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Alsayed AR, Abed A, Khader HA, Al-Shdifat LMH, Hasoun L, Al-Rshaidat MMD, Alkhatib M, Zihlif M. Molecular Accounting and Profiling of Human Respiratory Microbial Communities: Toward Precision Medicine by Targeting the Respiratory Microbiome for Disease Diagnosis and Treatment. Int J Mol Sci 2023; 24:4086. [PMID: 36835503 PMCID: PMC9966333 DOI: 10.3390/ijms24044086] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/05/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
The wide diversity of microbiota at the genera and species levels across sites and individuals is related to various causes and the observed differences between individuals. Efforts are underway to further understand and characterize the human-associated microbiota and its microbiome. Using 16S rDNA as a genetic marker for bacterial identification improved the detection and profiling of qualitative and quantitative changes within a bacterial population. In this light, this review provides a comprehensive overview of the basic concepts and clinical applications of the respiratory microbiome, alongside an in-depth explanation of the molecular targets and the potential relationship between the respiratory microbiome and respiratory disease pathogenesis. The paucity of robust evidence supporting the correlation between the respiratory microbiome and disease pathogenesis is currently the main challenge for not considering the microbiome as a novel druggable target for therapeutic intervention. Therefore, further studies are needed, especially prospective studies, to identify other drivers of microbiome diversity and to better understand the changes in the lung microbiome along with the potential association with disease and medications. Thus, finding a therapeutic target and unfolding its clinical significance would be crucial.
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Affiliation(s)
- Ahmad R. Alsayed
- Department of Clinical Pharmacy and Therapeutics, Faculty of Pharmacy, Applied Science Private University, Amman 11931, Jordan
| | - Anas Abed
- Pharmacological and Diagnostic Research Centre, Faculty of Pharmacy, Al-Ahliyya Amman University, Amman 11931, Jordan
| | - Heba A. Khader
- Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmaceutical Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan
| | - Laith M. H. Al-Shdifat
- Department of Pharmaceutical Chemistry and Pharmacognosy, Faculty of Pharmacy, Applied Science Private University, Amman 11931, Jordan
| | - Luai Hasoun
- Department of Clinical Pharmacy and Therapeutics, Faculty of Pharmacy, Applied Science Private University, Amman 11931, Jordan
| | - Mamoon M. D. Al-Rshaidat
- Laboratory for Molecular and Microbial Ecology (LaMME), Department of Biological Sciences, School of Sciences, The University of Jordan, Amman 11942, Jordan
| | - Mohammad Alkhatib
- Department of Experimental Medicine, University of Rome “Tor Vergata”, 00133 Roma, Italy
| | - Malek Zihlif
- Department of Pharmacology, School of Medicine, The University of Jordan, Amman 11942, Jordan
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102
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Regueira-Iglesias A, Vázquez-González L, Balsa-Castro C, Blanco-Pintos T, Vila-Blanco N, Carreira MJ, Tomás I. Impact of 16S rRNA Gene Redundancy and Primer Pair Selection on the Quantification and Classification of Oral Microbiota in Next-Generation Sequencing. Microbiol Spectr 2023; 11:e0439822. [PMID: 36779795 PMCID: PMC10101033 DOI: 10.1128/spectrum.04398-22] [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: 10/27/2022] [Accepted: 01/16/2023] [Indexed: 02/14/2023] Open
Abstract
This study aimed to evaluate the number of 16S rRNA genes in the complete genomes of the bacterial and archaeal species inhabiting the human mouth and to assess how the use of different primer pairs would affect the detection and classification of redundant amplicons and matching amplicons (MAs) from different taxa. A total of 518 oral-bacterial and 191 oral-archaeal complete genomes were downloaded from the NCBI database, and their complete 16S rRNA genes were extracted. The numbers of genes and variants per genome were calculated. Next, 39 primer pairs were used to search for matches in the genomes and obtain amplicons. For each primer, we calculated the number of gene amplicons, variants, genomes, and species detected and the percentage of coverage at the species level with no MAs (SC-NMA). The results showed that 94.09% of oral bacteria and 52.59% of oral archaea had more than one intragenomic 16S rRNA gene. From 1.29% to 46.70% of bacterial species and from 4.65% to 38.89% of archaea detected by the primers had MAs. The best primers were the following (SC-NMA; region; position for Escherichia coli [GenBank version no. J01859.1]): KP_F048-OP_R030 for bacteria (93.55%; V3 to V7; 342 to 1079), KP_F018-KP_R063 for archaea (89.63%; V3 to V9; undefined to 1506), and OP_F114-OP_R121 for both domains (92.52%; V3 to V9; 340 to 1405). In addition to 16S rRNA gene redundancy, the presence of MAs must be controlled to ensure an accurate interpretation of microbial diversity data. The SC-NMA is a more useful parameter than the conventional coverage percentage for selecting the best primer pairs. The pairs used the most in the oral microbiome literature were not among the best performers. IMPORTANCE Hundreds of publications have studied the oral microbiome through 16S rRNA gene sequencing. However, none have assessed the number of 16S rRNA genes in the genomes of oral microbes, or how the use of primer pairs targeting different regions affects the detection of MAs from different taxa. Here, we found that almost all oral bacteria and more than half of oral archaea have more than one intragenomic 16S rRNA gene. The performance of the primer pairs in not detecting MAs increases as the length of the amplicon augments. As none of those most employed in the oral literature were among the best performers, we selected a series of primers to detect bacteria and/or archaea based on their percentage of species detected without MAs. The intragenomic 16S rRNA gene redundancy and the presence of MAs between distinct taxa need to be considered to ensure an accurate interpretation of microbial diversity data.
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Affiliation(s)
- Alba Regueira-Iglesias
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute Foundation of Santiago (FIDIS), Santiago de Compostela, Spain
| | - Lara Vázquez-González
- Centro Singular de Investigación en Tecnoloxías Intelixentes and Departamento de Electrónica e Computación, Universidade de Santiago de Compostela, Health Research Institute Foundation of Santiago (FIDIS), Santiago de Compostela, Spain
| | - Carlos Balsa-Castro
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute Foundation of Santiago (FIDIS), Santiago de Compostela, Spain
| | - Triana Blanco-Pintos
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute Foundation of Santiago (FIDIS), Santiago de Compostela, Spain
| | - Nicolás Vila-Blanco
- Centro Singular de Investigación en Tecnoloxías Intelixentes and Departamento de Electrónica e Computación, Universidade de Santiago de Compostela, Health Research Institute Foundation of Santiago (FIDIS), Santiago de Compostela, Spain
| | - Maria José Carreira
- Centro Singular de Investigación en Tecnoloxías Intelixentes and Departamento de Electrónica e Computación, Universidade de Santiago de Compostela, Health Research Institute Foundation of Santiago (FIDIS), Santiago de Compostela, Spain
| | - Inmaculada Tomás
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute Foundation of Santiago (FIDIS), Santiago de Compostela, Spain
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103
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Nuppunen-Puputti M, Kietäväinen R, Kukkonen I, Bomberg M. Implications of a short carbon pulse on biofilm formation on mica schist in microcosms with deep crystalline bedrock groundwater. Front Microbiol 2023; 14:1054084. [PMID: 36819068 PMCID: PMC9932282 DOI: 10.3389/fmicb.2023.1054084] [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: 09/26/2022] [Accepted: 01/06/2023] [Indexed: 02/05/2023] Open
Abstract
Microbial life in the deep subsurface occupies rock surfaces as attached communities and biofilms. Previously, epilithic Fennoscandian deep subsurface bacterial communities were shown to host genetic potential, especially for heterotrophy and sulfur cycling. Acetate, methane, and methanol link multiple biogeochemical pathways and thus represent an important carbon and energy source for microorganisms in the deep subsurface. In this study, we examined further how a short pulse of low-molecular-weight carbon compounds impacts the formation and structure of sessile microbial communities on mica schist surfaces over an incubation period of ∼3.5 years in microcosms containing deep subsurface groundwater from the depth of 500 m, from Outokumpu, Finland. The marker gene copy counts in the water and rock phases were estimated with qPCR, which showed that bacteria dominated the mica schist communities with a relatively high proportion of epilithic sulfate-reducing bacteria in all microcosms. The dominant bacterial phyla in the microcosms were Proteobacteria, Firmicutes, and Actinobacteria, whereas most fungal genera belonged to Ascomycota and Basidiomycota. Dissimilarities between planktic and sessile rock surface microbial communities were observed, and the supplied carbon substrates led to variations in the bacterial community composition.
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Affiliation(s)
- Maija Nuppunen-Puputti
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland,*Correspondence: Maija Nuppunen-Puputti,
| | | | - Ilmo Kukkonen
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Malin Bomberg
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
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104
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Hajdu-Rahkama R, Özkaya B, Lakaniemi AM, Puhakka JA. Potential of biological sulphur recovery from thiosulphate by haloalkaliphilic Thioalkalivibrio denitrificans. ENVIRONMENTAL TECHNOLOGY 2023; 44:804-816. [PMID: 34615437 DOI: 10.1080/09593330.2021.1985620] [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: 04/26/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
The aim of this study was to investigate the potential for elemental sulphur recovery from sulphurous solutions under aerobic and anoxic conditions by haloalkalophilic Thioalkalivibrio denitrificans at 0.8-19.6 g S2O32--S L-1 and 0.2-0.58 g NO2 L-1, respectively. The experiments were conducted as batch assays with haloalkaline (pH 10 and ≥ 14 g Na+ L-1) thiosulphate solution. Aerobically, the highest biotransformation rate of thiosulphate obtained was 0.03 h-1 at 8.5 g L S2O32--S. Based on Monod model, the maximum substrate utilisation rate (qm) was 0.024 h-1 with half saturation constant (Ks) 0.42 g S2O32--S L-1 at initial [S2O32--S] of 14 g L-1. S0 accumulated at [S2O32--S] ≥ 1.5 g L-1 (10% yield at initial 9.5 g S2O32--S L-1) and the highest S0 yield estimated with the model was 61% with initial [S2O32--S] of 16.5 g L-1. Anoxically, the maximum nitrite removal rate based on Monod modelling was 0.011 h-1 with Ks = 0.84 g NO2- L-1. Aerobically and anoxically the maximum specific growth rates (µm) were 0.046 and 0.022 h-1, respectively. In summary, high-rate aerobic biotransformation kinetics of thiosulphate were demonstrated, whereas the rates were slower and no S0 accumulated under anoxic conditions. Thus, future developments of biotechnical applications for the recovery of S0 from haloalkaline streams from the process industry should focus on aerobic treatment.HighlightsHaloalkaline S2O32- biotransformations kinetics by Thioalkalivibrio denitrificansAerobic thiosulphate-S bioconversion up to 0.024 h-1 with Ks = 0.42 g S2O32--S L-110% S0 yield with initial 9.5 g S2O32--S L-1 in aerobic conditionAnoxic NO2 removal up to 0.01 h-1 with Ks = 0.84 g NO2- L-1.
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Affiliation(s)
- Réka Hajdu-Rahkama
- Faculty of Engineering and Natural Sciences, Bio- and Circular Economy Research Group, Tampere University, Tampere, Finland
| | - Bestamin Özkaya
- Faculty of Engineering and Natural Sciences, Bio- and Circular Economy Research Group, Tampere University, Tampere, Finland
- Department of Environmental Engineering, Yildiz Technical University, Istanbul, Turkey
| | - Aino-Maija Lakaniemi
- Faculty of Engineering and Natural Sciences, Bio- and Circular Economy Research Group, Tampere University, Tampere, Finland
| | - Jaakko A Puhakka
- Faculty of Engineering and Natural Sciences, Bio- and Circular Economy Research Group, Tampere University, Tampere, Finland
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105
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Hillyer KE, Raes E, Bissett A, Beale DJ. Multi-omics eco-surveillance of bacterial community function in legacy contaminated estuary sediments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 318:120857. [PMID: 36513173 DOI: 10.1016/j.envpol.2022.120857] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Complex legacy contamination is a major issue for many estuaries, with toxicity affecting change in bacterial communities, and their provision of associated goods and services. Sequencing surveys of bacterial community composition provide inferred function; however, additional insights may be generated by measurement of realised metabolic phenotypes. We apply multi-omics (genomics, lipidomics, and metabolomics), with traditional sediment quality analyses, to characterise sediment-associated bacterial communities in an estuary subject to legacy metal contamination (Zn, Hg, As, Cd, Cu and Pb). Analyses of bacterial composition and inferred function (genomics) are coupled with measurements of realised bacterial phenotype (metabolomics and lipidomics) at multiple industrialised and reference sites. At sites with the highest sediment metal concentrations (NTB), we also observed increased abundances of hydrocarbon and sulphuric acid metabolites, indicating additional sediment contamination. Bacterial phyla across sampled sites were dominated by Proteobacteria and Desulfobacteria. NTB sites were enriched with metabolically versatile, cooperative and biofilm forming phyla including, Zixibacteria, Spirochaetota, SAR324 clade, Proteobacteria, Latescibacterota, Desulfobacterota, Deferrisomtota and Acidobateriota; with inferred functions characterised by sulphur metabolism, pathways associated with the degradation of complex organic molecules, and fermentation. Reference sites were characterised by enhanced vitamin biosynthesis, cell wall, cofactor and carbohydrate biosynthesis, and CO2 fixation. Measured metabolic phenotypes at NTB sites supported predicted functions, with most consistent change observed to naphthalene and aminobenzoate degradation pathways and carbohydrate metabolism (galactose, amino and nucleotide sugar). Change in NTB metabolite profiles was most highly correlated with sediment Hg concentrations, indicative of toxic exposure and potential for Hg methylation. Lipid profiles generated further insight into potential functional (hydroxy fatty acids) and community level change (ceramide phosphoethanolamines, unsaturated glycerides). Multi-omics outputs provided insights into bacterial community functions, modes of contaminant toxicity and expressed mechanisms of adaptation, necessary to better inform management decisions and predictive models in increasingly human-influenced environments.
