xia H, Song S, Chen W, Zhao D. Effect of wastewater treatment plant discharge on the bacterial community in a receiving river. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 239:113641. [PMID: 35597140 DOI: 10.1016/j.ecoenv.2022.113641] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/29/2022] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
The effluent of wastewater treatment plants (WWTPs) is an important water resource for some rivers in regions with relatively low precipitation, which may pose ecological risks. Various pollutants and microorganisms are discharged into rivers, along with the WWTP effluent, but this process has not been thoroughly studied. The objective of this study was to evaluate the effect of WWTP effluent on the bacterial community in the sediment and water column of an urban river and to identify the relationship between the total and active bacterial communities. Five sites were sampled in the river, including the most upstream site of the river (Up-most), 200 m upstream of the WWTP (Up-200), at the point of effluent discharge of the WWTP (Eff-pl) and 50 m (Down-50) and 1000 m (Down-1000) downstream of the WWTP. Compared with the two upstream sites (Up-most and Up-200), the bacterial species composition of Eff-pl was significantly different (p < 0.05) in both the sediment and water columns, while the bacterial species composition at Down-1000 was significantly different (p < 0.05) in the sediment but not in the water. The relative abundance of Proteobacteria, Actinobacteriota and Verrucomicrobiota was significantly different (p < 0.05) at Eff-pl in both the sediment and water columns compared with that at the upstream sites. The shared bacterial species between the DNA and RNA 16 S rRNA analyses were only 45.5-62.2% and 43.2-52.3% for the sediment and water, respectively. Accordingly, WWTP effluent drainage significantly alters (p < 0.05) the bacterial composition in the receiving river but can be recovered in water within a short distance. However, in sediment, a longer recovery space is probably needed. Analyses of the combination of total and active bacterial compositions are recommended to evaluate the ecological consequences of WWTP effluent drainage on the bacterial composition.
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Affiliation(s)
- Qianqian Lu
- Department of Biological Science and Technology, Nanjing University, Nanjing 210093, PR China
| | - Junbo Mao
- Sinohydro Bureau 11 Co., Ltd, Zhengzhou 450001, PR China
| | - Haijun Xia
- Sinohydro Bureau 11 Co., Ltd, Zhengzhou 450001, PR China
| | - Siyuan Song
- Huadong Engineering Corporation Limited, Hangzhou 311122, PR China
| | - Wenjuan Chen
- Sinohydro Bureau 11 Co., Ltd, Zhengzhou 450001, PR China
| | - Dehua Zhao
- Department of Biological Science and Technology, Nanjing University, Nanjing 210093, PR China.
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28
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Li X, Liu D. Effects of wheat bran co-fermentation on the quality and bacterial community succession during radish fermentation. Food Res Int 2022; 157:111229. [DOI: 10.1016/j.foodres.2022.111229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 04/04/2022] [Accepted: 04/05/2022] [Indexed: 11/04/2022]
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29
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Devi P, Maurya R, Mehta P, Shamim U, Yadav A, Chattopadhyay P, Kanakan A, Khare K, Vasudevan JS, Sahni S, Mishra P, Tyagi A, Jha S, Budhiraja S, Tarai B, Pandey R. Increased Abundance of Achromobacter xylosoxidans and Bacillus cereus in Upper Airway Transcriptionally Active Microbiome of COVID-19 Mortality Patients Indicates Role of Co-Infections in Disease Severity and Outcome. Microbiol Spectr 2022; 10:e0231121. [PMID: 35579429 PMCID: PMC9241827 DOI: 10.1128/spectrum.02311-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 04/17/2022] [Indexed: 12/13/2022] Open
Abstract
The modulators of severe COVID-19 have emerged as the most intriguing features of SARS-CoV-2 pathogenesis. This is especially true as we are encountering variants of concern (VOC) with increased transmissibility and vaccination breakthroughs. Microbial co-infections are being investigated as one of the crucial factors for exacerbation of disease severity and complications of COVID-19. A key question remains whether early transcriptionally active microbial signature/s in COVID-19 patients can provide a window for future disease severity susceptibility and outcome? Using complementary metagenomics sequencing approaches, respiratory virus oligo panel (RVOP) and Holo-seq, our study highlights the possible functional role of nasopharyngeal early resident transcriptionally active microbes in modulating disease severity, within recovered patients with sub-phenotypes (mild, moderate, severe) and mortality. The integrative analysis combines patients' clinical parameters, SARS-CoV-2 phylogenetic analysis, microbial differential composition, and their functional role. The clinical sub-phenotypes analysis led to the identification of transcriptionally active bacterial species associated with disease severity. We found significant transcript abundance of Achromobacter xylosoxidans and Bacillus cereus in the mortality, Leptotrichia buccalis in the severe, Veillonella parvula in the moderate, and Actinomyces meyeri and Halomonas sp. in the mild COVID-19 patients. Additionally, the metabolic pathways, distinguishing the microbial functional signatures between the clinical sub-phenotypes, were also identified. We report a plausible mechanism wherein the increased transcriptionally active bacterial isolates might contribute to enhanced inflammatory response and co-infections that could modulate the disease severity in these groups. Current study provides an opportunity for potentially using these bacterial species for screening and identifying COVID-19 patient sub-groups with severe disease outcome and priority medical care. IMPORTANCE COVID-19 is invariably a disease of diverse clinical manifestation, with multiple facets involved in modulating the progression and outcome. In this regard, we investigated the role of transcriptionally active microbial co-infections as possible modulators of disease pathology in hospital admitted SARS-CoV-2 infected patients. Specifically, can there be early nasopharyngeal microbial signatures indicative of prospective disease severity? Based on disease severity symptoms, the patients were segregated into clinical sub-phenotypes: mild, moderate, severe (recovered), and mortality. We identified significant presence of transcriptionally active isolates, Achromobacter xylosoxidans and Bacillus cereus in the mortality patients. Importantly, the bacterial species might contribute toward enhancing the inflammatory responses as well as reported to be resistant to common antibiotic therapy, which together hold potential to alter the disease severity and outcome.
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Affiliation(s)
- Priti Devi
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ranjeet Maurya
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Priyanka Mehta
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Uzma Shamim
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Aanchal Yadav
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Partha Chattopadhyay
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Akshay Kanakan
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Kriti Khare
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Janani Srinivasa Vasudevan
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Shweta Sahni
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Pallavi Mishra
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Akansha Tyagi
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Delhi, India
| | - Sujeet Jha
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Delhi, India
| | - Sandeep Budhiraja
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Delhi, India
| | - Bansidhar Tarai
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Delhi, India
| | - Rajesh Pandey
- INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Niestępski S, Harnisz M, Korzeniewska E, Filipkowska Z. An improved selective/differential medium for culturing the Bacteroides fragilis group from wastewater. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:2083-2089. [PMID: 35551562 DOI: 10.1039/d2ay00526c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The aim of this study was to develop an effective selective/differential medium for culturing environmental strains of the Bacteroides fragilis group (BFG). This goal was achieved by modifying standard commercial Bacteroides Bile Esculin Agar (BBE Agar). Bacteroides Bile Esculin Agar was combined with substances that inhibit the growth of non-BFG bacteria, mostly Klebsiella pneumoniae and Fusobacterium mortiferum. The strains isolated from standard and modified BBE Agar were identified as BFG strains by PCR and 16S rRNA gene sequencing. The supplementation of standard BBE Agar with colistin (40 mg L-1), kanamycin (400 mg L-1) and vancomycin (7.5 mg L-1) increases the effectiveness of BFG bacteria isolation from <10% to 35%, and additional Gram staining improves the effectiveness of bacterial isolation five-fold relative to standard BBE Agar. The results of the present study also suggest that the presence of the bfr gene is not a reliable indicator for the identification of BFG strains.
