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Nagar S, Talwar C, Motelica-Heino M, Richnow HH, Shakarad M, Lal R, Negi RK. Microbial Ecology of Sulfur Biogeochemical Cycling at a Mesothermal Hot Spring Atop Northern Himalayas, India. Front Microbiol 2022; 13:848010. [PMID: 35495730 PMCID: PMC9044081 DOI: 10.3389/fmicb.2022.848010] [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: 01/03/2022] [Accepted: 03/09/2022] [Indexed: 11/13/2022] Open
Abstract
Sulfur related prokaryotes residing in hot spring present good opportunity for exploring the limitless possibilities of integral ecosystem processes. Metagenomic analysis further expands the phylogenetic breadth of these extraordinary sulfur (S) metabolizing microorganisms as well as their complex metabolic networks and syntrophic interactions in environmental biosystems. Through this study, we explored and expanded the microbial genetic repertoire with focus on S cycling genes through metagenomic analysis of S contaminated hot spring, located at the Northern Himalayas. The analysis revealed rich diversity of microbial consortia with established roles in S cycling such as Pseudomonas, Thioalkalivibrio, Desulfovibrio, and Desulfobulbaceae (Proteobacteria). The major gene families inferred to be abundant across microbial mat, sediment, and water were assigned to Proteobacteria as reflected from the reads per kilobase (RPKs) categorized into translation and ribosomal structure and biogenesis. An analysis of sequence similarity showed conserved pattern of both dsrAB genes (n = 178) retrieved from all metagenomes while other S disproportionation proteins were diverged due to different structural and chemical substrates. The diversity of S oxidizing bacteria (SOB) and sulfate reducing bacteria (SRB) with conserved (r)dsrAB suggests for it to be an important adaptation for microbial fitness at this site. Here, (i) the oxidative and reductive dsr evolutionary time-scale phylogeny proved that the earliest (but not the first) dsrAB proteins belong to anaerobic Thiobacillus with other (rdsr) oxidizers, also we confirm that (ii) SRBs belongs to δ-Proteobacteria occurring independent lateral gene transfer (LGT) of dsr genes to different and few novel lineages. Further, the structural prediction of unassigned DsrAB proteins confirmed their relatedness with species of Desulfovibrio (TM score = 0.86, 0.98, 0.96) and Archaeoglobus fulgidus (TM score = 0.97, 0.98). We proposed that the genetic repertoire might provide the basis of studying time-scale evolution and horizontal gene transfer of these genes in biogeochemical S cycling.
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Affiliation(s)
- Shekhar Nagar
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, New Delhi, India
| | - Chandni Talwar
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, New Delhi, India
| | - Mikael Motelica-Heino
- UMR 7327, Centre National de la Recherche Scientifique, Institut des Sciences de la Terre D'Orleans (ISTO), Université d'Orleans-Brgm, Orleans, France
| | - Hans-Hermann Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Mallikarjun Shakarad
- Evolutionary Biology Laboratory, Department of Zoology, University of Delhi, New Delhi, India
| | - Rup Lal
- NASI Senior Scientist Platinum Jubilee Fellow, The Energy and Resources Institute, New Delhi, India
| | - Ram Krishan Negi
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, New Delhi, India
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202
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Chen H, Ma K, Lu C, Fu Q, Qiu Y, Zhao J, Huang Y, Yang Y, Schadt CW, Chen H. Functional Redundancy in Soil Microbial Community Based on Metagenomics Across the Globe. Front Microbiol 2022; 13:878978. [PMID: 35586865 PMCID: PMC9108720 DOI: 10.3389/fmicb.2022.878978] [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: 02/18/2022] [Accepted: 04/13/2022] [Indexed: 12/30/2022] Open
Abstract
Understanding the contribution of soil microbial communities to ecosystem processes is critical for predicting terrestrial ecosystem feedbacks under changing climate. Our current understanding lacks a consistent strategy to formulate the linkage between microbial systems and ecosystem processes due to the presumption of functional redundancy in soil microbes. Here we present a global soil microbial metagenomic analysis to generalize patterns of microbial taxonomic compositions and functional potentials across climate and geochemical gradient. Our analyses show that soil microbial taxonomic composition varies widely in response to climate and soil physicochemical gradients, while microbial functional attributes based on metagenomic gene abundances are redundant. Among 17 climate zones, microbial taxonomic compositions were more distinct than functional potentials, as climate and edaphic properties showed more significant influence on microbial taxonomic compositions than on functional potentials. Microbial taxonomies formed a larger and more complex co-occurrence network with more module structures than functional potentials. Functional network was strongly inter-connected among different categories, whereas taxonomic network was more positively interactive in the same taxonomic groups. This study provides strong evidence to support the hypothesis of functional redundancy in soil microbes, as microbial taxonomic compositions vary to a larger extent than functional potentials based on metagenomic gene abundances in terrestrial ecosystems across the globe.