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Affiliation(s)
- Katie E Hillyer
- Land and Water, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Ecosciences Precinct, Dutton Park, QLD, Australia
| | - Eric Raes
- Oceans and Atmosphere, CSIRO, Battery Point, Hobart, TAS, Australia; Flourishing Oceans, Minderoo Foundation, Broadway, Nedlands, WA, Australia
| | - Andrew Bissett
- Oceans and Atmosphere, CSIRO, Battery Point, Hobart, TAS, Australia
| | - David J Beale
- Land and Water, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Ecosciences Precinct, Dutton Park, QLD, Australia.
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106
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Yuan B, Guo M, Wu W, Zhou X, Li M, Xie S. Spatial and Seasonal Patterns of Sediment Bacterial Communities in Large River Cascade Reservoirs: Drivers, Assembly Processes, and Co-occurrence Relationship. MICROBIAL ECOLOGY 2023; 85:586-603. [PMID: 35338380 DOI: 10.1007/s00248-022-01999-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
Sediment bacteria play an irreplaceable role in promoting the function and biogeochemical cycle of the freshwater ecosystem; however, little is known about their biogeographical patterns and community assembly mechanisms in large river suffering from cascade development. Here, we investigated the spatiotemporal distribution patterns of bacterial communities employing next-generation sequencing analysis and multivariate statistical analyses from the Lancang River cascade reservoirs during summer and winter. We found that sediment bacterial composition has a significant seasonal turnover due to the modification of cascade reservoirs operation mode, and the spatial consistency of biogeographical models (including distance-decay relationship and covariation of community composition with geographical distance) also has subtle changes. The linear regression between the dissimilarity of bacterial communities in sediments, geographical and environmental distance showed that the synergistic effects of geographical and environmental factors explained the influence on bacterial communities. Furthermore, the environmental difference explained little variations (19.40%) in community structure, implying the homogeneity of environmental conditions across the cascade reservoirs of Lancang River. From the quantification of the ecological process, the homogeneous selection was recognized as the dominating factor of bacterial community assembly. The co-occurrence topological network analyses showed that the key genera were more important than the most connected genera. In general, the assembly of bacterial communities in sediment of cascade reservoirs was mediated by both deterministic and stochastic processes and is always dominated by homogeneous selection with the seasonal switching, but the effects of dispersal limitation and ecological drift cannot be ignored.
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Affiliation(s)
- Bo Yuan
- College of Geology and Environment, Xi'an University of Science and Technology, Xi'an, 710054, Shaanxi, China.
| | - Mengjing Guo
- State Key Laboratory of Eco-Hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an, 710048, Shaanxi, China
| | - Wei Wu
- State Key Laboratory of Eco-Hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an, 710048, Shaanxi, China
| | - Xiaode Zhou
- State Key Laboratory of Eco-Hydraulics in Northwest Arid Region, Xi'an University of Technology, Xi'an, 710048, Shaanxi, China
| | - Miaojie Li
- College of Geology and Environment, Xi'an University of Science and Technology, Xi'an, 710054, Shaanxi, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
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107
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C-, N-, S-, and P-Substrate Spectra in and the Impact of Abiotic Factors on Assessing the Biotechnological Potential of Paracoccus pantotrophus. Appl Microbiol 2023. [DOI: 10.3390/applmicrobiol3010013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Modern biotechnology benefits from the introduction of novel chassis organisms in remedying the limitations of already-established strains. For this, Paracoccus pantotrophus was chosen for in-depth assessment. Its unique broad metabolism and robustness against abiotic stressors make this strain a well-suited chassis candidate. This study set out to comprehensively overview abiotic influences on the growth performance of five P. pantotrophus strains. These data can aid in assessing the suitability of this genus for chassis development by using the type strain as a preliminary model organism. The five P. pantotrophus strains DSM 2944T, DSM 11072, DSM 11073, DSM 11104, and DSM 65 were investigated regarding their growth on various carbon sources and other nutrients. Our data show a high tolerance against osmotic pressure for the type strain with both salts and organic osmolytes. It was further observed that P. pantotrophus prefers organic acids over sugars. All of the tested strains were able to grow on short-chain alkanes, which would make P. pantotrophus a candidate for bioremediation and the upcycling of plastics. In conclusion, we were able to gain insights into several P. pantotrophus strains, which will aid in further introducing this species, or even another species from this genus, as a candidate for future biotechnological processes.
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108
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Ohkusu K. Enterococcus faecium 129 BIO 3B is classified as Enterococcus lactis 129 BIO 3B. BIOSCIENCE OF MICROBIOTA, FOOD AND HEALTH 2023; 42:180-185. [PMID: 37404571 PMCID: PMC10315194 DOI: 10.12938/bmfh.2022-088] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/10/2023] [Indexed: 07/06/2023]
Abstract
Enterococcus faecium 129 BIO 3B is a lactic acid bacterium that has been safely used as a probiotic product for over 100 years. Recently, concerns about its safety have arisen because some species of E. faecium belong to the vancomycin-resistant enterococci. The groups of E. faecium with less pathogenic potential have been split into a separate species (Enterococcus lactis). In this study, I investigated the phylogenetic classification and safety of E. faecium 129 BIO 3B as well as E. faecium 129 BIO 3B-R, which is naturally resistant to ampicillin. Mass spectrometry and basic local alignment search tool analysis using specific gene regions failed to differentiate 3B and 3B-R into E. faecium or E. lactis. However, multilocus sequence typing successfully identified 3B and 3B-R as the same sequence types as E. lactis. Overall genome relatedness indices showed that 3B and 3B-R have high degrees of homology with E. lactis. Gene amplification was confirmed for 3B and 3B-R with E. lactis species-specific primers. The minimum inhibitory concentration of ampicillin was confirmed to be 2 µg/mL for 3B, which is within the safety standard for E. faecium set by the European Food Safety Authority. Based on the above results, E. faecium 129 BIO 3B and E. faecium 129 BIO 3B-R were classified as E. lactis. The absence of pathogenic genes except for fms21 in this study demonstrates that these bacteria are safe for use as probiotics.
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Affiliation(s)
- Kiyofumi Ohkusu
- Department of Microbiology, Tokyo Medical University, 6-1-1 Shinjuku-ku, Shinjuku, Tokyo 160-8402, Japan
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109
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Morrison AG, Sarkar S, Umar S, Lee STM, Thomas SM. The Contribution of the Human Oral Microbiome to Oral Disease: A Review. Microorganisms 2023; 11:318. [PMID: 36838283 PMCID: PMC9962706 DOI: 10.3390/microorganisms11020318] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/16/2023] [Accepted: 01/20/2023] [Indexed: 01/28/2023] Open
Abstract
The oral microbiome is an emerging field that has been a topic of discussion since the development of next generation sequencing and the implementation of the human microbiome project. This article reviews the current literature surrounding the oral microbiome, briefly highlighting most recent methods of microbiome characterization including cutting edge omics, databases for the microbiome, and areas with current gaps in knowledge. This article also describes reports on microorganisms contained in the oral microbiome which include viruses, archaea, fungi, and bacteria, and provides an in-depth analysis of their significant roles in tissue homeostasis. Finally, we detail key bacteria involved in oral disease, including oral cancer, and the current research surrounding their role in stimulation of inflammatory cytokines, the role of gingival crevicular fluid in periodontal disease, the creation of a network of interactions between microorganisms, the influence of the planktonic microbiome and cospecies biofilms, and the implications of antibiotic resistance. This paper provides a comprehensive literature analysis while also identifying gaps in knowledge to enable future studies to be conducted.
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Affiliation(s)
- Austin Gregory Morrison
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Soumyadev Sarkar
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Shahid Umar
- Department of General Surgery, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Sonny T. M. Lee
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
- 1717 Claflin Road, 136 Ackert Hall, Manhattan, KS 66506, USA
| | - Sufi Mary Thomas
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Departments of Otolaryngology, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Departments of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
- 3901 Rainbow Blvd., 4031 Wahl Hall East, MS 3040, Kansas City, KS 66160, USA
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110
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Anderson KE, Copeland DC, Erickson RJ, Floyd AS, Maes PC, Mott BM. A high-throughput sequencing survey characterizing European foulbrood disease and Varroosis in honey bees. Sci Rep 2023; 13:1162. [PMID: 36670153 PMCID: PMC9859799 DOI: 10.1038/s41598-023-28085-2] [Citation(s) in RCA: 4] [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: 03/09/2022] [Accepted: 01/12/2023] [Indexed: 01/21/2023] Open
Abstract
As essential pollinators of ecosystems and agriculture, honey bees (Apis mellifera) are host to a variety of pathogens that result in colony loss. Two highly prevalent larval diseases are European foulbrood (EFB) attributed to the bacterium Melissococcus plutonius, and Varroosis wherein larvae can be afflicted by one or more paralytic viruses. Here we used high-throughput sequencing and qPCR to detail microbial succession of larval development from six diseased, and one disease-free apiary. The disease-free larval microbiome revealed a variety of disease-associated bacteria in early larval instars, but later developmental stages were dominated by beneficial symbionts. Microbial succession associated with EFB pathology differed by apiary, characterized by associations with various gram-positive bacteria. At one apiary, diseased larvae were uniquely described as "melting and deflated", symptoms associated with Varroosis. We found that Acute Bee Paralysis Virus (ABPV) levels were significantly associated with these symptoms, and various gram-negative bacteria became opportunistic in the guts of ABPV afflicted larvae. Perhaps contributing to disease progression, the ABPV associated microbiome was significantly depleted of gram-positive bacteria, a likely result of recent antibiotic application. Our results contribute to the understanding of brood disease diagnosis and treatment, a growing problem for beekeeping and agriculture worldwide.
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Affiliation(s)
- Kirk E Anderson
- Carl Hayden Bee Research Center, USDA Agricultural Research Service, 2000 E. Allen Rd., Tucson, AZ, 85719, USA.
| | - Duan C Copeland
- Carl Hayden Bee Research Center, USDA Agricultural Research Service, 2000 E. Allen Rd., Tucson, AZ, 85719, USA
- Department of Microbiology, School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Robert J Erickson
- Carl Hayden Bee Research Center, USDA Agricultural Research Service, 2000 E. Allen Rd., Tucson, AZ, 85719, USA
| | - Amy S Floyd
- Carl Hayden Bee Research Center, USDA Agricultural Research Service, 2000 E. Allen Rd., Tucson, AZ, 85719, USA
- Department of Entomology and Center for Insect Science, University of Arizona, Tucson, AZ, 85721, USA
| | - Patrick C Maes
- Department of Entomology and Center for Insect Science, University of Arizona, Tucson, AZ, 85721, USA
| | - Brendon M Mott
- Carl Hayden Bee Research Center, USDA Agricultural Research Service, 2000 E. Allen Rd., Tucson, AZ, 85719, USA
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111
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Amin H, Marshall IPG, Bertelsen RJ, Wouters IM, Schlünssen V, Sigsgaard T, Šantl-Temkiv T. Optimization of bacterial DNA and endotoxin extraction from settled airborne dust. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159455. [PMID: 36252657 DOI: 10.1016/j.scitotenv.2022.159455] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/03/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Collecting and obtaining sufficient amount of airborne particles for multiple microbial component assessments can be challenging. A passive dust sampling device, the electrostatic dust fall collector (EDC) has been established for assessing airborne exposures including endotoxin and glucans. Recently, with advances in next-generation sequencing techniques, EDCs were used to collect microbial cells for DNA sequencing analysis to promote the study of airborne bacterial and fungal communities. However, low DNA yields have been problematic when employing passive sampling with EDC. To address this challenge, we attempted to increase the efficiency of extraction. We compared DNA extraction efficiency of bacterial components from EDCs captured on filters through filtration using five extraction techniques. By measuring the abundance, diversity and structure of bacterial communities using qPCR and amplicon sequencing targeting 16S rRNA genes, we found that two techniques outperformed the rest. Furthermore, we developed protocols to simultaneously extract both DNA and endotoxin from a single EDC cloth. Our technique promotes a high quality to price ratio and may be employed in large epidemiological studies addressing airborne bacterial exposure where a large number of samples is needed.
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Affiliation(s)
- Hesham Amin
- Department of Clinical Science, University of Bergen, Bergen, Norway.
| | - Ian P G Marshall
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Randi J Bertelsen
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Inge M Wouters
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Vivi Schlünssen
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Torben Sigsgaard
- Department of Public Health, Environment, Work and Health, Danish Ramazzini Centre, Aarhus University, Aarhus, Denmark
| | - Tina Šantl-Temkiv
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
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Feng A, Akter S, Leigh SA, Wang H, Pharr GT, Evans J, Branton SL, Landinez MP, Pace L, Wan XF. Genomic diversity, pathogenicity and antimicrobial resistance of Escherichia coli isolated from poultry in the southern United States. BMC Microbiol 2023; 23:15. [PMID: 36647025 PMCID: PMC9841705 DOI: 10.1186/s12866-022-02721-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 11/30/2022] [Indexed: 01/18/2023] Open
Abstract
Escherichia coli (E. coli) are typically present as commensal bacteria in the gastro-intestinal tract of most animals including poultry species, but some avian pathogenic E. coli (APEC) strains can cause localized and even systematic infections in domestic poultry. Emergence and re-emergence of antimicrobial resistant isolates (AMR) constrain antibiotics usage in poultry production, and development of an effective vaccination program remains one of the primary options in E. coli disease prevention and control for domestic poultry. Thus, understanding genetic and pathogenic diversity of the enzootic E. coli isolates, particularly APEC, in poultry farms is the key to designing an optimal vaccine candidate and to developing an effective vaccination program. This study explored the genomic and pathogenic diversity among E. coli isolates in southern United States poultry. A total of nine isolates were recovered from sick broilers from Mississippi, and one from Georgia, with epidemiological variations among clinical signs, type of housing, and bird age. The genomes of these isolates were sequenced by using both Illumina short-reads and Oxford Nanopore long-reads, and our comparative analyses suggested data from both platforms were highly consistent. The 16 s rRNA based phylogenetic analyses showed that the 10 bacteria strains are genetically closer to each other than those in the public database. However, whole genome analyses showed that these 10 isolates encoded a diverse set of reported virulence and AMR genes, belonging to at least nine O:H serotypes, and are genetically clustered with at least five different groups of E. coli isolates reported by other states in the United States. Despite the small sample size, this study suggested that there was a large extent of genomic and serological diversity among E. coli isolates in southern United States poultry. A large-scale comprehensive study is needed to understand the overall genomic diversity and the associated virulence, and such a study will be important to develop a broadly protective E. coli vaccine.