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Affiliation(s)
- Sebastian Niestępski
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720 Olsztyn, Poland.
- Division of Reproductive Biology, Reproductive Immunology and Pathology, Institute of Animal Reproduction and Food Research of Polish Academy of Sciences, Bydgoska 7, 10-243 Olsztyn, Poland
| | - Monika Harnisz
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720 Olsztyn, Poland.
| | - Ewa Korzeniewska
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720 Olsztyn, Poland.
| | - Zofia Filipkowska
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1, 10-720 Olsztyn, Poland.
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Vega M, Ontiveros-Valencia A, Vargas IT, Nerenberg R. Chlorate addition enhances perchlorate reduction in denitrifying membrane-biofilm reactors. Appl Microbiol Biotechnol 2022; 106:4341-4350. [PMID: 35612628 DOI: 10.1007/s00253-022-11976-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 11/29/2022]
Abstract
Perchlorate is a widespread drinking water contaminant with regulatory standards ranging from 2 to 18 μg/L. The hydrogen-based membrane-biofilm reactor (MBfR) can effectively reduce perchlorate, but it is challenging to achieve low-µg/L levels. We explored chlorate addition to increase the abundance of perchlorate-reducing bacteria (PRB) and improve removals. MBfR reactors were operated with and without chlorate addition. Results show that chlorate doubled the abundance of putative PRB (e.g., Rhodocyclales) and improved perchlorate reduction to 23 ± 17 µg/L, compared to 53 ± 37 µg/L in the control. Sulfate reduction was substantially inhibited during chlorate addition, but quickly recovered once suspended. Our results suggest that chlorate addition can enhance perchlorate reduction by providing a selective pressure for PRB. It also decreases net sulfate reduction. KEY POINTS: • Chlorate increased the abundance of perchlorate-reducing bacteria • Chlorate addition improved perchlorate removal • Chlorate appeared to suppress sulfate reduction.
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Affiliation(s)
- Marcela Vega
- Departamento de Ingeniería Hidráulica y Ambiental, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago, Chile.,Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, 156 Fitzpatrick Hall of Engineering, South Bend, IN, 46556, USA.,Centro de Desarrollo Urbano Sustentable (CEDEUS), Av. Vicuña Mackenna 4860, Macul, Santiago, Chile
| | - Aura Ontiveros-Valencia
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, 156 Fitzpatrick Hall of Engineering, South Bend, IN, 46556, USA.,División de Ciencias Ambientales, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa de San José 2055, CP 78216, San Luis Potosí, México
| | - Ignacio T Vargas
- Departamento de Ingeniería Hidráulica y Ambiental, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago, Chile.,Centro de Desarrollo Urbano Sustentable (CEDEUS), Av. Vicuña Mackenna 4860, Macul, Santiago, Chile
| | - Robert Nerenberg
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, 156 Fitzpatrick Hall of Engineering, South Bend, IN, 46556, USA.
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Differences in the Active Endometrial Microbiota across Body Weight and Cancer in Humans and Mice. Cancers (Basel) 2022; 14:cancers14092141. [PMID: 35565271 PMCID: PMC9100094 DOI: 10.3390/cancers14092141] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/21/2022] [Accepted: 04/23/2022] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Of all cancers, endometrial cancer has the greatest association with obesity. Obesity causes dysbiosis of intestinal microbiota, but little is known about whether obesity is associated with dysbiosis of the female genital tract. Therefore, the aim of this study was to determine whether obesity and cancer were associated with altered microbiota profiles in the endometrium. 16S rRNA transcript amplicon sequencing (which captures actively replicating bacteria) of endometrial tissues showed that obesity and cancer were associated with the prevalence of microbial community types in the human endometrium. However, obesity was not associated with microbial community types in the mouse endometrium. The presence of endometrial cancer (but not obesity) was associated with decreased abundance of the Lactobacillus genus in the human endometrium. In mice, an enrichment of Lactobacillus was associated with lower prevalence of disease (normal uterine histology). These results suggest that obesity and cancer may influence microbiota community types in the endometrium (at least in humans) and Lactobacillus may be protective in the endometrium. This study therefore supports further research into the role of microbiota in endometrial cancer development. Abstract Obesity is a risk factor for endometrial cancer. The aim of this study was to determine whether actively replicating microbiota in the endometrium differ between obese vs. lean and cancer vs. benign states. We performed 16S rRNA amplicon sequencing on endometrial tissues from lean and obese women with and without endometrial cancer, and lean and obese mice. Results displayed human endometrial microbiota clustered into three community types (R = 0.363, p = 0.001). Lactobacillus was dominant in community type 1 (C1) while community type 2 (C2) had high levels of Proteobacteria and more cancer samples when compared to C1 (p = 0.007) and C3 (p = 0.0002). A significant increase in the prevalence of the C2 community type was observed across body mass index and cancer (χ2 = 14.24, p = 0.0002). The relative abundance of Lactobacillus was lower in cancer samples (p = 0.0043), and an OTU with 100% similarity to Lactobacillus iners was enriched in control samples (p = 0.0029). Mouse endometrial microbiota also clustered into three community types (R = 0.419, p = 0.001) which were not influenced by obesity. In conclusion, obesity and cancer are associated with community type prevalence in the human endometrium, and Lactobacillus abundance is associated with normal uterine histologies in humans and mice.
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Morales Medina WR, Eramo A, Fahrenfeld NL. Metabolically Active Prokaryotes and Actively Transcribed Antibiotic Resistance Genes in Sewer Systems: Implications for Public Health and Microbially Induced Corrosion. MICROBIAL ECOLOGY 2022; 83:583-595. [PMID: 34117524 PMCID: PMC8195243 DOI: 10.1007/s00248-021-01775-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 05/13/2021] [Indexed: 05/11/2023]
Abstract
Sewer systems are reservoirs of pathogens and bacteria carrying antibiotic resistance genes (ARGs). However, most recent high-throughput studies rely on DNA-based techniques that cannot provide information on the physiological state of the cells nor expression of ARGs. In this study, wastewater and sewer sediment samples were collected from combined and separate sanitary sewer systems. The metabolically active prokaryote community was evaluated using 16S rRNA amplicon sequencing and actively transcribed ARG abundance was measured using mRNA RT-qPCR. Three (sul1, blaTEM, tet(G)) of the eight tested ARGs were quantifiable in select samples. Sewer sediment samples had greater abundance of actively transcribed ARGs compared to wastewater. Microbiome analysis showed the presence of metabolically active family taxa that contain clinically relevant pathogens (Pseudomonadaceae, Enterobacteraceae, Streptococcaceae, Arcobacteraceae, and Clostridiaceae) and corrosion-causing prokaryotes (Desulfobulbaceae and Desulfovibrionaceae) in both matrices. Spirochaetaceae and methanogens were more common in the sediment matrix while Mycobacteraceae were more common in wastewater. The microbiome obtained from 16S rRNA sequencing had a significantly different structure from the 16S rRNA gene microbiome. Overall, this study demonstrates active transcription of ARGs in sewer systems and provides insight into the abundance and physiological state of taxa of interest in the different sewer matrices and sewer types relevant for wastewater-based epidemiology, corrosion, and understanding the hazard posed by different matrices during sewer overflows.