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Affiliation(s)
- Huaihai Chen
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Kayan Ma
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Caiyan Lu
- Key Laboratory of Pollution Ecology and Environment Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- Key Lab of Conservation Tillage and Ecological Agriculture, Shenyang, China
| | - Qi Fu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Yingbo Qiu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Jiayi Zhao
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Yu Huang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Yuchun Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | | | - Hao Chen
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
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203
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Co-culturing of microalgae and bacteria in real wastewaters alters indigenous bacterial communities enhancing effluent bioremediation. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102705] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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204
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Chaitra HS, Singh A, Pandiyan K, Kalia VK. Sex Biased Variance in the Structural and Functional Diversity of the Midgut Bacterial Community of Last Instar Larvae of Pectinophora gossypiella (Lepidoptera: Gelechiidae). MICROBIAL ECOLOGY 2022; 83:1112-1122. [PMID: 34345962 DOI: 10.1007/s00248-021-01829-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
Elucidating the midgut bacterial diversity in an important cotton bollworm Pectinophora gossypiella can be a stepping stone in understanding the possible role of midgut bacteria in field evolved resistance against Bt cotton as well as to commonly used insecticides. Present study targeted metagenomics of 16S rRNA V3-V4 region to understand the influence of sex, if exists, in community diversity of gut microbes vis a vis their function in pink bollworm larvae. The results of the present study revealed that Proteobacteria, Firmicutes, and Actinobacteria were the predominant phyla in the midgut of pink bollworm. Distinctive differences were found in the Shannon and Simpson diversity indices, ChaoI and ACE richness estimates in male and female larvae. The alpha diversity analysis showed that the gut bacteria of male were diverse and rich as compared to that of female. Further, beta diversity analysis indicated that the gut bacterial communities of both larval groups were unique from each other. These findings are the maiden report on sex-based variation in gut bacteria in P. gossypiella larvae. Role of candidate phyla OD1 (Parcubacteria) and TM7 (Saccharibacteria) in the living organisms needs to be studied, and their fairly significant composition in male and negligible composition in female larva raises question on their obvious role. Taxonomic to phenotypic mapping revealed that these gut bacteria play vital role in many metabolic and physiological activities of pink bollworm. Difference in potential functions of gut bacteria also varied with the sex.
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Affiliation(s)
- H S Chaitra
- Division of Entomology, Indian Agricultural Research Institute, New Delhi, India
| | - Arjun Singh
- ICAR-Central Soil Salinity Research Institute, RRS, Lucknow, India
- ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, Mau, India
| | - Kuppusamy Pandiyan
- ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, Mau, India
- Ginning Training Centre, ICAR-Central Institute for Research on Cotton Technology, Nagpur, India
| | - Vinay K Kalia
- Division of Entomology, Indian Agricultural Research Institute, New Delhi, India.