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Affiliation(s)
- Aijing Feng
- grid.134936.a0000 0001 2162 3504Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO USA ,grid.134936.a0000 0001 2162 3504Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO USA ,grid.134936.a0000 0001 2162 3504Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO USA
| | - Sadia Akter
- grid.134936.a0000 0001 2162 3504Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO USA ,grid.134936.a0000 0001 2162 3504Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO USA ,grid.134936.a0000 0001 2162 3504Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO USA
| | - Spencer A. Leigh
- Poultry Research Unit, USDA Agricultural Research Service, Mississippi State, MS USA
| | - Hui Wang
- grid.260120.70000 0001 0816 8287Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS USA
| | - G. Todd Pharr
- grid.260120.70000 0001 0816 8287Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS USA
| | - Jeff Evans
- Poultry Research Unit, USDA Agricultural Research Service, Mississippi State, MS USA
| | - Scott L. Branton
- Poultry Research Unit, USDA Agricultural Research Service, Mississippi State, MS USA
| | - Martha Pulido Landinez
- grid.260120.70000 0001 0816 8287Poultry Research and Diagnostic Laboratory, College of Veterinary Medicine, Mississippi State University, Pearl, MS USA
| | - Lanny Pace
- grid.260120.70000 0001 0816 8287Mississippi Veterinary Research and Diagnostic Laboratory System, College of Veterinary Medicine, Mississippi State University, Pearl, MS USA
| | - Xiu-Feng Wan
- grid.134936.a0000 0001 2162 3504Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO USA ,grid.134936.a0000 0001 2162 3504Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO USA ,grid.134936.a0000 0001 2162 3504Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO USA
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Kurnijasanti R, Rais M, Sudjarwo SA. Screening for Anti Mycobacterium tuberculosis Activity of Streptomyces sp. from Lapindo Mud in Sidoarjo, Indonesia. Open Access Maced J Med Sci 2023. [DOI: 10.3889/oamjms.2023.10765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023] Open
Abstract
BACKGROUND: Streptomyces sp. from Indonesian soil have not been explored and isolated to find new strains as a source of antibiotics for the treatment of tuberculosis (TB) disease.
AIM: In this study, the effect of Streptomyces spp. from Lapindo mud in Sidoarjo, Indonesia be observed, to find out whether Streptomyces spp. has anti-TB activity.
METHODS: The primers Strep F; 5-AGAGTTTGAT CCTGKGTCAG-3 and Strep R; 5-AAGGGAG GTGATCCAKKGKGA-3 were used in polymerase chain reaction amplification of the 16S rRNA gene against Streptomyces strains. The anti-TB activity of Streptomyces sp. was determined by broth dilution method using Middlebrook 7H9 media.
RESULTS: The results showed that new types of Streptomyces spp., namely, Streptomyces A, Streptomyces D, Streptomyces Ea, Streptomyces Ep, Streptomyces I, Streptomyces F, and Streptomyces G from garbage dump soils. This result also showed that the activity of Streptomyces I, Streptomyces F, and Streptomyces G could inhibit the Mycobacterium TB growth by with inhibitory zones, respectively, 2 ± 0.3; 8 ± 0.7 and 15 ± 0.9mm, while Streptomyces A, Streptomyces D, Streptomyces Ea, and Streptomyces Ep did not inhibit M. TB.
CONCLUSION: Thus, from the results obtained, it can be concluded that Streptomyces extract mainly Streptomyces G has promising anti-TB activity by preliminary in vitro techniques. Therefore, it has the definite potential as a source of compounds that may be developed further into antimycobacterial drugs.
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Berland M, Meslier V, Berreira Ibraim S, Le Chatelier E, Pons N, Maziers N, Thirion F, Gauthier F, Plaza Oñate F, Furet JP, Leboime A, Said-Nahal R, Levenez F, Galleron N, Quinquis B, Langella P, Ehrlich SD, Breban M. Both Disease Activity and HLA-B27 Status Are Associated With Gut Microbiome Dysbiosis in Spondyloarthritis Patients. Arthritis Rheumatol 2023; 75:41-52. [PMID: 35818337 PMCID: PMC10099252 DOI: 10.1002/art.42289] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 04/27/2022] [Accepted: 06/30/2022] [Indexed: 02/04/2023]
Abstract
OBJECTIVE Gut microbiome dysbiosis has previously been reported in spondyloarthritis (SpA) patients and could be critically involved in the pathogenesis of this disorder. The objectives of this study were to further characterize the microbiota structure in SpA patients and to investigate the relationship between dysbiosis and disease activity in light of the putative influence of the genetic background. METHODS Shotgun sequencing was performed on fecal DNA isolated from stool samples from 2 groups of adult volunteers: SpA patients (n = 102) and healthy controls (n = 63). A subset of the healthy controls comprised the age-matched siblings of patients whose HLA-B27 status was known. Changes in gut microbiota composition were assessed based on species diversity, enterotypes, and taxonomic and functional differences. RESULTS Dysbiosis was confirmed in SpA patients as compared to healthy controls. The restriction of microbiota diversity was detected in patients with the most active disease, and the abundance of several bacterial species was correlated with Bath Ankylosing Spondylitis Disease Activity Index score. Among healthy controls, significant differences in microbiota composition were also detected between the HLA-B27-positive and the HLA-B27-negative siblings of SpA patients. We highlighted a decreased abundance of several species of bacteria in SpA patients, especially those bacteria belonging to the Clostridiales order. Among the few species of bacteria showing increased abundance, Ruminococcus gnavus was one of the top differentiating species. CONCLUSION These findings reveal that genetic background and level of disease activity are likely to influence the composition of the gut microbiota of patients with SpA. It may be appropriate for further research on chronic arthritis to focus on these key parameters.
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Affiliation(s)
- Magali Berland
- Université Paris-Saclay and MetaGenoPolis, INRAE, Jouy-en-Josas, France
| | - Victoria Meslier
- Université Paris-Saclay and MetaGenoPolis, INRAE, Jouy-en-Josas, France
| | | | | | - Nicolas Pons
- Université Paris-Saclay and MetaGenoPolis, INRAE, Jouy-en-Josas, France
| | - Nicolas Maziers
- Université Paris-Saclay and MetaGenoPolis, INRAE, Jouy-en-Josas, France
| | - Florence Thirion
- Université Paris-Saclay and MetaGenoPolis, INRAE, Jouy-en-Josas, France
| | - Franck Gauthier
- Université Paris-Saclay and MetaGenoPolis, INRAE, Jouy-en-Josas, France
| | | | - Jean-Pierre Furet
- AgroParisTech, Université Paris-Saclay and the Micalis Institute, INRAE, Jouy-en-Josas, France, and Paris Center for Microbiome Medicine (PaCeMM) FHU, Paris, France
| | - Ariane Leboime
- Service de Rhumatologie, Hôpital Ambroise Paré, AP-HP, Boulogne, France
| | - Roula Said-Nahal
- Service de Rhumatologie, Hôpital Ambroise Paré, AP-HP, Boulogne, France
| | - Florence Levenez
- Université Paris-Saclay and MetaGenoPolis, INRAE, Jouy-en-Josas, France
| | - Nathalie Galleron
- Université Paris-Saclay and MetaGenoPolis, INRAE, Jouy-en-Josas, France
| | - Benoît Quinquis
- Université Paris-Saclay and MetaGenoPolis, INRAE, Jouy-en-Josas, France
| | - Philippe Langella
- AgroParisTech, Université Paris-Saclay and the Micalis Institute, INRAE, Jouy-en-Josas, France, and Paris Center for Microbiome Medicine (PaCeMM) FHU, Paris, France
| | - Stanislav Dusko Ehrlich
- Université Paris-Saclay, MetaGenoPolis, INRAE, Jouy-en-Josas, France, and the Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK, and Paris Center for Microbiome Medicine (PaCeMM) FHU, Paris, France
| | - Maxime Breban
- Service de Rhumatologie, Hôpital Ambroise Paré, AP-HP, Boulogne, France, Infection & Inflammation, UMR 1173, Inserm, Université de Versailles-Paris-Saclay, Montigny-le-Bretonneux, France, and Laboratoire d'Excellence Inflamex, Université Paris Descartes, Sorbonne Paris Cité, and Paris Center for Microbiome Medicine (PaCeMM) FHU, Paris, France
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Pible O, Petit P, Steinmetz G, Rivasseau C, Armengaud J. Taxonomical composition and functional analysis of biofilms sampled from a nuclear storage pool. Front Microbiol 2023; 14:1148976. [PMID: 37125163 PMCID: PMC10133526 DOI: 10.3389/fmicb.2023.1148976] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/27/2023] [Indexed: 05/02/2023] Open
Abstract
Sampling small amounts of biofilm from harsh environments such as the biofilm present on the walls of a radioactive material storage pool offers few analytical options if taxonomic characterization and estimation of the different biomass contributions are the objectives. Although 16S/18S rRNA amplification on extracted DNA and sequencing is the most widely applied method, its reliability in terms of quantitation has been questioned as yields can be species-dependent. Here, we propose a tandem-mass spectrometry proteotyping approach consisting of acquiring peptide data and interpreting then against a generalist database without any a priori. The peptide sequence information is transformed into useful taxonomical information that allows to obtain the different biomass contributions at different taxonomical ranks. This new methodology is applied for the first time to analyze the composition of biofilms from minute quantities of material collected from a pool used to store radioactive sources in a nuclear facility. For these biofilms, we report the identification of three genera, namely Sphingomonas, Caulobacter, and Acidovorax, and their functional characterization by metaproteomics which shows that these organisms are metabolic active. Differential expression of Gene Ontology GOslim terms between the two main microorganisms highlights their metabolic specialization.
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Affiliation(s)
- Olivier Pible
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, France
| | - Pauline Petit
- Université Grenoble Alpes, CEA, CNRS, IRIG, Grenoble, France
| | - Gérard Steinmetz
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, France
| | - Corinne Rivasseau
- Université Grenoble Alpes, CEA, CNRS, IRIG, Grenoble, France
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, France
- *Correspondence: Jean Armengaud,
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Andrianjakarivony HF, Bettarel Y, Armougom F, Desnues C. Phage-Host Prediction Using a Computational Tool Coupled with 16S rRNA Gene Amplicon Sequencing. Viruses 2022; 15:76. [PMID: 36680116 PMCID: PMC9862649 DOI: 10.3390/v15010076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/13/2022] [Accepted: 12/20/2022] [Indexed: 12/29/2022] Open
Abstract
Metagenomics studies have revealed tremendous viral diversity in aquatic environments. Yet, while the genomic data they have provided is extensive, it is unannotated. For example, most phage sequences lack accurate information about their bacterial host, which prevents reliable phage identification and the investigation of phage-host interactions. This study aimed to take this knowledge further, using a viral metagenomic framework to decipher the composition and diversity of phage communities and to predict their bacterial hosts. To this end, we used water and sediment samples collected from seven sites with varying contamination levels in the Ebrié Lagoon in Abidjan, Ivory Coast. The bacterial communities were characterized using the 16S rRNA metabarcoding approach, and a framework was developed to investigate the virome datasets that: (1) identified phage contigs with VirSorter and VIBRANT; (2) classified these contigs with MetaPhinder using the phage database (taxonomic annotation); and (3) predicted the phages' bacterial hosts with a machine learning-based tool: the Prokaryotic Virus-Host Predictor. The findings showed that the taxonomic profiles of phages and bacteria were specific to sediment or water samples. Phage sequences assigned to the Microviridae family were widespread in sediment samples, whereas phage sequences assigned to the Siphoviridae, Myoviridae and Podoviridae families were predominant in water samples. In terms of bacterial communities, the phyla Latescibacteria, Zixibacteria, Bacteroidetes, Acidobacteria, Calditrichaeota, Gemmatimonadetes, Cyanobacteria and Patescibacteria were most widespread in sediment samples, while the phyla Epsilonbacteraeota, Tenericutes, Margulisbacteria, Proteobacteria, Actinobacteria, Planctomycetes and Marinimicrobia were most prevalent in water samples. Significantly, the relative abundance of bacterial communities (at major phylum level) estimated by 16S rRNA metabarcoding and phage-host prediction were significantly similar. These results demonstrate the reliability of this novel approach for predicting the bacterial hosts of phages from shotgun metagenomic sequencing data.