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Affiliation(s)
- William R Morales Medina
- Microbiology & Molecular Genetics, Rutgers, The State University of New Jersey, 500 Bartholomew Dr, Piscataway, NJ, 08854, USA
| | - Alessia Eramo
- Civil & Environmental Engineering, Rutgers, The State University of New Jersey, 500 Bartholomew Dr, Piscataway, NJ, 08854, USA
| | - N L Fahrenfeld
- Civil & Environmental Engineering, Rutgers, The State University of New Jersey, 500 Bartholomew Dr, Piscataway, NJ, 08854, USA.
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Yang J, Lee J, Choi J, Ma L, Heaton EA, Howe A. Response of Total (DNA) and Metabolically Active (RNA) Microbial Communities in Miscanthus × Giganteus Cultivated Soil to Different Nitrogen Fertilization Rates. Microbiol Spectr 2022; 10:e0211621. [PMID: 35170997 PMCID: PMC8849084 DOI: 10.1128/spectrum.02116-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/19/2022] [Indexed: 11/20/2022] Open
Abstract
Miscanthus × giganteus is a promising high-yielding perennial plant to meet growing bioenergy demands; however, the degree to which the soil microbiome affects its nitrogen cycling and subsequently, biomass yield remains unclear. In this study, we hypothesize that contributions of metabolically active soil microbial membership may be underestimated with DNA-based approaches. We assessed the response of the soil microbiome to nitrogen availability in terms of both DNA and RNA soil microbial communities from the Long-term Assessment of Miscanthus Productivity and Sustainability (LAMPS) field trial. DNA and RNA were extracted from 271 samples, and 16S small subunit (SSU) rRNA amplicon sequencing was performed to characterize microbial community structure. Significant differences were observed in the resulting soil microbiomes and were best explained by the sequencing library of origin, either DNA or RNA. Similar numbers of membership were detected in DNA and RNA microbial communities, with more than 90% of membership shared. However, the profile of dominant membership within DNA and RNA differed, with varying proportions of Actinobacteria and Proteobacteria and Firmicutes and Proteobacteria. Only RNA microbial communities showed seasonal responses to nitrogen fertilization, and these differences were associated with nitrogen-cycling bacteria. The relative abundance of bacteria associated with nitrogen cycling was 7-fold higher in RNA than in DNA, and genes associated with denitrifying bacteria were significantly enriched in RNA, suggesting that these bacteria may be underestimated with DNA-only approaches. Our findings indicate that RNA-based SSU characterization can be a significant and complementing resource for understanding the role of soil microbiomes in bioenergy crop production. IMPORTANCEMiscanthus × giganteus is a promising candidate for bioeconomy cropping systems; however, it remains unclear how the soil microbiome supplies nitrogen to this low-input crop. DNA-based techniques are used to provide community characterization, but may miss important metabolically active taxa. By analyzing both DNA- and actively transcribed RNA-based microbial communities, we found that nitrogen cycling taxa in the soil microbiome may be underestimated using only DNA-based approaches. Accurately understanding the role of microbes and how they cycle nutrients is important for the development of sustainable bioenergy crops, and RNA-based approaches are recommended as a complement to DNA approaches to better understand the microbial, plant, and management interactions.
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Affiliation(s)
- Jihoon Yang
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, USA
- Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, Illinois, USA
| | - Jaejin Lee
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, USA
- Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, Illinois, USA
| | - Jinlyung Choi
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, USA
- Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, Illinois, USA
| | - Lanying Ma
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, USA
- Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, Illinois, USA
| | - Emily A. Heaton
- Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, Illinois, USA
- Department of Agronomy, Iowa State University, Ames, Iowa, USA
| | - Adina Howe
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa, USA
- Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, Illinois, USA
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Jang Y, Kim S, Kim N, Son H, Ha EJ, Koh EJ, Phi JH, Park C, Kim JE, Kim S, Lee SK, Cho W, Moon J, Chu K. Nanopore
16S
sequencing enhances the detection of bacterial meningitis after neurosurgery. Ann Clin Transl Neurol 2022; 9:312-325. [PMID: 35124895 PMCID: PMC8935320 DOI: 10.1002/acn3.51517] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 01/10/2022] [Accepted: 01/25/2022] [Indexed: 12/19/2022] Open
Abstract
Objective Nosocomial bacterial meningitis is one of the major complications after neurosurgery. We performed nanopore 16S amplicon sequencing from cerebrospinal fluid (CSF) to evaluate bacterial meningitis in patients who underwent neurosurgery. Methods Among the patients who visited the neurosurgery department of Seoul National University Hospital between July 2017 and June 2020, those with clinically suspected bacterial meningitis were included. 16S rDNA PCR was performed from the CSF, and nanopore sequencing was performed for up to 3 h. The reads were aligned to the BLAST database. In each case, the culture and the 16S rRNA gene amplicon analysis were simultaneously performed and compared with each other, and we retrospectively reviewed the medical records. Genuine infection was determined by the identical results between conventional culture study and the sequencing, or clinically determined in cases with inconsistent results between the two methods. Results Of the 285 samples obtained from 178 patients who had 16S rDNA PCR, 41 samples (14.4%) were diagnosed with genuine infection. A total of 56.1% (23/41) of the samples with genuine infection showed a false‐negative culture test. In particular, 16S amplicon sequencing was useful in evaluating patients at the initial tests who had infection with intraventricular hemorrhage (Culture false‐negative rate = 100%), subarachnoid hemorrhage (Culture false‐negative rate = 77.8%), and systemic cancer (Culture false‐negative rate = 100%), which are risk factors for central fever. Moreover, 16S amplicon sequencing could suggest the possibility of persistent bacterial meningitis in empirical antibiotic use. Conclusion CSF nanopore 16S sequencing was more effective than conventional CSF culture studies in postoperative bacterial meningitis and may contribute to evidence‐based decisions for antibiotic maintenance and discontinuation.
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Affiliation(s)
- Yoonhyuk Jang
- Department of Neurology Seoul National University College of Medicine Seoul National University Hospital Seoul South Korea
| | - Seondeuk Kim
- Department of Neurology Seoul National University College of Medicine Seoul National University Hospital Seoul South Korea
| | - Narae Kim
- Department of Neurology Seoul National University College of Medicine Seoul National University Hospital Seoul South Korea
| | - Hyoshin Son
- Department of Neurosurgery Seoul National University College of Medicine, Seoul National University Hospital Seoul South Korea
| | - Eun Jin Ha
- Department of Neurosurgery Seoul National University College of Medicine, Seoul National University Hospital Seoul South Korea
| | - Eun Jung Koh
- Department of Neurosurgery Seoul National University College of Medicine, Seoul National University Hospital Seoul South Korea
- Division of Pediatric Neurosurgery Seoul National University Children's Hospital Seoul South Korea
| | - Ji Hoon Phi
- Department of Neurosurgery Seoul National University College of Medicine, Seoul National University Hospital Seoul South Korea
- Division of Pediatric Neurosurgery Seoul National University Children's Hospital Seoul South Korea
| | - Chul‐Kee Park
- Department of Neurosurgery Seoul National University College of Medicine, Seoul National University Hospital Seoul South Korea
| | - Jeong Eun Kim
- Department of Neurosurgery Seoul National University College of Medicine, Seoul National University Hospital Seoul South Korea
| | - Seung‐Ki Kim
- Department of Neurosurgery Seoul National University College of Medicine, Seoul National University Hospital Seoul South Korea
- Division of Pediatric Neurosurgery Seoul National University Children's Hospital Seoul South Korea
| | - Sang Kun Lee
- Department of Neurology Seoul National University College of Medicine Seoul National University Hospital Seoul South Korea
| | - Won‐Sang Cho
- Department of Neurosurgery Seoul National University College of Medicine, Seoul National University Hospital Seoul South Korea
| | - Jangsup Moon
- Department of Neurology Seoul National University College of Medicine Seoul National University Hospital Seoul South Korea
- Department of Genomic Medicine Seoul National University Hospital Seoul South Korea
| | - Kon Chu
- Department of Neurology Seoul National University College of Medicine Seoul National University Hospital Seoul South Korea
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Blais MA, Matveev A, Lovejoy C, Vincent WF. Size-Fractionated Microbiome Structure in Subarctic Rivers and a Coastal Plume Across DOC and Salinity Gradients. Front Microbiol 2022; 12:760282. [PMID: 35046910 PMCID: PMC8762315 DOI: 10.3389/fmicb.2021.760282] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/01/2021] [Indexed: 11/16/2022] Open
Abstract
Little is known about the microbial diversity of rivers that flow across the changing subarctic landscape. Using amplicon sequencing (rRNA and rRNA genes) combined with HPLC pigment analysis and physicochemical measurements, we investigated the diversity of two size fractions of planktonic Bacteria, Archaea and microbial eukaryotes along environmental gradients in the Great Whale River (GWR), Canada. This large subarctic river drains an extensive watershed that includes areas of thawing permafrost, and discharges into southeastern Hudson Bay as an extensive plume that gradually mixes with the coastal marine waters. The microbial communities differed by size-fraction (separated with a 3-μm filter), and clustered into three distinct environmental groups: (1) the GWR sites throughout a 150-km sampling transect; (2) the GWR plume in Hudson Bay; and (3) small rivers that flow through degraded permafrost landscapes. There was a downstream increase in taxonomic richness along the GWR, suggesting that sub-catchment inputs influence microbial community structure in the absence of sharp environmental gradients. Microbial community structure shifted across the salinity gradient within the plume, with changes in taxonomic composition and diversity. Rivers flowing through degraded permafrost had distinct physicochemical and microbiome characteristics, with allochthonous dissolved organic carbon explaining part of the variation in community structure. Finally, our analyses of the core microbiome indicated that while a substantial part of all communities consisted of generalists, most taxa had a more limited environmental range and may therefore be sensitive to ongoing change.
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Affiliation(s)
- Marie-Amélie Blais
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS) and Takuvik Joint International Laboratory, Université Laval, Quebec City, QC, Canada.,Centre for Northern Studies (CEN), Université Laval, Quebec City, QC, Canada
| | - Alex Matveev
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS) and Takuvik Joint International Laboratory, Université Laval, Quebec City, QC, Canada.,Centre for Northern Studies (CEN), Université Laval, Quebec City, QC, Canada
| | - Connie Lovejoy
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS) and Takuvik Joint International Laboratory, Université Laval, Quebec City, QC, Canada.,Québec-Océan, Université Laval, Quebec City, QC, Canada
| | - Warwick F Vincent
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS) and Takuvik Joint International Laboratory, Université Laval, Quebec City, QC, Canada.,Centre for Northern Studies (CEN), Université Laval, Quebec City, QC, Canada
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Honey Bee Larval and Adult Microbiome Life Stages Are Effectively Decoupled with Vertical Transmission Overcoming Early Life Perturbations. mBio 2021; 12:e0296621. [PMID: 34933445 PMCID: PMC8689520 DOI: 10.1128/mbio.02966-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Microbiomes provide a range of benefits to their hosts which can lead to the coevolution of a joint ecological niche. However, holometabolous insects, some of the most successful organisms on Earth, occupy different niches throughout development, with larvae and adults being physiologically and morphologically highly distinct. Furthermore, transition between the stages usually involves the loss of the gut microbiome since the gut is remodeled during pupation. Most eusocial organisms appear to have evolved a workaround to this problem by sharing their communal microbiome across generations. However, whether this vertical microbiome transmission can overcome perturbations of the larval microbiome remains untested. Honey bees have a relatively simple, conserved, coevolved adult microbiome which is socially transmitted and affects many aspects of their biology. In contrast, larval microbiomes are more variable, with less clear roles. Here, we manipulated the gut microbiome of in vitro-reared larvae, and after pupation of the larvae, we inoculated the emerged bees with adult microbiome to test whether adult and larval microbiome stages may be coupled (e.g., through immune priming). Larval treatments differed in bacterial composition and abundance, depending on diet, which also drove larval gene expression. Nonetheless, adults converged on the typical core taxa and showed limited gene expression variation. This work demonstrates that honey bee adult and larval stages are effectively microbiologically decoupled, and the core adult microbiome is remarkably stable to early developmental perturbations. Combined with the transmission of the microbiome in early adulthood, this allows the formation of long-term host-microbiome associations. IMPORTANCE This work investigated host-microbiome interactions during a crucial developmental stage-the transition from larvae to adults, which is a challenge to both, the insect host and its microbiome. Using the honey bee as a tractable model system, we showed that microbiome transfer after emergence overrides any variation in the larvae, indicating that larval and adult microbiome stages are effectively decoupled. Together with the reliable vertical transfer in the eusocial system, this decoupling ensures that the adults are colonized with a consistent and derived microbiome after eclosion. Taken all together, our data provide additional support that the evolution of sociality, at least in the honey bee system tested here, is linked with host-microbiome relationships.
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Biogeochemical Niches of Fe-cycling Communities Influencing Heavy Metal Transport Along the Rio Tinto, Spain. Appl Environ Microbiol 2021; 88:e0229021. [PMID: 34910570 DOI: 10.1128/aem.02290-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the mining-impacted Rio Tinto, Spain, Fe-cycling microorganisms influence the transport of heavy metals (HMs) into the Atlantic Ocean. However, it remains largely unknown how spatial and temporal hydrogeochemical gradients along the Rio Tinto shape the composition of Fe-cycling microbial communities and how this in turn affects HM mobility. Using a combination of DNA- and RNA-based 16S rRNA (gene) amplicon sequencing and hydrogeochemical analyses, we explored the impact of pH, Fe(III), Fe(II) and Cl- on Fe-cycling microorganisms. We showed that the water column at the acidic (pH 2.2) middle course of the river was colonized by Fe(II) oxidizers affiliating with Acidithiobacillus and Leptospirillum. At the upper estuary, daily fluctuations of pH (2.7-3.7) and Cl- (6.9-16.6 g/L) contributed to the establishment of a unique microbial community, including Fe(II) oxidizers belonging to Acidihalobacter, Marinobacter and Mariprofundus identified at this site. Furthermore, DNA- and RNA-based profiles of the benthic community suggested that acidophilic and neutrophilic Fe(II) oxidizers (e.g., Acidihalobacter, Marinobacter and Mariprofundus), Fe(III) reducers (e.g., Thermoanaerobaculum) and sulfate-reducing bacteria drive the Fe cycle in the estuarine sediments. RNA-based relative abundances of Leptospirillum at the middle course as well as abundances of Acidohalobacter and Mariprofundus at the upper estuary were higher, compared to DNA-based results, suggesting potentially higher level of activity of these taxa. Based on our findings, we propose a model of how tidal water affects the composition and activity of the Fe-cycling taxa, playing an important role in the transport of HMs (e.g., As, Cd, Cr and Pb) along the Rio Tinto. Importance The estuary of the Rio Tinto is a unique environment in which extremely acidic, heavy metal- and especially iron-rich river water is mixed with seawater. Due to the mixing events, the estuarine water is characterized by a low pH, almost sea water salinity and high concentrations of bioavailable iron. The unusual hydrogeochemistry maintains unique microbial communities in the estuarine water and in the sediment. These communities include halotolerant iron-oxidizing microorganisms which typically inhabit acidic saline environments and marine iron-oxidizing microorganisms, which, in opposite, are not typically found in acidic environments. Furthermore, highly saline estuarine water favored the prosperity of acidophilic heterotrophs, typically inhabiting brackish and saline environments. The Rio Tinto estuarine sediment harbored a diverse microbial community with both, acidophilic and neutrophilic members that can mediate the iron cycle, and in turn, can directly impact the mobility and transport of heavy metals in the Rio Tinto estuary.