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Affiliation(s)
- Harilanto Felana Andrianjakarivony
- Microbes, Evolution, Phylogeny, and Infection (MEΦI), IHU—Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
- Microbiologie Environnementale Biotechnologie (MEB), Mediterranean Institute of Oceanography (MIO), 163 Avenue de Luminy, 13009 Marseille, France
| | - Yvan Bettarel
- MARBEC, Marine Biodiversity, Exploitation & Conservation, Université de Montpellier, CNRS, Ifremer, IRD, 093 Place Eugène Bataillon, 34090 Montpellier, France
| | - Fabrice Armougom
- Microbiologie Environnementale Biotechnologie (MEB), Mediterranean Institute of Oceanography (MIO), 163 Avenue de Luminy, 13009 Marseille, France
| | - Christelle Desnues
- Microbes, Evolution, Phylogeny, and Infection (MEΦI), IHU—Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
- Microbiologie Environnementale Biotechnologie (MEB), Mediterranean Institute of Oceanography (MIO), 163 Avenue de Luminy, 13009 Marseille, France
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Miller S, Greenwald H, Kennedy LC, Kantor RS, Jiang R, Pisarenko A, Chen E, Nelson KL. Microbial Water Quality through a Full-Scale Advanced Wastewater Treatment Demonstration Facility. ACS ES&T ENGINEERING 2022; 2:2206-2219. [PMID: 36530600 PMCID: PMC9745798 DOI: 10.1021/acsestengg.2c00198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 06/17/2023]
Abstract
The fates of viruses, bacteria, and antibiotic resistance genes during advanced wastewater treatment are important to assess for implementation of potable reuse systems. Here, a full-scale advanced wastewater treatment demonstration facility (ozone, biological activated carbon filtration, micro/ultrafiltration, reverse osmosis, and advanced oxidation) was sampled over three months. Atypically, no disinfectant residual was applied before the microfiltration step. Microbial cell concentrations and viability were assessed via flow cytometry and adenosine triphosphate (ATP). Concentrations of bacteria (16S rRNA gene), viruses (human adenovirus and JC polyomavirus), and antibiotic resistance genes (sul1 and bla TEM ) were assessed via quantitative PCR following the concentration of large sample volumes by dead-end ultrafiltration. In all membrane filtration permeates, microbial concentrations were higher than previously reported for chloraminated membranes, and log10 reduction values were lower than expected. Concentrations of 16S rRNA and sul1 genes were reduced by treatment but remained quantifiable in reverse osmosis permeate. It is unclear whether sul1 in the RO permeate was from the passage of resistance genes or new growth of microorganisms, but the concentrations were on the low end of those reported for conventional drinking water distribution systems. Adenovirus, JC polyomavirus, and bla TEM genes were reduced below the limit of detection (∼10-2 gene copies per mL) by microfiltration. The results provide insights into how treatment train design and operation choices affect microbial water quality as well as the use of flow cytometry and ATP for online monitoring and process control.
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Affiliation(s)
- Scott Miller
- Department
of Civil and Environmental Engineering, College of Engineering, University of California, Berkeley, Berkeley, California 94720, United States
- National
Science Foundation Engineering Research Center for Re-inventing the
Nation’s Urban Water Infrastructure (ReNUWIt), Berkeley, California 94720, United States
| | - Hannah Greenwald
- Department
of Civil and Environmental Engineering, College of Engineering, University of California, Berkeley, Berkeley, California 94720, United States
- National
Science Foundation Engineering Research Center for Re-inventing the
Nation’s Urban Water Infrastructure (ReNUWIt), Berkeley, California 94720, United States
| | - Lauren C. Kennedy
- Department
of Civil and Environmental Engineering, College of Engineering, University of California, Berkeley, Berkeley, California 94720, United States
- National
Science Foundation Engineering Research Center for Re-inventing the
Nation’s Urban Water Infrastructure (ReNUWIt), Berkeley, California 94720, United States
- Department
of Civil and Environmental Engineering, College of Engineering, Stanford University, Stanford, California 94305, United States
| | - Rose S. Kantor
- Department
of Civil and Environmental Engineering, College of Engineering, University of California, Berkeley, Berkeley, California 94720, United States
- National
Science Foundation Engineering Research Center for Re-inventing the
Nation’s Urban Water Infrastructure (ReNUWIt), Berkeley, California 94720, United States
| | - Renjing Jiang
- Department
of Civil and Environmental Engineering, College of Engineering, University of California, Berkeley, Berkeley, California 94720, United States
- National
Science Foundation Engineering Research Center for Re-inventing the
Nation’s Urban Water Infrastructure (ReNUWIt), Berkeley, California 94720, United States
| | - Aleksey Pisarenko
- Trussell
Technologies, Inc., Solana
Beach, California 92075, United States
| | - Elise Chen
- Trussell
Technologies, Inc., Solana
Beach, California 92075, United States
| | - Kara L. Nelson
- Department
of Civil and Environmental Engineering, College of Engineering, University of California, Berkeley, Berkeley, California 94720, United States
- National
Science Foundation Engineering Research Center for Re-inventing the
Nation’s Urban Water Infrastructure (ReNUWIt), Berkeley, California 94720, United States
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Mao B, Cui T, Su T, Xu Q, Lu F, Su H, Zhang J, Xiao S. Mixed-litter effects of fresh leaf semi-decomposed litter and fine root on soil enzyme activity and microbial community in an evergreen broadleaf karst forest in southwest China. FRONTIERS IN PLANT SCIENCE 2022; 13:1065807. [PMID: 36570900 PMCID: PMC9780490 DOI: 10.3389/fpls.2022.1065807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Litter decomposition is the main process that affects nutrient cycling and carbon budgets in mixed forests. However, knowledge of the response of the soil microbial processes to the mixed-litter decomposition of fresh leaf, semi-decomposed leaf and fine root is limited. Thus, a laboratory microcosm experiment was performed to explore the mixed-litter effects of fresh leaf, semi-decomposed leaf and fine root on the soil enzyme activity and microbial community in an evergreen broadleaf karst forest in Southwest China. Fresh leaf litter, semi-decomposed litter and fine root in the Parakmeria nitida and Dayaoshania cotinifolia forests, which are unique protective species and dominant species in the evergreen broadleaf forest, were decomposed alone and in all possible combinations, respectively. Our results showed that the mass loss of fresh leaf litter in three mixed-litter treatment was significantly higher than that in two mixed-litter treatment in the P. nitida and D. cotinifolia forests. Mass loss of fine root in the single litter treatment was significantly lower in the P. nitida forest and higher in the D. cotinifolia forest compared to that in the other litter treatments. There were insignificant differences in the activities of β-glucosidase (BG) and leucine aminopeptidase (LAP) between control and mixed-litter treatment in the P. nitida forest and between control and single litter treatment in the D. cotinifolia forest. The N-acetyl-β-D-glucosaminidase (NAG) activity was significantly increased by the single litter decomposition of fresh leaf and fine root and three mixed-litter decomposition in the P. nitida and D. cotinifolia forests. The activity of acid phospomonoesterase (AP) in the decomposition of fresh leaf litter was lower in the P. nitida forest and higher in the D. cotinifolia forest compared to that in control. The most dominant soil bacteria were Proteobacteria in the P. nitida forest and were Actinobacteria and Proteobacteria in the D. cotinifolia forest. Shannon, Chao1, ACE and PD indexes in the mixed-litter decomposition of fresh leaf and semi-decomposition litter were higher than that in control in P. nitida forest. There were insignificant differences in observed species and indexes of Chao1, ACE and PD between litter treatments in the D. cotinifolia forest. Richness of mixed-litter significantly affected mass loss, soil enzyme activity and microbial diversity in the P. nitida forest. Litter N concentration and the presence of fresh leaf litter were significantly correlated with the mass loss and soil enzyme activity in the P. nitida and D. cotinifolia forests. These results indicated that the presence of fresh leaf litter showed a non-negligible influence on mixed-litter decomposition and soil enzyme activity, which might be partly explained by litter initial quality in the P. nitida and D. cotinifolia forests.
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Affiliation(s)
- Bing Mao
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning, China
- Institute of Ecology, College of Urban and Environmental Sciences and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing, China
| | - Tingting Cui
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning, China
| | - Tongqing Su
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning, China
| | - Qiangsheng Xu
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning, China
| | - Feng Lu
- Laibin Jinxiu Dayaoshan Forest Ecosystem Observation and Research Station of Guangxi, Laibin, China
| | - Hongxin Su
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning, China
- Laibin Jinxiu Dayaoshan Forest Ecosystem Observation and Research Station of Guangxi, Laibin, China
| | - Jianbing Zhang
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning, China
| | - Shuangshuang Xiao
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning, China
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Loganathan T, Priya Doss C G. The influence of machine learning technologies in gut microbiome research and cancer studies - A review. Life Sci 2022; 311:121118. [DOI: 10.1016/j.lfs.2022.121118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/19/2022] [Accepted: 10/19/2022] [Indexed: 11/18/2022]
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Liu W, Du Q, Zhang H, Han D. The gut microbiome and obstructive sleep apnea syndrome in children. Sleep Med 2022; 100:462-471. [PMID: 36252415 DOI: 10.1016/j.sleep.2022.09.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/23/2022] [Accepted: 09/24/2022] [Indexed: 01/11/2023]
Abstract
Obstructive sleep apnea syndrome (OSAS) in children has become a major public health problem that affects the physical and mental growth of children. OSAS can result in adverse outcomes during growth and development, inhibiting the normal development of the metabolic, cardiovascular, and immune systems. OSAS is characterized by partial or complete obstruction of the upper airway, and prolonged obstruction that causes intermittent hypoxia and sleep fragmentation in children. The human microbiota is a complex community that is in dynamic equilibrium in the human body. Intermittent hypoxia and sleep fragmentation induced by childhood OSAS alter the composition of the gut microbiome. At the same time, changes in the gut microbiome affect sleep patterns in children through immunomodulatory and metabolic mechanisms, and induce further comorbidities, such as obesity, hypertension, and cardiovascular disease. This article discusses recent progress in research into the mechanisms of OSAS-induced changes in the gut microbiota and its pathophysiology in children.
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Affiliation(s)
- Wenxin Liu
- Children's Hospital of Shanghai Jiao Tong University, Clinical Lab in Children's Hospital of Shanghai, Shanghai, 200040, China; Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, 200062, Shanghai, China
| | - Qingqing Du
- Children's Hospital of Shanghai Jiao Tong University, Clinical Lab in Children's Hospital of Shanghai, Shanghai, 200040, China; Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, 200062, Shanghai, China
| | - Hong Zhang
- Children's Hospital of Shanghai Jiao Tong University, Clinical Lab in Children's Hospital of Shanghai, Shanghai, 200040, China; Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, 200062, Shanghai, China.
| | - Dingding Han
- Children's Hospital of Shanghai Jiao Tong University, Clinical Lab in Children's Hospital of Shanghai, Shanghai, 200040, China; Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, 200062, Shanghai, China.
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van Dongen KCW, Ioannou A, Wesseling S, Beekmann K, Belzer C. Differences in gut microbial fructoselysine degradation activity between breast-fed and formula-fed infants. FEMS Microbiol Ecol 2022; 99:6849965. [PMID: 36442156 PMCID: PMC9749803 DOI: 10.1093/femsec/fiac145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 11/10/2022] [Accepted: 11/25/2022] [Indexed: 11/29/2022] Open
Abstract
The Amadori product fructoselysine is formed upon heating of food products and is abundantly present in infant formula while being almost absent in breast milk. The human gut microbiota can degrade fructoselysine for which interindividual differences have been described for adults. The aim of this study is to compare functional differences in microbial fructoselysine degradation between breast-fed and formula-fed infants, in view of their different diets and resulting different fructoselysine exposures. First, a publicly available metagenomic dataset with metagenome-assembled genomes (MAGs) from infant fecal samples was analyzed and showed that query genes involved in fructoselysine degradation (frlD/yhfQ) were abundantly present in multiple bacterial taxa in the fecal samples, with a higher prevalence in the formula-fed infants. Next, fecal samples collected from exclusively breast-fed and formula-fed infants were anaerobically incubated with fructoselysine. Both groups degraded fructoselysine, however the fructoselysine degradation activity was significantly higher by fecal samples from formula-fed infants. Overall, this study provides evidence that infant formula feeding, leading to increased dietary fructoselysine exposure, seems to result in an increased fructoselysine degradation activity in the gut microbiota of infants. This indicates that the infant gut microbiota adapts towards dietary fructoselysine exposure.
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Affiliation(s)
- Katja C W van Dongen
- Division of Toxicology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Athanasia Ioannou
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Sebastiaan Wesseling
- Division of Toxicology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Karsten Beekmann
- Wageningen Food Safety Research, Wageningen University and Research, Akkermaalsbos 2, 6708 WB, Wageningen, The Netherlands
| | - Clara Belzer
- Corresponding author: Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, the Netherlands. Tel: +31317482795; E-mail:
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El Hamss H, Maruthi MN, Ally HM, Omongo CA, Wang HL, van Brunschot S, Colvin J, Delatte H. Spatio-temporal changes in endosymbiont diversity and composition in the African cassava whitefly, Bemisia tabaci SSA1. Front Microbiol 2022; 13:986226. [DOI: 10.3389/fmicb.2022.986226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 09/29/2022] [Indexed: 11/20/2022] Open
Abstract
Sap-sucking insects, including whiteflies, are amongst the most devastating and widely distributed organisms on the planet. They are often highly invasive and endosymbiont communities within these insects help them adapt to new or changing environments. Bemisia tabaci (Gennadius; Hemiptera: Aleyrodidae) whitefly species are vectors of more than 500 known plant-viruses and harbour highly diverse endosymbionts communities. To date, however, whitefly–endosymbiont interactions, community structure and their spatio-temporal changes are still poorly understood. In this study, we investigated the spatio-temporal changes in the composition and diversity of bacterial endosymbionts in the agricultural crop pest whitefly species, Bemisia tabaci sub-Saharan Africa 1-subgroup 1 and 2 (SSA1-SG1 and SSA1-SG2). 16S rRNA amplicon sequencing analysis was carried out to characterise endosymbiont compositionsin field-collected SSA1 (SSA1-SG1 and SSA1-SG2) populations infesting cassava in Uganda in 1997 and 2017. We detected Portiera, Arsenophonus, Wolbachia, Hamiltonella and Hemipteriphilus, with Arsenophonus and Wolbachia infections being predominant. Hemipteriphilus and Hamiltonella frequencies were very low and were detected in seven and two samples, respectively. Bacterial diversity based on three independent parameters including Simpson index, number of haplotypes and Bray–Curtis dissimilarity matrix was significantly higher in 1997 than in 2017. This period also coincided with the advent of super-abundant cassava-whitefly populations on cassava crops in Uganda. We discuss how endosymbionts may influence the biology and behaviour of whiteflies leading to population explosions.