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Mongodin EF, Saxena V, Iyyathurai J, Lakhan R, Ma B, Silverman E, Lee ZL, Bromberg JS. Chronic rejection as a persisting phantom menace in organ transplantation: a new hope in the microbiota? Curr Opin Organ Transplant 2021; 26:567-581. [PMID: 34714788 PMCID: PMC8556501 DOI: 10.1097/mot.0000000000000929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW The microbiota plays an important role in health and disease. During organ transplantation, perturbations in microbiota influence transplant outcome. We review recent advances in characterizing microbiota and studies on regulation of intestinal epithelial barrier function and mucosal and systemic immunity by microbiota and their metabolites. We discuss implications of these interactions on transplant outcomes. RECENT FINDINGS Metagenomic approaches have helped the research community identify beneficial and harmful organisms. Microbiota regulates intestinal epithelial functions. Signals released by epithelial cells or microbiota trigger pro-inflammatory or anti-inflammatory effects on innate and adaptive immune cells, influencing the structure and function of the immune system. Assessment and manipulation of microbiota can be used for biomarkers for diagnosis, prognosis, and therapy. SUMMARY The bidirectional dialogue between the microbiota and immune system is a major influence on immunity. It can be targeted for biomarkers or therapy. Recent studies highlight a close association of transplant outcomes with microbiota, suggesting exciting potential avenues for management of host physiology and organ transplantation.
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Affiliation(s)
- Emmanuel F. Mongodin
- University of Maryland School of Medicine, Institute for Genome Sciences and Department of Microbiology & Immunology, Baltimore, MD, USA
| | - Vikas Saxena
- University of Maryland School of Medicine, Center for Vascular and Inflammatory Diseases, Departments of Surgery, Microbiology and Immunology, Baltimore, MD, USA
| | - Jegan Iyyathurai
- University of Maryland School of Medicine, Center for Vascular and Inflammatory Diseases, Departments of Surgery, Microbiology and Immunology, Baltimore, MD, USA
| | - Ram Lakhan
- University of Maryland School of Medicine, Center for Vascular and Inflammatory Diseases, Departments of Surgery, Microbiology and Immunology, Baltimore, MD, USA
| | - Bing Ma
- University of Maryland School of Medicine, Institute for Genome Sciences and Department of Microbiology & Immunology, Baltimore, MD, USA
| | - Emma Silverman
- University of Maryland School of Medicine, Center for Vascular and Inflammatory Diseases, Departments of Surgery, Microbiology and Immunology, Baltimore, MD, USA
| | - Zachariah L. Lee
- University of Maryland School of Medicine, Center for Vascular and Inflammatory Diseases, Departments of Surgery, Microbiology and Immunology, Baltimore, MD, USA
| | - Jonathan S. Bromberg
- University of Maryland School of Medicine, Center for Vascular and Inflammatory Diseases, Departments of Surgery, Microbiology and Immunology, Baltimore, MD, USA
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Slinger J, Wynne JW, Adams MB. Profiling Branchial Bacteria of Atlantic Salmon (Salmo salar L.) Following Exposure to Antimicrobial Agents. FRONTIERS IN ANIMAL SCIENCE 2021. [DOI: 10.3389/fanim.2021.756101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Microbial gill diseases caused by either opportunistic or specific pathogens are an emerging area of concern for aquaculture producers in part due to their sometimes complex and/or cryptic nature. Many antimicrobial treatments used in aquacultural settings are broad spectrum in nature. The effect of such therapeutics upon reduction and recolonization of commensal or pathogenic microbiota post-treatment has received little attention to date. Commensal bacteria are an integral component of the barrier function of mucosal surfaces in animals. This study evaluated the effect of several commercially relevant antimicrobial treatments upon the diversity and composition of branchial bacteria of Atlantic salmon. Here we exposed Atlantic salmon smolt to a number of commercially relevant antimicrobial treatments including chemotherapeutants (chloramine-t and hydrogen peroxide) and antibiotics (oxytetracycline and florfenicol) in vivo. Subsequently we examined the change in bacterial load, 16S rRNA gene expression, and taxonomic diversity post-treatment upon the gills. Results revealed a decrease in cultivable bacterial colonies after antimicrobial treatment, and a downstream decrease in bacterial richness and abundance post-treatment, with colonization of several prominent pathogenic taxa including Vibrio and Tenacibaculum. Temporal tracing over a 14-day period demonstrated that the bacteriome of gill mucus is sensitive to change, and altered by antimicrobial treatment and handling. This study identified candidate antimicrobial treatments which could be implemented in future studies to illustrate the effect of dysbiosis on microbial gill diseases.
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Nagarkar M, Keely SP, Brinkman NE, Garland JL. Human- and infrastructure-associated bacteria in greywater. J Appl Microbiol 2021; 131:2178-2192. [PMID: 33905584 PMCID: PMC8682149 DOI: 10.1111/jam.15118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 04/01/2021] [Accepted: 04/21/2021] [Indexed: 01/12/2023]
Abstract
Greywater, the wastewater from sinks, showers and laundry, is an understudied environment for bacterial communities. Most greywater studies focus on quantifying pathogens, often via proxies used in other wastewater, like faecal indicator bacteria; there is a need to identify more greywater-appropriate surrogates, like Staphylococcus sp. Sequencing-based studies have revealed distinct communities in different types of greywater as well as in different parts of greywater infrastructure, including biofilms on pipes, holding tanks and filtration systems. The use of metagenomic sequencing provides high resolution on both the taxa and genes present, which may be of interest in cases like identifying pathogens and surrogates relevant to different matrices, monitoring antibiotic resistance genes and understanding metabolic processes occurring in the system. Here, we review what is known about bacterial communities in different types of greywater and its infrastructure. We suggest that wider adoption of environmental sequencing in greywater research is important because it can describe the entire bacterial community along with its metabolic capabilities, including pathways for removal of nutrients and organic materials. We briefly describe a metagenomic dataset comparing different types of greywater samples in a college dormitory building to highlight the type of questions these methods can address. Metagenomic sequencing can help further the understanding of greywater treatment for reuse because it allows for identification of new pathogens or genes of concern.