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123
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Montero-Calasanz MDC, Yaramis A, Rohde M, Schumann P, Klenk HP, Meier-Kolthoff JP. Genotype-phenotype correlations within the Geodermatophilaceae. Front Microbiol 2022; 13:975365. [PMID: 36439792 PMCID: PMC9686282 DOI: 10.3389/fmicb.2022.975365] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 10/11/2022] [Indexed: 11/11/2022] Open
Abstract
The integration of genomic information into microbial systematics along with physiological and chemotaxonomic parameters provides for a reliable classification of prokaryotes. In silico analysis of chemotaxonomic traits is now being introduced to replace characteristics traditionally determined in the laboratory with the dual goal of both increasing the speed of the description of taxa and the accuracy and consistency of taxonomic reports. Genomics has already successfully been applied in the taxonomic rearrangement of Geodermatophilaceae (Actinomycetota) but in the light of new genomic data the taxonomy of the family needs to be revisited. In conjunction with the taxonomic characterisation of four strains phylogenetically located within the family, we conducted a phylogenetic analysis of the whole proteomes of the sequenced type strains and established genotype-phenotype correlations for traits related to chemotaxonomy, cell morphology and metabolism. Results indicated that the four isolates under study represent four novel species within the genus Blastococcus. Additionally, the genera Blastococcus, Geodermatophilus and Modestobacter were shown to be paraphyletic. Consequently, the new genera Trujillonella, Pleomorpha and Goekera were proposed within the Geodermatophilaceae and Blastococcus endophyticus was reclassified as Trujillonella endophytica comb. nov., Geodermatophilus daqingensis as Pleomorpha daqingensis comb. nov. and Modestobacter deserti as Goekera deserti comb. nov. Accordingly, we also proposed emended descriptions of Blastococcus aggregatus, Blastococcus jejuensis, Blastococcus saxobsidens and Blastococcus xanthilyniticus. In silico chemotaxonomic results were overall consistent with wet-lab results. Even though in silico discriminatory levels varied depending on the respective chemotaxonomic trait, this approach is promising for effectively replacing and/or complementing chemotaxonomic analyses at taxonomic ranks above the species level. Finally, interesting but previously overlooked insights regarding morphology and ecology were revealed by the presence of a repertoire of genes related to flagellum synthesis, chemotaxis, spore production and pilus assembly in all representatives of the family. A rich carbon metabolism including four different CO2 fixation pathways and a battery of enzymes able to degrade complex carbohydrates were also identified in Blastococcus genomes.
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Affiliation(s)
- Maria del Carmen Montero-Calasanz
- IFAPA Las Torres-Andalusian Institute of Agricultural and Fisheries Research and Training, Junta de Andalucía, Seville, Spain
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Adnan Yaramis
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Manfred Rohde
- Central Facility for Microscopy, HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Peter Schumann
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jan P. Meier-Kolthoff
- Department Bioinformatics and Databases, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Abstract
Until recently, bacteria have been studied in terms of their roles in infectious diseases and mainly by using isolation and culture methods. However, in practice, many bacteria existing on the earth are difficult to isolate and culture, and thus only a limited number of them have been studied to date. On the other hand, in 2005, the next-generation sequencing technology became generally available, and since then genomic analysis of bacterial flora has become widespread. As a result, it has been revealed that the lower respiratory tract, which was previously thought to be sterile, in fact has bacterial flora (a microbiome) with a high level of biodiversity. In addition, it has been found that various diseases develop and worsen depending on the balance of the bacterial flora, and in recent years, a relationship has been established between various disorders. Recent research on cancer-associated microbial communities has elucidated the reciprocal interactions among bacteria, tumors and immune cells, the bacterial pathways associated with induction of oncogenesis, and their translational significance. Nevertheless, despite the increasing evidence showing that dysbiosis is associated with lung oncogenesis, the detailed mechanisms remain to be fully elucidated. Microorganisms seem to trigger tumor initiation and progression, presumably through the production of bacterio-toxins and other pro-inflammatory factors. The purpose of this review is to present a context for the basic mechanisms and molecular functions of the airway microbiome in oncogenesis, in an effort to prevent cancer by strategies utilizing the airway microbiota, as well as summarizing the mechanisms wherein the microbiome acts as a modulator of immunotherapies in lung cancer.
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125
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Kim CY, Ma J, Lee I. HiFi metagenomic sequencing enables assembly of accurate and complete genomes from human gut microbiota. Nat Commun 2022; 13:6367. [PMID: 36289209 PMCID: PMC9606305 DOI: 10.1038/s41467-022-34149-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 10/12/2022] [Indexed: 12/25/2022] Open
Abstract
Advances in metagenomic assembly have led to the discovery of genomes belonging to uncultured microorganisms. Metagenome-assembled genomes (MAGs) often suffer from fragmentation and chimerism. Recently, 20 complete MAGs (cMAGs) have been assembled from Oxford Nanopore long-read sequencing of 13 human fecal samples, but with low nucleotide accuracy. Here, we report 102 cMAGs obtained by Pacific Biosciences (PacBio) high-accuracy long-read (HiFi) metagenomic sequencing of five human fecal samples, whose initial circular contigs were selected for complete prokaryotic genomes using our bioinformatics workflow. Nucleotide accuracy of the final cMAGs was as high as that of Illumina sequencing. The cMAGs could exceed 6 Mbp and included complete genomes of diverse taxa, including entirely uncultured RF39 and TANB77 orders. Moreover, cMAGs revealed that regions hard to assemble by short-read sequencing comprised mostly genomic islands and rRNAs. HiFi metagenomic sequencing will facilitate cataloging accurate and complete genomes from complex microbial communities, including uncultured species.
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Affiliation(s)
- Chan Yeong Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Junyeong Ma
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Insuk Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea.
- POSTECH Biotech Center, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea.
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126
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Lin JN, Lai CH, Lin SY, Lee CC, Lee NY, Liu PY, Yang CH, Huang YH. Effect of Intragenomic Sequence Heterogeneity among Multiple 16S rRNA Genes on Species Identification of Elizabethkingia. Microbiol Spectr 2022; 10:e0133822. [PMID: 36036645 PMCID: PMC9604143 DOI: 10.1128/spectrum.01338-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 08/15/2022] [Indexed: 12/30/2022] Open
Abstract
Accurate identification of Elizabethkingia species mostly requires the use of molecular techniques, and 16S rRNA gene sequencing is generally considered the method of choice. In this study, we evaluated the effect of intraspecific diversity among the multiple copies of the 16S rRNA gene on the accuracy of species identification in the genus Elizabethkingia. Sequences of 16S rRNA genes obtained from the 32 complete whole-genome sequences of Elizabethkingia deposited in GenBank and from 218 clinical isolates collected from 5 hospitals in Taiwan were analyzed. Four or five copies of 16S rRNA were identified in the Elizabethkingia species with complete genome sequences. The dissimilarity among the copies of the16S rRNA gene was <1% in all Elizabethkingia strains. E. meningoseptica demonstrated a significantly higher rate of nucleotide variations in the 16S rRNA than did E. anophelis (P = 0.011). Nucleotide alterations occurred more frequently in regions V2 and V6 than in other hypervariable regions (P < 0.001). E. meningoseptica, E. anophelis, and E. argenteiflava strains were clustered distinctly in the phylogenetic tree inferred from 16S rRNA genes, and the intragenomic variation of gene sequences had no profound effect on the classification of taxa. However, E. miricola, E. bruuniana, E. ursingii, and E. occulta were grouped closely in the phylogenetic analysis, and the variation among the multiple copies of the 16S rRNA in one E. ursingii strain affected species classification. Other marker genes may be required to supplement the species classification of closely related taxa in the genus Elizabethkingia. IMPORTANCE Incorrect identification of bacterial species would influence the epidemiology and clinical analysis of patients infected with Elizabethkingia. The results of the present study suggest that 16S rRNA gene sequencing should not be considered the gold standard for the accurate identification of Elizabethkingia species.
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Affiliation(s)
- Jiun-Nong Lin
- College of Medical Science and Technology, I-Shou University, Kaohsiung, Taiwan
- Department of Critical Care Medicine, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
- Division of Infectious Diseases, Department of Internal Medicine, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
- School of Medicine, College of Medicine, I-Shou University, Kaohsiung, Taiwan
| | - Chung-Hsu Lai
- Division of Infectious Diseases, Department of Internal Medicine, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
- School of Medicine, College of Medicine, I-Shou University, Kaohsiung, Taiwan
| | - Shang-Yi Lin
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ching-Chi Lee
- Clinical Medicine Research Center, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Nan-Yao Lee
- Division of Infectious Diseases, Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
- School of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Po-Yu Liu
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Chih-Hui Yang
- Department of Biological Science and Technology, Meiho University, Pingtung, Taiwan
| | - Yi-Han Huang
- College of Medical Science and Technology, I-Shou University, Kaohsiung, Taiwan
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127
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Özkurt E, Fritscher J, Soranzo N, Ng DYK, Davey RP, Bahram M, Hildebrand F. LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis. MICROBIOME 2022; 10:176. [PMID: 36258257 PMCID: PMC9580208 DOI: 10.1186/s40168-022-01365-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 09/01/2022] [Indexed: 05/02/2023]
Abstract
BACKGROUND Amplicon sequencing is an established and cost-efficient method for profiling microbiomes. However, many available tools to process this data require both bioinformatics skills and high computational power to process big datasets. Furthermore, there are only few tools that allow for long read amplicon data analysis. To bridge this gap, we developed the LotuS2 (less OTU scripts 2) pipeline, enabling user-friendly, resource friendly, and versatile analysis of raw amplicon sequences. RESULTS In LotuS2, six different sequence clustering algorithms as well as extensive pre- and post-processing options allow for flexible data analysis by both experts, where parameters can be fully adjusted, and novices, where defaults are provided for different scenarios. We benchmarked three independent gut and soil datasets, where LotuS2 was on average 29 times faster compared to other pipelines, yet could better reproduce the alpha- and beta-diversity of technical replicate samples. Further benchmarking a mock community with known taxon composition showed that, compared to the other pipelines, LotuS2 recovered a higher fraction of correctly identified taxa and a higher fraction of reads assigned to true taxa (48% and 57% at species; 83% and 98% at genus level, respectively). At ASV/OTU level, precision and F-score were highest for LotuS2, as was the fraction of correctly reported 16S sequences. CONCLUSION LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes. AVAILABILITY LotuS2 is available from GitHub, conda, or via a Galaxy web interface, documented at http://lotus2.earlham.ac.uk/ . Video Abstract.
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Affiliation(s)
- Ezgi Özkurt
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
- Earlham Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UZ, UK
| | - Joachim Fritscher
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
- Earlham Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UZ, UK
| | - Nicola Soranzo
- Earlham Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UZ, UK
| | - Duncan Y K Ng
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Robert P Davey
- Earlham Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UZ, UK
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 756 51, Uppsala, Sweden
- Institute of Ecology and Earth Sciences, University of Tartu, Lai St, 40, Tartu, Estonia
| | - Falk Hildebrand
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK.
- Earlham Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UZ, UK.
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128
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Sezgin E, Terlemez G, Bozkurt B, Bengi G, Akpinar H, Büyüktorun İ. Quantitative real-time PCR analysis of bacterial biomarkers enable fast and accurate monitoring in inflammatory bowel disease. PeerJ 2022; 10:e14217. [PMID: 36275453 PMCID: PMC9586115 DOI: 10.7717/peerj.14217] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/20/2022] [Indexed: 01/24/2023] Open
Abstract
Inflammatory bowel diseases (IBD) affect millions of people worldwide with increasing incidence. Ulcerative colitis (UC) and Crohn's disease (CD) are the two most common IBDs. There is no definite cure for IBD, and response to treatment greatly vary among patients. Therefore, there is urgent need for biomarkers to monitor therapy efficacy, and disease prognosis. We aimed to test whether qPCR analysis of common candidate bacteria identified from a patient's individual fecal microbiome can be used as a fast and reliable personalized microbial biomarker for efficient monitoring of disease course in IBD. Next generation sequencing (NGS) of 16S rRNA gene region identified species level microbiota profiles for a subset of UC, CD, and control samples. Common high abundance bacterial species observed in all three groups, and reported to be associated with IBD are chosen as candidate marker species. These species, and total bacteria amount are quantified in all samples with qPCR. Relative abundance of anti-inflammatory, beneficial Faecalibacterium prausnitzii, Akkermansia muciniphila, and Streptococcus thermophilus was significantly lower in IBD compared to control samples. Moreover, the relative abundance of the examined common species was correlated with the severity of IBD disease. The variance in qPCR data was much lower compared to NGS data, and showed much higher statistical power for clinical utility. The qPCR analysis of target common bacterial species can be a powerful, cost and time efficient approach for monitoring disease status and identify better personalized treatment options for IBD patients.