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Affiliation(s)
- M Nagarkar
- Office of Research and Development, United States Environmental Protection Agency, Cincinnati, OH, USA
| | - S P Keely
- Office of Research and Development, United States Environmental Protection Agency, Cincinnati, OH, USA
| | - N E Brinkman
- Office of Research and Development, United States Environmental Protection Agency, Cincinnati, OH, USA
| | - J L Garland
- Office of Research and Development, United States Environmental Protection Agency, Cincinnati, OH, USA
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Habibi N, Uddin S, Al‐Salameen F, Al‐Amad S, Kumar V, Al‐Otaibi M, Razzack NA, Shajan A, Shirshikar F. SARS-CoV-2, other respiratory viruses and bacteria in aerosols: Report from Kuwait's hospitals. INDOOR AIR 2021; 31:1815-1825. [PMID: 34121237 PMCID: PMC8447393 DOI: 10.1111/ina.12871] [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: 02/24/2021] [Revised: 05/23/2021] [Accepted: 05/27/2021] [Indexed: 05/08/2023]
Abstract
The role of airborne particles in the spread of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) is well explored. The novel coronavirus can survive in aerosol for extended periods, and its interaction with other viral communities can cause additional virulence and infectivity. This baseline study reports concentrations of SARS-CoV-2, other respiratory viruses, and pathogenic bacteria in the indoor air from three major hospitals (Sheikh Jaber, Mubarak Al-Kabeer, and Al-Amiri) in Kuwait dealing with coronavirus disease 2019 (COVID-19) patients. The indoor aerosol samples showed 12-99 copies of SARS-CoV-2 per m3 of air. Two non-SARS-coronavirus (strain HKU1 and NL63), respiratory syncytial virus (RSV), and human bocavirus, human rhinoviruses, Influenza B (FluB), and human enteroviruses were also detected in COVID-positive areas of Mubarak Al Kabeer hospital (MKH). Pathogenic bacteria such as Mycoplasma pneumonia, Streptococcus pneumonia and, Haemophilus influenza were also found in the hospital aerosols. Our results suggest that the existing interventions such as social distancing, use of masks, hand hygiene, surface sanitization, and avoidance of crowded indoor spaces are adequate to prevent the spread of SARS-CoV-2 in enclosed areas. However, increased ventilation can significantly reduce the concentration of SARS-CoV-2 in indoor aerosols. The synergistic or inhibitory effects of other respiratory pathogens in the spread, severity, and complexity of SARS-CoV-2 need further investigation.
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Affiliation(s)
- N. Habibi
- Environment and Life Sciences Research CenterKuwait Institute for Scientific ResearchSafatKuwait
| | - S. Uddin
- Environment and Life Sciences Research CenterKuwait Institute for Scientific ResearchSafatKuwait
| | - F. Al‐Salameen
- Environment and Life Sciences Research CenterKuwait Institute for Scientific ResearchSafatKuwait
| | - S. Al‐Amad
- Environment and Life Sciences Research CenterKuwait Institute for Scientific ResearchSafatKuwait
| | - V. Kumar
- Environment and Life Sciences Research CenterKuwait Institute for Scientific ResearchSafatKuwait
| | - M. Al‐Otaibi
- Environment and Life Sciences Research CenterKuwait Institute for Scientific ResearchSafatKuwait
| | - N. Abdul Razzack
- Environment and Life Sciences Research CenterKuwait Institute for Scientific ResearchSafatKuwait
| | - A. Shajan
- Environment and Life Sciences Research CenterKuwait Institute for Scientific ResearchSafatKuwait
| | - F. Shirshikar
- Environment and Life Sciences Research CenterKuwait Institute for Scientific ResearchSafatKuwait
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Mancabelli L, Milani C, Anzalone R, Alessandri G, Lugli GA, Tarracchini C, Fontana F, Turroni F, Ventura M. Free DNA and Metagenomics Analyses: Evaluation of Free DNA Inactivation Protocols for Shotgun Metagenomics Analysis of Human Biological Matrices. Front Microbiol 2021; 12:749373. [PMID: 34691000 PMCID: PMC8527314 DOI: 10.3389/fmicb.2021.749373] [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: 07/29/2021] [Accepted: 09/09/2021] [Indexed: 12/16/2022] Open
Abstract
Culture-independent approaches now represent the gold standard for the investigation of both environmental and host-associated complex microbial communities. Nevertheless, despite the great advantages offered by these novel methodologies based on the use of next-generation DNA sequencing approaches, a number of bias sources have been identified. Among the latter, free DNA contained in biological matrices is one of the main sources of inaccuracy in reconstructing the resident microbial population of viable cells. For this reason, the photoreactive DNA-binding dye propidium monoazide (PMAxx™) has been developed by improving standard PMA. This compound binds and inactivates free DNA, thus preventing its amplification and sequencing. While the performances of PMA have been previously investigated, the efficiency with PMAxx™ has been tested mainly for amplicon-based profiling approaches on a limited number of biological matrices. In this study, we validated the performance of PMAxx™ for shotgun metagenomics approaches employing various human-associated matrices. Notably, results revealed that the effectiveness of PMAxx™ in inactivating free DNA of prokaryotes and eukaryotes tends to vary significantly based on the biological matrices analyzed.
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Affiliation(s)
- Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.,Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
| | | | - Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Chiara Tarracchini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Federico Fontana
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.,Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.,Interdepartmental Research Centre "Microbiome Research Hub", University of Parma, Parma, Italy
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Wolf EA, Rettig HC, Lupatsii M, Schlüter B, Schäfer K, Friedrich D, Graspeuntner S, Rupp J. Culturomics Approaches Expand the Diagnostic Accuracy for Sexually Transmitted Infections. Int J Mol Sci 2021; 22:ijms221910815. [PMID: 34639153 PMCID: PMC8509341 DOI: 10.3390/ijms221910815] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 09/26/2021] [Accepted: 10/01/2021] [Indexed: 02/07/2023] Open
Abstract
Sexually transmitted infections (STIs) are a major health concern with clinical manifestations being acknowledged to cause severe reproductive impairment. Research in infectious diseases has been centered around the known major pathogens for decades. However, we have just begun to understand that the microbiota of the female genital tract is of particular importance for disease initiation, infection progression, and pathological outcome. Thus, we are now aware that many poorly described, partially not yet known, or cultured bacteria may pave the way for an infection and/or contribute to disease severity. While sequencing-based methods are an important step in diagnosing STIs, culture-based methods are still the gold-standard method in diagnostic routine, providing the opportunity to distinguish phenotypic traits of bacteria. However, current diagnostic culture routines suffer from several limitations reducing the content of information about vaginal microbiota. A detailed characterization of microbiota-associated factors is needed to assess the impact of single-bacterial isolates from the vaginal community on vaginal health and the containment of STIs. Here we provide current concepts to enable modern culture routines and create new ideas to improve diagnostic approaches with a conjunct usage of bioinformatics. We aim to enable scientists and physicians alike to overcome long-accepted limitations in culturing bacteria of interest to the human health. Eventually, this may improve the quality of culture-based diagnostics, facilitate a research interface, and lead to a broader understanding of the role of vaginal microbiota in reproductive health and STIs.