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Affiliation(s)
- Efe Sezgin
- Izmir Institute of Technology, Izmir, Turkey
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129
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Budimir I, Giampieri E, Saccenti E, Suarez-Diez M, Tarozzi M, Dall'Olio D, Merlotti A, Curti N, Remondini D, Castellani G, Sala C. Intraspecies characterization of bacteria via evolutionary modeling of protein domains. Sci Rep 2022; 12:16595. [PMID: 36198716 PMCID: PMC9534902 DOI: 10.1038/s41598-022-21036-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 09/22/2022] [Indexed: 12/04/2022] Open
Abstract
The ability to detect and characterize bacteria within a biological sample is crucial for the monitoring of infections and epidemics, as well as for the study of human health and its relationship with commensal microorganisms. To this aim, a commonly used technique is the 16S rRNA gene targeted sequencing. PCR-amplified 16S sequences derived from the sample of interest are usually clustered into the so-called Operational Taxonomic Units (OTUs) based on pairwise similarities. Then, representative OTU sequences are compared with reference (human-made) databases to derive their phylogeny and taxonomic classification. Here, we propose a new reference-free approach to define the phylogenetic distance between bacteria based on protein domains, which are the evolving units of proteins. We extract the protein domain profiles of 3368 bacterial genomes and we use an ecological approach to model their Relative Species Abundance distribution. Based on the model parameters, we then derive a new measurement of phylogenetic distance. Finally, we show that such model-based distance is capable of detecting differences between bacteria in cases in which the 16S rRNA-based method fails, providing a possibly complementary approach , which is particularly promising for the analysis of bacterial populations measured by shotgun sequencing.
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Affiliation(s)
- Iva Budimir
- Department of Physics and Astronomy 'Augusto Righi', University of Bologna, 40127, Bologna, Italy
| | - Enrico Giampieri
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138, Bologna, Italy
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, 6708 WE, Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, 6708 WE, Wageningen, The Netherlands
| | - Martina Tarozzi
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138, Bologna, Italy
| | - Daniele Dall'Olio
- Department of Physics and Astronomy 'Augusto Righi', University of Bologna, 40127, Bologna, Italy
| | - Alessandra Merlotti
- Department of Physics and Astronomy 'Augusto Righi', University of Bologna, 40127, Bologna, Italy
| | - Nico Curti
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138, Bologna, Italy
| | - Daniel Remondini
- Department of Physics and Astronomy 'Augusto Righi', University of Bologna, 40127, Bologna, Italy
| | - Gastone Castellani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138, Bologna, Italy.
| | - Claudia Sala
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138, Bologna, Italy
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130
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Kong J, Fan C, Liao X, Chen A, Yang S, Zhao L, Li H. Accurate detection of Escherichia coli O157:H7 and Salmonella enterica serovar typhimurium based on the combination of next-generation sequencing and droplet digital PCR. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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131
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The Wheat Head Blight Pathogen Fusarium graminearum Can Recruit Collaborating Bacteria from Soil. Cells 2022; 11:cells11193004. [PMID: 36230966 PMCID: PMC9563980 DOI: 10.3390/cells11193004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/15/2022] [Accepted: 09/21/2022] [Indexed: 11/17/2022] Open
Abstract
In nature, fungal endophytes often have facultative endohyphal bacteria (FEB). Can a model plant pathogenic fungus have them, and does it affect their phenotype? We constructed a growth system/microcosm to allow an F. graminearum isolate to grow through natural soil and then re-isolated it on a gentamicin-containing medium, allowing endohyphal growth of bacteria while killing other bacteria. F. graminearum PH-1 labelled with a His1mCherry gene staining the fungal nuclei fluorescent red was used to confirm the re-isolation of the fungus. Most new re-isolates contained about 10 16SrRNA genes per fungal mCherry gene determined by qPCR. The F. graminearum + FEB holobiont isolates containing the bacteria were sub-cultured several times, and their bacterial contents were stable. Sequencing the bacterial 16SrRNA gene from several Fg-FEB holobiont isolates revealed endophytic bacteria known to be capable of nitrogen fixation. We tested the pathogenicity of one common Fg-FEB holobiont association, F. graminearum + Stenatrophomonas maltophilia, and found increased pathogenicity. The 16SrRNA gene load per fungal His1mCherry gene inside the wheat stayed the same as previously found in vitro. Finally, strong evidence was found for Fg-S. maltophilia symbiotic nitrogen fixation benefitting the fungus.
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132
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Stinson LF, Ma J, Sindi AS, Geddes DT. Methodological approaches for studying the human milk microbiome. Nutr Rev 2022; 81:705-715. [PMID: 36130405 DOI: 10.1093/nutrit/nuac082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Human milk contains a low-biomass, low-diversity microbiome, consisting largely of bacteria. This community is of great research interest in the context of infant health and maternal and mammary health. However, this sample type presents many unique methodological challenges. In particular, there are numerous technical considerations relating to sample collection and storage, DNA extraction and sequencing, viability, and contamination. Failure to properly address these challenges may lead to distortion of bacterial DNA profiles generated from human milk samples, ultimately leading to spurious conclusions. Here, these technical challenges are discussed, and various methodological approaches used to address them are analyzed. Data were collected from studies in which a breadth of methodological approaches were used, and recommendations for robust and reproducible analysis of the human milk microbiome are proposed. Such methods will ensure high-quality data are produced in this field, ultimately supporting better research outcomes for mothers and infants.
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Affiliation(s)
- Lisa F Stinson
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
| | - Jie Ma
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
| | - Azhar S Sindi
- Division of Obstetrics and Gynaecology, School of Medicine, The University of Western Australia, Perth, Australia.,is with the College of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Donna T Geddes
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
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Bacteria communities and water quality parameters in riverine water and sediments near wastewater discharges. Sci Data 2022; 9:578. [PMID: 36130969 PMCID: PMC9492694 DOI: 10.1038/s41597-022-01686-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 09/04/2022] [Indexed: 11/24/2022] Open
Abstract
Wastewater treatment plant (WWTP) discharges alter water quality and microbial communities by introducing human-associated bacteria in the environment and by altering microbial communities. To fully understand this impact, it is crucial to study whether WWTP discharges affect water and sediments microbial communities in comparable ways and whether such effects depend on specific environmental variables. Here, we present a dataset investigating the impact of a WWTP on water quality and bacterial communities by comparing samples collected directly from the WWTP outflow to surface waters and sediments at two sites above and two sites below it over a period of five months. When possible, we measured five physicochemical variables (e.g., temperature, turbidity, conductivity, dissolved oxygen, and salinity), four bioindicators (e.g., Escherichia coli, total coliforms, Enterococcus sp., and endotoxins), and two molecular indicators (e.g., intI1’s relative abundance, and 16S rRNA gene profiling). Preliminary results suggest that bioindicators correlate with environmental variables and that bacterial communities present in the water tables, sediments, and treated water differ greatly in composition and structure. Measurement(s) | temperature of water • conductivity of water • dissolved oxygen in water • salinity of water • Concentration of Escherichia coli in water • Concentration of total coliforms in water • Concentration of Enterococcus sp. • Concentration of endotoxins in water • Relative abundance of integron 1 in water • Bacterial 16S RNA | Technology Type(s) | YSI field probe • Colilert dection system • Enterolert dection system • Charles River Endosafe system • quantitative PCR • Illumina Sequencing | Sample Characteristic - Organism | Bacteria | Sample Characteristic - Environment | Fresh water river | Sample Characteristic - Location | United States |
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134
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van Dongen KCW, Belzer C, Bakker W, Rietjens IMCM, Beekmann K. Inter- and Intraindividual Differences in the Capacity of the Human Intestinal Microbiome in Fecal Slurries to Metabolize Fructoselysine and Carboxymethyllysine. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:11759-11768. [PMID: 36069406 PMCID: PMC9501902 DOI: 10.1021/acs.jafc.2c05756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 08/27/2022] [Accepted: 08/28/2022] [Indexed: 06/15/2023]
Abstract
The advanced glycation endproduct carboxymethyllysine and its precursor fructoselysine are present in heated, processed food products and are considered potentially hazardous for human health. Upon dietary exposure, they can be degraded by human colonic gut microbiota, reducing internal exposure. Pronounced interindividual and intraindividual differences in these metabolic degradations were found in anaerobic incubations with human fecal slurries in vitro. The average capacity to degrade fructoselysine was 27.7-fold higher than that for carboxymethyllysine, and degradation capacities for these two compounds were not correlated (R2 = 0.08). Analysis of the bacterial composition revealed that interindividual differences outweighed intraindividual differences, and multiple genera were correlated with the individuals' carboxymethyllysine and fructoselysine degradation capacities (e.g., Akkermansia, Alistipes).
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Affiliation(s)
- Katja C. W. van Dongen
- Division
of Toxicology, Wageningen University and
Research, P.O. Box 8000, Wageningen 6700 EA, The
Netherlands
| | - Clara Belzer
- Laboratory
of Microbiology, Wageningen University and
Research, P.O. Box 8033, Wageningen 6700 EH, The
Netherlands
| | - Wouter Bakker
- Division
of Toxicology, Wageningen University and
Research, P.O. Box 8000, Wageningen 6700 EA, The
Netherlands
| | - Ivonne M. C. M. Rietjens
- Division
of Toxicology, Wageningen University and
Research, P.O. Box 8000, Wageningen 6700 EA, The
Netherlands
| | - Karsten Beekmann
- Wageningen
Food Safety Research (WFSR), Part of Wageningen University and Research, P.O. Box 230, Wageningen 700 AE, The Netherlands
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135
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Claesson R, Johansson A, Belibasakis GN. Clinical laboratory diagnostics in dentistry: Application of microbiological methods. FRONTIERS IN ORAL HEALTH 2022; 3:983991. [PMID: 36160119 PMCID: PMC9493047 DOI: 10.3389/froh.2022.983991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/10/2022] [Indexed: 12/05/2022] Open
Abstract
Diagnosis and treatment in dentistry are based on clinical examination of the patients. Given that the major oral diseases are of microbial biofilm etiology, it can be expected that performing microbiological analysis on samples collected from the patient could deliver supportive evidence to facilitate the decision-making process by the clinician. Applicable microbiological methods range from microscopy, to culture, to molecular techniques, which can be performed easily within dedicated laboratories proximal to the clinics, such as ones in academic dental institutions. Periodontal and endodontic infections, along with odontogenic abscesses, have been identified as conditions in which applied clinical microbiology may be beneficial for the patient. Administration of antimicrobial agents, backed by microbiological analysis, can yield more predictable treatment outcomes in refractory or early-occurring forms of periodontitis. Confirming a sterile root canal using a culture-negative sample during endodontic treatment may ensure the longevity of its outcome and prevent secondary infections. Susceptibility testing of samples obtained from odontogenic abscesses may facilitate the selection of the appropriate antimicrobial treatment to prevent further spread of the infection.
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Affiliation(s)
- Rolf Claesson
- Division of Oral Microbiology, Department of Odontology, Umeå University, Umeå, Sweden
- *Correspondence: Rolf Claesson
| | - Anders Johansson
- Division of Oral Microbiology, Department of Odontology, Umeå University, Umeå, Sweden
| | - Georgios N. Belibasakis
- Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden
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136
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Halla FF, Massawa SM, Joseph EK, Acharya K, Sabai SM, Mgana SM, Werner D. Attenuation of bacterial hazard indicators in the subsurface of an informal settlement and their application in quantitative microbial risk assessment. ENVIRONMENT INTERNATIONAL 2022; 167:107429. [PMID: 35914337 DOI: 10.1016/j.envint.2022.107429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
Pit latrines provide essential onsite sanitation services to over a billion people, but there are concerns about their role in infectious disease transmission, and impacts on groundwater resources. We conducted fieldwork in an informal settlement in Dar es Salaam, where cholera is endemic. We combined plate counting with portable MinION sequencing and quantitative polymerase chain reaction (qPCR) methods for characterization of bacteria in pit latrine sludge, leachate, shallow and deep groundwater resources. Pit latrine sludge was characterized by log10 marker gene concentrations per 100 mL of 11.2 ± 0.2, 9.9 ± 0.9, 6.0 ± 0.3, and 4.4 ± 0.8, for total bacteria (16S rRNA), E. coli (rodA), human-host-associated Bacteroides (HF183), and Vibrio cholerae (ompW), respectively. The ompW gene observations suggested 5 % asymptomatic Vibrio cholerae carriers amongst pit latrine users. Pit leachate percolation through one-meter-thick sand beds attenuated bacterial hazard indicators by 1 to 4 log10 units. But first-order removal rates derived from these data substantially overestimated the longer-range hazard attenuation in the sand aquifers. Cooccurrence of human sewage marker gene HF183 in all shallow groundwater samples testing positive for ompW genes demonstrated the human origin of Vibrio cholerae hazards in the subsurface. All borehole water samples tested negative for ompW and HF183 genes, but 16S rRNA gene sequencing data suggested ingress of faecal pollution into boreholes at the peak of the "long rainy season". Quantitative microbial risk assessment (QMRA) predicted a gastrointestinal disease burden of 0.05 DALY per person per year for the community, well above WHO targets of 10-4-10-6 DALY for disease related to drinking water.