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Affiliation(s)
- Ellinor Anna Wolf
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
| | - Hannah Clara Rettig
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
| | - Mariia Lupatsii
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
| | - Britta Schlüter
- Department of Gynecology and Obstetrics, University Medical Center Schleswig-Holstein, 23538 Lübeck, Germany;
| | - Kathrin Schäfer
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
| | - Dirk Friedrich
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
| | - Simon Graspeuntner
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 23538 Lübeck, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 23538 Lübeck, Germany
- Correspondence:
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Ren Q, Wei F, Yuan C, Zhu C, Zhang Q, Quan J, Sun X, Zheng S. The effects of removing dead bacteria by propidium monoazide on the profile of salivary microbiome. BMC Oral Health 2021; 21:460. [PMID: 34551743 PMCID: PMC8456568 DOI: 10.1186/s12903-021-01832-5] [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: 03/09/2021] [Accepted: 09/16/2021] [Indexed: 12/22/2022] Open
Abstract
Background Oral microbiome played an important role in maintaining healthy state and might exhibit certain changes under circumstances of diseases. However, current microbiological research using sequencing techniques did not regard dead bacteria as a separate part, causing findings based on subsequent analyses on dynamic equilibrium and functional pathways of microbes somewhat questionable. Since treatment by propidium monoazide (PMA) was able to remove dead bacteria effectively, it would be worth studying how the sequencing results after PMA treatment differed from those focusing on the whole microbiota. Methods Unstimulated whole saliva samples were obtained from 18 healthy people from 3 age groups (children, adults, and the elderly). After removal of dead bacteria by propidium monoazide (PMA), changes in the profile of salivary microbiome were detected using 16S rRNA sequencing technology, and differences among age groups were compared subsequently. Results Dead bacteria accounted for nearly a half of the whole bacteria flora in saliva, while freezing had little effect on the proportion of deaths. After treatment with PMA, the numbers of OTUs reduced by 4.4–14.2%, while the Shannon diversity indices decreased significantly (P < 0.01). Only 35.2% of positive and 6.1% of negative correlations were found to be shared by the whole microbiota and that with dead bacteria removed. Differences in significantly changed OTUs and functional pathways among different age groups were also observed between the group of PMA and the control. Conclusions It was necessary to take the influence of living state of bacteria into account in analytic studies of salivary microbiome. Supplementary Information The online version contains supplementary material available at 10.1186/s12903-021-01832-5.
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Affiliation(s)
- Qidi Ren
- Department of Preventive Dentistry, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing, People's Republic of China
| | - Fangqiao Wei
- Department of Preventive Dentistry, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing, People's Republic of China
| | - Chao Yuan
- Department of Preventive Dentistry, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing, People's Republic of China
| | - Ce Zhu
- Department of Preventive Dentistry, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing, People's Republic of China.,Department of Preventive Dentistry, Shanghai Jiao Tong University School of Dentistry, Shanghai Ninth People's Hospital, Shanghai, People's Republic of China
| | - Qian Zhang
- Central Laboratory, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing, People's Republic of China
| | - Junkang Quan
- Department of Preventive Dentistry, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing, People's Republic of China
| | - Xiangyu Sun
- Department of Preventive Dentistry, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing, People's Republic of China.
| | - Shuguo Zheng
- Department of Preventive Dentistry, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing, People's Republic of China.
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Nakai R, Wakana I, Niki H. Internal microbial zonation during the massive growth of marimo, a lake ball of Aegagropila linnaei in Lake Akan. iScience 2021; 24:102720. [PMID: 34258554 PMCID: PMC8253969 DOI: 10.1016/j.isci.2021.102720] [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: 03/20/2021] [Revised: 05/24/2021] [Accepted: 06/09/2021] [Indexed: 11/16/2022] Open
Abstract
Marimo (lake ball) is an uncommon ball-like aggregation of the green alga, Aegagropila linnaei. Although A. linnaei is distributed in fresh and brackish waters in the northern hemisphere, marimo colonies are found only in particular habitats. Here, we report the bacterial communities inside various sizes and aggregating structures of natural marimo collected from Lake Akan, Japan. We observed multi-layers composed of sediment particles only in the sizable radial-type marimo with >20 cm diameter and not in the tangled-type marimo. The deeper layers were enriched by Nitrospira, potential sulfur-oxidizing bacteria, and sulfate-reducing bacteria. Microorganisms of the multi-layers would form biofilms incorporating nearby sediment, which would function as microbial “seals” within large radial-type marimo. These findings provide clues to deciphering the growth of endangered marimo. The radial type of marimo (lake ball) can grow to over 20 cm in diameter The sizable radial-type marimo develops the internal multi-layers and hollow structure The layers provide different diverse microbiomes and structural strength The internal multi-layers support the massive growth of the radial-type marimo
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Affiliation(s)
- Ryosuke Nakai
- Microbial Physiology Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, 1111, Yata, Mishima, Shizuoka 411-8540 Japan
| | - Isamu Wakana
- Kushiro International Wetland Center, 7-5 Kuroganecho, Kushiro, Hokkaido 085-8505, Japan
| | - Hironori Niki
- Microbial Physiology Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, 1111, Yata, Mishima, Shizuoka 411-8540 Japan.,Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), 1111, Yata, Mishima, Shizuoka 411-8540 Japan
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47
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Al-Ahmad A, Wollensak K, Rau S, Guevara Solarte DL, Paschke S, Lienkamp K, Staszewski O. How Do Polymer Coatings Affect the Growth and Bacterial Population of a Biofilm Formed by Total Human Salivary Bacteria?-A Study by 16S-RNA Sequencing. Microorganisms 2021; 9:1427. [PMID: 34361863 PMCID: PMC8304871 DOI: 10.3390/microorganisms9071427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/25/2021] [Accepted: 06/26/2021] [Indexed: 11/23/2022] Open
Abstract
Antimicrobial surface modifications are required to prevent biomaterial-associated biofilm infections, which are also a major concern for oral implants. The aim of this study was to evaluate the influence of three different coatings on the biofilm formed by human saliva. Biofilms grown from human saliva on three different bioactive poly(oxanorbornene)-based polymer coatings (the protein-repellent PSB: poly(oxanorbornene)-based poly(sulfobetaine), the protein-repellent and antimicrobial PZI: poly(carboxyzwitterion), and the mildly antimicrobial and protein-adhesive SMAMP: synthetic mimics of antimicrobial peptides) were analyzed and compared with the microbial composition of saliva, biofilms grown on uncoated substrates, and biofilms grown in the presence of chlorhexidine digluconate. It was found that the polymer coatings significantly reduced the amount of adherent bacteria and strongly altered the microbial composition, as analyzed by 16S RNA sequencing. This may hold relevance for maintaining oral health and the outcome of oral implants due to the existing synergism between the host and the oral microbiome. Especially the reduction of some bacterial species that are associated with poor oral health such as Tannerella forsythia and Fusobacterium nucleatum (observed for PSB and SMAMP), and Prevotella denticola (observed for all coatings) may positively modulate the oral biofilm, including in situ.
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Affiliation(s)
- Ali Al-Ahmad
- Medical Center, Department of Operative Dentistry and Periodontology, Faculty of Medicine, University of Freiburg, Hugstetter Strasse 55, 79106 Freiburg, Germany; (K.W.); (S.R.); (D.L.G.S.)
| | - Kira Wollensak
- Medical Center, Department of Operative Dentistry and Periodontology, Faculty of Medicine, University of Freiburg, Hugstetter Strasse 55, 79106 Freiburg, Germany; (K.W.); (S.R.); (D.L.G.S.)
- Bioactive Polymer Synthesis and Surface Engineering Group, Department of Microsystems Engineering (IMTEK) and Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany; (S.P.); (K.L.)
| | - Sibylle Rau
- Medical Center, Department of Operative Dentistry and Periodontology, Faculty of Medicine, University of Freiburg, Hugstetter Strasse 55, 79106 Freiburg, Germany; (K.W.); (S.R.); (D.L.G.S.)
| | - Diana Lorena Guevara Solarte
- Medical Center, Department of Operative Dentistry and Periodontology, Faculty of Medicine, University of Freiburg, Hugstetter Strasse 55, 79106 Freiburg, Germany; (K.W.); (S.R.); (D.L.G.S.)
| | - Stefan Paschke
- Bioactive Polymer Synthesis and Surface Engineering Group, Department of Microsystems Engineering (IMTEK) and Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany; (S.P.); (K.L.)
| | - Karen Lienkamp
- Bioactive Polymer Synthesis and Surface Engineering Group, Department of Microsystems Engineering (IMTEK) and Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany; (S.P.); (K.L.)
- Institut für Materialwissenschaft und Werkstoffkunde, Universität des Saarlandes, Campus, 66123 Saarbrücken, Germany
| | - Ori Staszewski
- Medical Center, Institute of Neuropathology, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany;
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Malayil L, Chattopadhyay S, Mongodin EF, Sapkota AR. Coupled DNA-labeling and sequencing approach enables the detection of viable-but-non-culturable Vibrio spp. in irrigation water sources in the Chesapeake Bay watershed. ENVIRONMENTAL MICROBIOME 2021; 16:13. [PMID: 34158117 PMCID: PMC8218497 DOI: 10.1186/s40793-021-00382-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 06/01/2021] [Indexed: 06/01/2023]
Abstract
Nontraditional irrigation water sources (e.g., recycled water, brackish water) may harbor human pathogens, including Vibrio spp., that could be present in a viable-but-nonculturable (VBNC) state, stymieing current culture-based detection methods. To overcome this challenge, we coupled 5-bromo-2'-deoxyuridine (BrdU) labeling, enrichment techniques, and 16S rRNA sequencing to identify metabolically-active Vibrio spp. in nontraditional irrigation water (recycled water, pond water, non-tidal freshwater, and tidal brackish water). Our coupled BrdU-labeling and sequencing approach revealed the presence of metabolically-active Vibrio spp. at all sampling sites. Whereas, the culture-based method only detected vibrios at three of the four sites. We observed the presence of V. cholerae, V. vulnificus, and V. parahaemolyticus using both methods, while V. aesturianus and V. shilonii were detected only through our labeling/sequencing approach. Multiple other pathogens of concern to human health were also identified through our labeling/sequencing approach including P. shigelloides, B. cereus and E. cloacae. Most importantly, 16S rRNA sequencing of BrdU-labeled samples resulted in Vibrio spp. detection even when our culture-based methods resulted in negative detection. This suggests that our novel approach can effectively detect metabolically-active Vibrio spp. that may have been present in a VBNC state, refining our understanding of the prevalence of vibrios in nontraditional irrigation waters.
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Affiliation(s)
- Leena Malayil
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD, USA
| | - Suhana Chattopadhyay
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD, USA
| | - Emmanuel F Mongodin
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Amy R Sapkota
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, MD, USA.
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Kim E, Yang SM, Kim HY. Analysis of Cultivable Microbial Community during Kimchi Fermentation Using MALDI-TOF MS. Foods 2021; 10:foods10051068. [PMID: 34066045 PMCID: PMC8151656 DOI: 10.3390/foods10051068] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 04/28/2021] [Accepted: 05/08/2021] [Indexed: 12/31/2022] Open
Abstract
Kimchi, a traditional Korean fermented vegetable, has received considerable attention for its health-promoting effects. This study analyzes the cultivable microbial community in kimchi fermented at different temperatures using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to comprehensively understand the factors affecting the quality of kimchi. Of the 5204 strains isolated from kimchi, aligned with the in-house database, 4467 (85.8%) were correctly identified at the species level. The fermentation temperature affected the microbial community by varying the pH and acidity, which was mainly caused by temperature-dependent competition between the different lactic acid bacteria (LAB) species in kimchi. LAB, such as Levilactobacillus (Lb.) brevis and Lactiplantibacillus (Lpb.) plantarum associated with rancidity and tissue softening, proliferated faster at higher temperatures than at low temperature. In addition, LAB, such as Latilactobacillus (Lat.) sakei and Leuconostoc (Leu.) mesenteroides, which produce beneficial substances and flavor, were mainly distributed in kimchi fermented at 4 °C. This study shows as a novelty that MALDI-TOF MS is a robust and economically affordable method for investigating viable microbial communities in kimchi.
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Affiliation(s)
| | | | - Hae-Yeong Kim
- Correspondence: ; Tel.: +82-31-201-2600; Fax: +82-31-204-8116
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Mycobactericidal Effects of Different Regimens Measured by Molecular Bacterial Load Assay among People Treated for Multidrug-Resistant Tuberculosis in Tanzania. J Clin Microbiol 2021; 59:JCM.02927-20. [PMID: 33536294 PMCID: PMC8092737 DOI: 10.1128/jcm.02927-20] [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: 11/19/2020] [Accepted: 01/28/2021] [Indexed: 12/17/2022] Open
Abstract
Rifampin or multidrug-resistant tuberculosis (RR/MDR-TB) treatment has largely transitioned to regimens free of the injectable aminoglycoside component, despite the drug class’ purported bactericidal activity early in treatment. We tested whether Mycobacterium tuberculosis Rifampin or multidrug-resistant tuberculosis (RR/MDR-TB) treatment has largely transitioned to regimens free of the injectable aminoglycoside component, despite the drug class’ purported bactericidal activity early in treatment. We tested whether Mycobacterium tuberculosis killing rates measured by tuberculosis molecular bacterial load assay (TB-MBLA) in sputa correlate with composition of the RR/MDR-TB regimen. Serial sputa were collected from patients with RR/MDR- and drug-sensitive TB at days 0, 3, 7, and 14, and then monthly for 4 months of anti-TB treatment. TB-MBLA was used to quantify viable M. tuberculosis 16S rRNA in sputum for estimation of colony forming units per ml (eCFU/ml). M. tuberculosis killing rates were compared among regimens using nonlinear-mixed-effects modeling of repeated measures. Thirty-seven patients produced 296 serial sputa and received treatment as follows: 13 patients received an injectable bedaquiline-free reference regimen, 9 received an injectable bedaquiline-containing regimen, 8 received an all-oral bedaquiline-based regimen, and 7 patients were treated for drug-sensitive TB with conventional rifampin/isoniazid/pyrazinamide/ethambutol (RHZE). Compared to the adjusted M. tuberculosis killing of −0.17 (95% confidence interval [CI] −0.23 to −0.12) for the injectable bedaquiline-free reference regimen, the killing rates were −0.62 (95% CI −1.05 to −0.20) log10 eCFU/ml for the injectable bedaquiline-containing regimen (P = 0.019), −0.35 (95% CI −0.65 to −0.13) log10 eCFU/ml for the all-oral bedaquiline-based regimen (P = 0.054), and −0.29 (95% CI −0.78 to +0.22) log10 eCFU/ml for the RHZE regimen (P = 0.332). Thus, M. tuberculosis killing rates from sputa were higher among patients who received bedaquiline but were further improved with the addition of an injectable aminoglycoside.
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