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Affiliation(s)
- Franella Francos Halla
- Department of Environmental Engineering, School of Environmental Science and Technology, Ardhi University, Dar es Salaam, Tanzania
| | - Said Maneno Massawa
- Department of Environmental Engineering, School of Environmental Science and Technology, Ardhi University, Dar es Salaam, Tanzania
| | - Elihaika Kengalo Joseph
- Department of Environmental Engineering, School of Environmental Science and Technology, Ardhi University, Dar es Salaam, Tanzania
| | - Kishor Acharya
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Shadrack Mwita Sabai
- Department of Environmental Engineering, School of Environmental Science and Technology, Ardhi University, Dar es Salaam, Tanzania
| | - Shaaban Mrisho Mgana
- Department of Environmental Engineering, School of Environmental Science and Technology, Ardhi University, Dar es Salaam, Tanzania.
| | - David Werner
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
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137
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Gonzalez-Nayeck AC, Mohr W, Tang T, Sattin S, Parenteau MN, Jahnke LL, Pearson A. Absence of canonical trophic levels in a microbial mat. GEOBIOLOGY 2022; 20:726-740. [PMID: 35831948 DOI: 10.1111/gbi.12511] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/16/2022] [Accepted: 06/26/2022] [Indexed: 06/15/2023]
Abstract
In modern ecosystems, the carbon stable isotope (δ13 C) ratios of consumers generally conform to the principle "you are what you eat, +1‰." However, this metric may not apply to microbial mat systems where diverse communities, using a variety of carbon substrates via multiple assimilation pathways, live in close physical association and phagocytosis is minimal or absent. To interpret the δ13 C record of the Proterozoic and early Paleozoic, when mat-based productivity likely was widespread, it is necessary to understand how a microbially driven producer-consumer structure affects the δ13 C compositions of biomass and preservable lipids. Protein Stable Isotope Fingerprinting (P-SIF) is a recently developed method that allows measurement of the δ13 C values of whole proteins, separated from environmental samples and identified taxonomically via proteomics. Here, we use P-SIF to determine the trophic relationships in a microbial mat sample from Chocolate Pots Hot Springs, Yellowstone National Park (YNP), USA. In this mat, proteins from heterotrophic bacteria are indistinguishable from cyanobacterial proteins, indicating that "you are what you eat, +1‰" is not applicable. To explain this finding, we hypothesize that sugar production and consumption dominate the net ecosystem metabolism, yielding a community in which producers and consumers share primary photosynthate as a common resource. This idea was validated by confirming that glucose moieties in exopolysaccharide were equal in δ13 C composition to both cyanobacterial and heterotrophic proteins, and by confirming that highly 13 C-depleted fatty acids (FAs) of Cyanobacteria dominate the lipid pool, consistent with flux-balance expectations for systems that overproduce primary photosynthate. Overall, the results confirm that the δ13 C composition of microbial biomass and lipids is tied to specific metabolites, rather than to autotrophy versus heterotrophy or to individual trophic levels. Therefore, we suggest that aerobic microbial heterotrophy is simply a case of "you are what you eat."
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Affiliation(s)
- Ana C Gonzalez-Nayeck
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - Wiebke Mohr
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
- Max-Planck-Institute for Marine Microbiology, Bremen, Germany
| | - Tiantian Tang
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
- State Key Laboratory of Marine Environmental Science (Xiamen University), Xiamen, Fujian, China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Sarah Sattin
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
| | | | - Linda L Jahnke
- NASA Ames Research Center, Moffett Field, California, USA
| | - Ann Pearson
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
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138
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Rabapane KJ, Ijoma GN, Matambo TS. Insufficiency in functional genomics studies, data, and applications: A case study of bio-prospecting research in ruminant microbiome. Front Genet 2022; 13:946449. [PMID: 36118848 PMCID: PMC9472250 DOI: 10.3389/fgene.2022.946449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 07/21/2022] [Indexed: 12/02/2022] Open
Abstract
Over the last two decades, biotechnology has advanced at a rapid pace, propelled by the incorporation of bio-products into various aspects of pharmaceuticals, industry, and the environment. These developments have sparked interest in the bioprospecting of microorganisms and their products in a variety of niche environments. Furthermore, the use of omics technologies has greatly aided our analyses of environmental samples by elucidating the microbial ecological framework, biochemical pathways, and bio-products. However, the more often overemphasis on taxonomic identification in most research publications, as well as the data associated with such studies, is detrimental to immediate industrial and commercial applications. This review identifies several factors that contribute to the complexity of sequence data analysis as potential barriers to the pragmatic application of functional genomics, utilizing recent research on ruminants to demonstrate these limitations in the hopes of broadening our horizons and drawing attention to this gap in bioprospecting studies for other niche environments as well. The review also aims to emphasize the importance of routinely incorporating functional genomics into environmental metagenomics analyses in order to improve solutions that drive rapid industrial biocatalysis developments from derived outputs with the aim of achieving potential benefits in energy-use reduction and environmental considerations for current and future applications.
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139
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A revisit to universal single-copy genes in bacterial genomes. Sci Rep 2022; 12:14550. [PMID: 36008577 PMCID: PMC9411617 DOI: 10.1038/s41598-022-18762-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/18/2022] [Indexed: 11/08/2022] Open
Abstract
Universal single-copy genes (USCGs) are widely used for species classification and taxonomic profiling. Despite many studies on USCGs, our understanding of USCGs in bacterial genomes might be out of date, especially how different the USCGs are in different studies, how well a set of USCGs can distinguish two bacterial species, whether USCGs can separate different strains of a bacterial species, to name a few. To fill the void, we studied USCGs in the most updated complete bacterial genomes. We showed that different USCG sets are quite different while coming from highly similar functional categories. We also found that although USCGs occur once in almost all bacterial genomes, each USCG does occur multiple times in certain genomes. We demonstrated that USCGs are reliable markers to distinguish different species while they cannot distinguish different strains of most bacterial species. Our study sheds new light on the usage and limitations of USCGs, which will facilitate their applications in evolutionary, phylogenomic, and metagenomic studies.
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140
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Baltrušis P, Halvarsson P, Höglund J. Estimation of the impact of three different bioinformatic pipelines on sheep nemabiome analysis. Parasit Vectors 2022; 15:290. [PMID: 35953825 PMCID: PMC9373329 DOI: 10.1186/s13071-022-05399-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 07/13/2022] [Indexed: 11/10/2022] Open
Abstract
Background Next-generation sequencing (NGS) has provided an alternative strategy to study the composition of nematode communities with increased resolution and sensitivity. However, the handling and processing of gigabytes worth of amplicon sequence data produced by an NGS platform is still a major hurdle, limiting the use and adoption of faster and more convenient analysis software. Methods In total 32 paired, fecal samples from Swedish sheep flocks were cultured and the larvae subsequently harvested subjected to internal transcribed spacer 2 (ITS2) amplicon sequencing using the PacBio platform. Samples were analyzed with three different bioinformatic pipelines, i.e. the DADA2, Mothur and SCATA pipelines, to determine species composition and richness. Results For the the major species tested in this study (Haemonchus contortus, Teladorsagia circumcinta and Trichostrongylus colubriformis) neither relative abundances nor species diversity differed significantly between the three pipelines, effectively showing that all three analysis pipelines, although different in their approaches, yield nearly identical outcomes. In addition, the samples analyzed here had especially high frequencies of H. contortus (90–95% across the three pipelines) both before and after sample treatment, followed by T. circumcinta (3.5–4%). This shows that H. contortus is the parasite of primary importance in contemporary Swedish sheep farms struggling with anthelmintic resistance. Finally, although on average a significant reduction in egg counts was achieved post-treatment, no significant shifts in major species relative frequencies occurred, indicating highly rigid community structures at sheep farms where anthelmintic resistance has been reported. Conclusions The findings presented here further contribute to the development and application of NGS technology to study nemabiome compositions in sheep, in addition to expanding our understanding about the most recent changes in parasite species abundances from Swedish sheep farms struggling with anthelmintic resistance. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05399-0.
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Affiliation(s)
- Paulius Baltrušis
- Section for Parasitology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | - Peter Halvarsson
- Section for Parasitology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Johan Höglund
- Section for Parasitology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
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141
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Hayat Z, Shahzad K, Ali H, Casini R, Naveed K, Hafeez A, El-Ansary DO, Elansary HO, Fiaz S, Abaid-Ullah M, Hafeez FY, Iqbal MS, Ullah A. 16S rRNA gene flow in Enterococcus spp. and SNP analysis: A reliable approach for specie level identification. BIOCHEM SYST ECOL 2022. [DOI: 10.1016/j.bse.2022.104445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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142
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Kumar MS, Slud EV, Hehnly C, Zhang L, Broach J, Irizarry RA, Schiff SJ, Paulson JN. Differential richness inference for 16S rRNA marker gene surveys. Genome Biol 2022; 23:166. [PMID: 35915508 PMCID: PMC9344657 DOI: 10.1186/s13059-022-02722-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 06/28/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Individual and environmental health outcomes are frequently linked to changes in the diversity of associated microbial communities. Thus, deriving health indicators based on microbiome diversity measures is essential. While microbiome data generated using high-throughput 16S rRNA marker gene surveys are appealing for this purpose, 16S surveys also generate a plethora of spurious microbial taxa. RESULTS When this artificial inflation in the observed number of taxa is ignored, we find that changes in the abundance of detected taxa confound current methods for inferring differences in richness. Experimental evidence, theory-guided exploratory data analyses, and existing literature support the conclusion that most sub-genus discoveries are spurious artifacts of clustering 16S sequencing reads. We proceed to model a 16S survey's systematic patterns of sub-genus taxa generation as a function of genus abundance to derive a robust control for false taxa accumulation. These controls unlock classical regression approaches for highly flexible differential richness inference at various levels of the surveyed microbial assemblage: from sample groups to specific taxa collections. The proposed methodology for differential richness inference is available through an R package, Prokounter. CONCLUSIONS False species discoveries bias richness estimation and confound differential richness inference. In the case of 16S microbiome surveys, supporting evidence indicate that most sub-genus taxa are spurious. Based on this finding, a flexible method is proposed and is shown to overcome the confounding problem noted with current approaches for differential richness inference. Package availability: https://github.com/mskb01/prokounter.
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Affiliation(s)
- M Senthil Kumar
- Department of Data Science, The Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Eric V Slud
- Department of Mathematics, University of Maryland, College Park, MD, USA
- Center for Statistical Research and Methodology U.S. Census Bureau, Suitland, MD, USA
| | - Christine Hehnly
- Penn State Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, PA, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Lijun Zhang
- Penn State Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - James Broach
- Penn State Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, PA, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Rafael A Irizarry
- Department of Data Science, The Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Steven J Schiff
- Department of Neurosurgery, Yale University, New Haven, CT, 06510, USA
| | - Joseph N Paulson
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA.
- Department of Data Sciences, Product Development, Genentech, South San Francisco, CA, USA.
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143
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Sharon I, Quijada NM, Pasolli E, Fabbrini M, Vitali F, Agamennone V, Dötsch A, Selberherr E, Grau JH, Meixner M, Liere K, Ercolini D, de Filippo C, Caderni G, Brigidi P, Turroni S. The Core Human Microbiome: Does It Exist and How Can We Find It? A Critical Review of the Concept. Nutrients 2022; 14:nu14142872. [PMID: 35889831 PMCID: PMC9323970 DOI: 10.3390/nu14142872] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 11/16/2022] Open
Abstract
The core microbiome, which refers to a set of consistent microbial features across populations, is of major interest in microbiome research and has been addressed by numerous studies. Understanding the core microbiome can help identify elements that lead to dysbiosis, and lead to treatments for microbiome-related health states. However, defining the core microbiome is a complex task at several levels. In this review, we consider the current state of core human microbiome research. We consider the knowledge that has been gained, the factors limiting our ability to achieve a reliable description of the core human microbiome, and the fields most likely to improve that ability. DNA sequencing technologies and the methods for analyzing metagenomics and amplicon data will most likely facilitate higher accuracy and resolution in describing the microbiome. However, more effort should be invested in characterizing the microbiome’s interactions with its human host, including the immune system and nutrition. Other components of this holobiontic system should also be emphasized, such as fungi, protists, lower eukaryotes, viruses, and phages. Most importantly, a collaborative effort of experts in microbiology, nutrition, immunology, medicine, systems biology, bioinformatics, and machine learning is probably required to identify the traits of the core human microbiome.
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Affiliation(s)
- Itai Sharon
- Migal-Galilee Research Institute, P.O. Box 831, Kiryat Shmona 11016, Israel
- Faculty of Sciences and Technology, Tel-Hai Academic College, Upper Galilee 1220800, Israel
- Correspondence:
| | - Narciso Martín Quijada
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, A-1210 Vienna, Austria; (N.M.Q.); (E.S.)
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, A-3430 Tulln an der Donau, Austria
| | - Edoardo Pasolli
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, 80055 Portici, Italy; (E.P.); (D.E.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80055 Portici, Italy
| | - Marco Fabbrini
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy; (M.F.); (S.T.)
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy;
| | - Francesco Vitali
- Institute of Agricultural Biology and Biotechnology (IBBA), National Research Council (CNR), Via Moruzzi 1, 56124 Pisa, Italy; (F.V.); (C.d.F.)
| | - Valeria Agamennone
- Microbiology and Systems Biology, Netherlands Organization for Applied Scientific Research (TNO), Utrechtseweg 48, 3704 HE Zeist, The Netherlands;
| | - Andreas Dötsch
- Department of Physiology and Biochemistry of Nutrition, Max Rubner-Institut (MRI)-Federal Research Institute of Nutrition and Food, 76131 Karlsruhe, Germany;
| | - Evelyne Selberherr
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, A-1210 Vienna, Austria; (N.M.Q.); (E.S.)
| | - José Horacio Grau
- Amedes Genetics, Amedes Medizinische Dienstleistungen GmbH, 10117 Berlin, Germany; (J.H.G.); (M.M.); (K.L.)
- Center for Species Survival, Smithsonian Conservation Biology Institute, Washington, DC 20008, USA
| | - Martin Meixner
- Amedes Genetics, Amedes Medizinische Dienstleistungen GmbH, 10117 Berlin, Germany; (J.H.G.); (M.M.); (K.L.)
| | - Karsten Liere
- Amedes Genetics, Amedes Medizinische Dienstleistungen GmbH, 10117 Berlin, Germany; (J.H.G.); (M.M.); (K.L.)
| | - Danilo Ercolini
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, 80055 Portici, Italy; (E.P.); (D.E.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80055 Portici, Italy
| | - Carlotta de Filippo
- Institute of Agricultural Biology and Biotechnology (IBBA), National Research Council (CNR), Via Moruzzi 1, 56124 Pisa, Italy; (F.V.); (C.d.F.)
| | - Giovanna Caderni
- NEUROFARBA Department, Pharmacology and Toxicology Section, University of Florence, Viale Pieraccini 6, 50139 Florence, Italy;
| | - Patrizia Brigidi
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy;
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy; (M.F.); (S.T.)
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Cao Y, Macori G, Naithani A, Tall BD, Gangiredla J, Srikumar S, Fanning S. A 16S rRNA Sequencing Study Describing the Environmental Microbiota of Two Powdered Infant Formula Built Facilities. Foodborne Pathog Dis 2022; 19:473-484. [PMID: 35766923 DOI: 10.1089/fpd.2021.0116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Microbial safety is critically important for powdered infant formula (PIF) fed to neonates, with under-developed immune systems. The quality and safety of food products are dictated by those microorganisms found in both raw materials and the built production environment. In this study, a 2-year monitoring program of a production environment was carried out in two PIF factories located in the Republic of Ireland, and the environmental microbiome in different care areas of these sites was studied by using a 16S ribosomal RNA (rRNA)-based sequencing technique. Results highlighted a core microbiome associated with the PIF factory environment containing 24 bacterial genera representing five phyla, with Acinetobacter and Pseudomonas as the predominant genera. In different care areas of the PIF factory, as hygiene standards increased, deciphered changes in microbial community compositions became smaller over time and approached stability, and bacteria dominating the care area became less influenced by the external environment and more by human interactions and raw materials. These observations indicated that the microbial composition can be altered in response to environmental interventions. Genera Cronobacter and Salmonella were observed in trace amounts in the PIF factory environment, and bacterial genera known to be persistent in a stressed environment, such as Acinetobacter, Bacillus, Streptococcus, and Clostridium, were likely to have higher abundances in dry environment-based care areas. To our knowledge, this is the first study to characterize the PIF production environment microbiome using 16S rRNA-based sequencing. This study described the composition and changing trends of the environmental microbial communities in different care areas of the PIF manufacturing facility, and it provided valuable information to support the safer production of PIF in the future.
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Affiliation(s)
- Yu Cao
- UCD-Centre for Food Safety, Science Centre South, University College Dublin, Dublin, Ireland
| | - Guerrino Macori
- UCD-Centre for Food Safety, Science Centre South, University College Dublin, Dublin, Ireland
| | - Ankita Naithani
- UCD-Centre for Food Safety, Science Centre South, University College Dublin, Dublin, Ireland
| | - Ben D Tall
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Jayanthi Gangiredla
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Shabarinath Srikumar
- UCD-Centre for Food Safety, Science Centre South, University College Dublin, Dublin, Ireland.,Department of Food, Nutrition and Health, College of Food and Agriculture, UAE University Al Ain Campus, Al Ain, United Arab Emirates
| | - Séamus Fanning
- UCD-Centre for Food Safety, Science Centre South, University College Dublin, Dublin, Ireland
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145
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Gao L, Cheng Z, Zhu F, Bi C, Shi Q, Chen X. The Oral Microbiome and Its Role in Systemic Autoimmune Diseases: A Systematic Review of Big Data Analysis. Front Big Data 2022; 5:927520. [PMID: 35844967 PMCID: PMC9277227 DOI: 10.3389/fdata.2022.927520] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 05/23/2022] [Indexed: 12/30/2022] Open
Abstract
Introduction Despite decades of research, systemic autoimmune diseases (SADs) continue to be a major global health concern and the etiology of these diseases is still not clear. To date, with the development of high-throughput techniques, increasing evidence indicated a key role of oral microbiome in the pathogenesis of SADs, and the alterations of oral microbiome may contribute to the disease emergence or evolution. This review is to present the latest knowledge on the relationship between the oral microbiome and SADs, focusing on the multiomics data generated from a large set of samples. Methodology By searching the PubMed and Embase databases, studies that investigated the oral microbiome of SADs, including systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), and Sjögren's syndrome (SS), were systematically reviewed according to the PRISMA guidelines. Results One thousand and thirty-eight studies were found, and 25 studies were included: three referred to SLE, 12 referred to RA, nine referred to SS, and one to both SLE and SS. The 16S rRNA sequencing was the most frequent technique used. HOMD was the most common database aligned to and QIIME was the most popular pipeline for downstream analysis. Alterations in bacterial composition and population have been found in the oral samples of patients with SAD compared with the healthy controls. Results regarding candidate pathogens were not always in accordance, but Selenomonas and Veillonella were found significantly increased in three SADs, and Streptococcus was significantly decreased in the SADs compared with controls. Conclusion A large amount of sequencing data was collected from patients with SAD and controls in this systematic review. Oral microbial dysbiosis had been identified in these SADs, although the dysbiosis features were different among studies. There was a lack of standardized study methodology for each study from the inclusion criteria, sample type, sequencing platform, and referred database to downstream analysis pipeline and cutoff. Besides the genomics, transcriptomics, proteomics, and metabolomics technology should be used to investigate the oral microbiome of patients with SADs and also the at-risk individuals of disease development, which may provide us with a better understanding of the etiology of SADs and promote the development of the novel therapies.
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Affiliation(s)
- Lu Gao
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Clinical Research Center for Oral Diseases, Hangzhou, China
- Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou, China
| | - Zijian Cheng
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Clinical Research Center for Oral Diseases, Hangzhou, China
- Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou, China
| | - Fudong Zhu
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Clinical Research Center for Oral Diseases, Hangzhou, China
- Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou, China
| | - Chunsheng Bi
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Clinical Research Center for Oral Diseases, Hangzhou, China
- Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou, China
| | - Qiongling Shi
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Clinical Research Center for Oral Diseases, Hangzhou, China
- Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou, China
| | - Xiaoyan Chen
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Clinical Research Center for Oral Diseases, Hangzhou, China
- Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou, China
- *Correspondence: Xiaoyan Chen
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146
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Social microbiota and social gland gene expression of worker honey bees by age and climate. Sci Rep 2022; 12:10690. [PMID: 35739206 PMCID: PMC9226125 DOI: 10.1038/s41598-022-14442-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 06/07/2022] [Indexed: 11/08/2022] Open
Abstract
Winter forage dearth is a major contributor to honey bee colony loss and can influence disease susceptibility. Honey bees possess a secretory head gland that interfaces with the social environment on many levels. During winter or forage dearth, colonies produce a long-lived (diutinus) worker phenotype that survives until environmental conditions improve. We used a known-age worker cohort to investigate microbiome integrity and social gene expression of workers in early and late winter. We provide additional context by contrasting host-microbial interactions from warm outdoor and cold indoor environments. Our results provide novel evidence that social immune gene expression is associated with worker longevity, and highlight the midgut as a target of opportunistic disease during winter. Host microbial interactions suggest opportunistic disease progression and resistance in long-lived workers, but susceptibility to opportunistic disease in younger workers that emerged during the winter, including increases in Enterobacteriaceae, fungal load and non-core bacterial abundance. The results are consistent with increased social immunity, including host associations with the social microbiota, and a social immune response by long-lived workers to combat microbial opportunism. The cost/benefit ratio associated with limited expression of the diutinus phenotype may be a strong determinant of colony survival during winter forage dearth.
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147
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Nguyen PT, Tuz K, Restaino L, Juárez O. NRJ Media as the Gold-Standard Arcobacter-Specific Detection System: Applications in Poultry Testing. Front Microbiol 2022; 13:903079. [PMID: 35801110 PMCID: PMC9253625 DOI: 10.3389/fmicb.2022.903079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/25/2022] [Indexed: 11/24/2022] Open
Abstract
Arcobacter species are ubiquitous emerging pathogens with an impact that has been underestimated due to limitations in isolation and detection methods. Our group recently developed the novel NRJ Arcobacter-detection system, with major improvements in specificity and selectivity compared to other culture-based methods. In this work, the NRJ detection system was evaluated using retail whole broiler chicken carcass. Nanopore 16S rRNA gene amplicon sequencing demonstrated that Arcobacter species are found in very low abundance in retail chicken and that indigenous microbiota could be a major factor interfering with detection. Comparison of the microbiome obtained from modified Houf broth (HB) method, as the standard detection system, and the novel NRJ method, showed Arcobacter abundances of <15% and >97%, respectively. The NRJ system significantly inhibits the growth of non-target microbiota, and specifically allows the multiplication of Arcobacter species. In this report, we describe the gold-standard of Arcobacter-specific culture-based method to test food matrices, which can be used for other applications, such as clinical and environmental sampling.
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Affiliation(s)
- Paul T. Nguyen
- R & F Products, Inc., Downers Grove, IL, United States,Department of Biology, Illinois Institute of Technology, Chicago, IL, United States
| | - Karina Tuz
- Department of Biology, Illinois Institute of Technology, Chicago, IL, United States
| | - Lawrence Restaino
- R & F Products, Inc., Downers Grove, IL, United States,*Correspondence: Lawrence Restaino,
| | - Oscar Juárez
- Department of Biology, Illinois Institute of Technology, Chicago, IL, United States,Oscar Juárez,
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148
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Song W, Zhang S, Thomas T. MarkerMAG: linking metagenome-assembled genomes (MAGs) with 16S rRNA marker genes using paired-end short reads. Bioinformatics 2022; 38:3684-3688. [PMID: 35713513 DOI: 10.1093/bioinformatics/btac398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 06/08/2022] [Accepted: 06/15/2022] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Metagenome-assembled genomes (MAGs) have substantially extended our understanding of microbial functionality. However, 16S rRNA genes, which are commonly used in phylogenetic analysis and environmental surveys, are often missing from MAGs. Here, we developed MarkerMAG, a pipeline that links 16S rRNA genes to MAGs using paired-end sequencing reads. RESULTS Assessment of MarkerMAG on three benchmarking metagenomic datasets with various degrees of complexity shows substantial increases in the number of MAGs with 16S rRNA genes and a 100% assignment accuracy. MarkerMAG also estimates the copy number of 16S rRNA genes in MAGs with high accuracy. Assessments on three real metagenomic datasets demonstrates 1.1- to 14.2-fold increases in the number of MAGs with 16S rRNA genes. We also show that MarkerMAG-improved MAGs increase the accuracy of functional prediction from 16S rRNA gene amplicon data. MarkerMAG is helpful in connecting information in MAG database with those in 16S rRNA databases and surveys and hence contributes to our increasing understanding of microbial diversity, function, and phylogeny. AVAILABILITY MarkerMAG is implemented in Python3 and freely available at https://github.com/songweizhi/MarkerMAG. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Weizhi Song
- Centre for Marine Science & Innovation, University of New South Wales, Sydney, 2052, Australia.,School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, 2052, Australia
| | - Shan Zhang
- Centre for Marine Science & Innovation, University of New South Wales, Sydney, 2052, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia
| | - Torsten Thomas
- Centre for Marine Science & Innovation, University of New South Wales, Sydney, 2052, Australia.,School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, 2052, Australia
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149
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Nepel M, Pfeifer J, Oberhauser FB, Richter A, Woebken D, Mayer VE. Nitrogen fixation by diverse diazotrophic communities can support population growth of arboreal ants. BMC Biol 2022; 20:135. [PMID: 35681192 PMCID: PMC9185989 DOI: 10.1186/s12915-022-01289-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/31/2022] [Indexed: 11/17/2022] Open
Abstract
Background Symbiotic ant-plant associations, in which ants live on plants, feed on plant-provided food, and protect host trees against threats, are ubiquitous across the tropics, with the Azteca-Cecropia associations being amongst the most widespread interactions in the Neotropics. Upon colonization of Cecropia’s hollow internodes, Azteca queens form small patches with plant parenchyma, which are then used as waste piles when the colony grows. Patches—found in many ant-plant mutualisms—are present throughout the colony life cycle and may supplement larval food. Despite their initial nitrogen (N)-poor substrate, patches in Cecropia accommodate fungi, nematodes, and bacteria. In this study, we investigated the atmospheric N2 fixation as an N source in patches of early and established ant colonies. Results Via 15N2 tracer assays, N2 fixation was frequently detected in all investigated patch types formed by three Azteca ant species. Quantified fixation rates were similar in early and established ant colonies and higher than in various tropical habitats. Based on amplicon sequencing, the identified microbial functional guild—the diazotrophs—harboring and transcribing the dinitrogenase reductase (nifH) gene was highly diverse and heterogeneous across Azteca colonies. The community composition differed between early and established ant colonies and partly between the ant species. Conclusions Our data show that N2 fixation can result in reasonable amounts of N in ant colonies, which might not only enable bacterial, fungal, and nematode growth in the patch ecosystems but according to our calculations can even support the growth of ant populations. The diverse and heterogeneous diazotrophic community implies a functional redundancy, which could provide the ant-plant-patch system with a higher resilience towards changing environmental conditions. Hence, we propose that N2 fixation represents a previously unknown potential to overcome N limitations in arboreal ant colonies. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01289-0.
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Affiliation(s)
- Maximilian Nepel
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria. .,Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
| | - Josephine Pfeifer
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Felix B Oberhauser
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria.,Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany
| | - Andreas Richter
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Dagmar Woebken
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
| | - Veronika E Mayer
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
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150
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Investigating the microbial terroir of fermented foods produced in a professional kitchen. Int J Gastron Food Sci 2022. [DOI: 10.1016/j.ijgfs.2022.100509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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