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205
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Lu X, Wang K, Mou X. Metagenomes of polyamine-transforming bacterioplankton along a nearshore-open ocean transect. MARINE LIFE SCIENCE & TECHNOLOGY 2022; 4:268-276. [PMID: 37073219 PMCID: PMC10077212 DOI: 10.1007/s42995-021-00114-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/22/2021] [Indexed: 05/03/2023]
Abstract
Short-chained aliphatic polyamines (PAs) have recently been recognized as an important carbon, nitrogen, and/or energy source for marine bacterioplankton. To study the genes and taxa involved in the transformations of different PA compounds and their potential variations among marine systems, we collected surface bacterioplankton from nearshore, offshore, and open ocean stations in the Gulf of Mexico and examined their metagenomic responses to additions of single PA model compounds (putrescine, spermidine, or spermine). Genes affiliated with PA uptake and all three known PA degradation pathways, i.e., transamination, γ-glutamylation, and spermidine cleavage, were significantly enriched in most PA-treated metagenomes. In addition, identified PA-transforming taxa were mostly the alpha and gamma classes of Proteobacteria, with less important contributions from members of Betaproteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, and Planctomycetes. These findings suggest that PA transformations are ubiquitous, have diverse pathways, and are carried out by a broad range of the bacterioplankton taxa in the Gulf of Mexico. Identified PA-transforming bacterial genes and taxa were different among nearshore, offshore, and open ocean sites, but were little different among individual compound-amended metagenomes at any specific site. These observations further indicate that PA-transforming taxa and genes are site-specific and with high similarities among PA compounds. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-021-00114-x.
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Affiliation(s)
- Xinxin Lu
- Department of Biological Sciences, Kent State University, Kent, OH USA
| | - Kai Wang
- Department of Biological Sciences, Kent State University, Kent, OH USA
| | - Xiaozhen Mou
- Department of Biological Sciences, Kent State University, Kent, OH USA
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206
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Functional Diversity of Bacterial Communities in the Rhizosphere of Maize Grown on a Soil under Organic and Inorganic Fertilization. SCIENTIFIC AFRICAN 2022. [DOI: 10.1016/j.sciaf.2022.e01212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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207
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Influence of Fe2+ and Fe3+ on the Performance and Microbial Community Composition of a MFC Inoculated with Sulfate-Reducing Sludge and Acetate as Electron Donor. J CHEM-NY 2022. [DOI: 10.1155/2022/5685178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A sulfidogenic sludge supplemented with acetate was evaluated in the anodic chamber of microbial fuel cells (MFCs) in the presence of sulfate (SO4-2)/Fe3+ and sulfate (SO4-2)/Fe2+ to investigate the MFC performance and the effect of the iron ions on the composition of the microbial community since sulfate and iron ions are frequently present in wastewater derived from several anthropogenic activities. The current densities were up to 0.025 mA/cm2 and 0.017 mA/cm2 for MFCs with Fe2+ and Fe3+, respectively. Accordingly, the redox activity was slightly higher in the presence of Fe2+ than Fe3+. In general, the metabolic activity of the MFC supplemented with Fe2+ was higher than the system with Fe3+ reaching a percentage of sulfate reduction (% SR), sulfide concentration (mg/L HS-), and removal of chemical oxygen demand (% COD removal) of
,
, and
for % SR, HS-, and % COD, respectively, whereas in the MFC with Fe3+, the percentages were of
,
, and
for % SR, HS-, and % COD, respectively. The microbial population determined in each system was also correlated to the metabolic activity. Rhodospirillales, Caulobacterales, and Burkholderiales were the most abundant orders of bacteria in the MFC with Fe3+, whereas with Fe2+, Rhodobacterales, Sphingomonadales, and Rhizobiales. Desulfohalobiaceae and Desulfovibrionaceae were identified in the presence of Fe2+. Unexpected interactions and combinations of microorganisms were observed in a relatively short culturing time, demonstrating the importance of characterizing the anode biofilm prior to shifts in iron ion concentrations on a long-term basis.
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208
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Hernandez AR, Kemp KM, Burke SN, Buford TW, Carter CS. Influence of Aging, Macronutrient Composition and Time-Restricted Feeding on the Fischer344 x Brown Norway Rat Gut Microbiota. Nutrients 2022; 14:nu14091758. [PMID: 35565725 PMCID: PMC9105022 DOI: 10.3390/nu14091758] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/19/2022] [Accepted: 04/21/2022] [Indexed: 02/01/2023] Open
Abstract
Both ketogenic diets (KD) and time-restricted feeding (TRF) regimens have the ability to influence several parameters of physical health, including gut microbiome composition and circulating cytokine concentration. Moreover, both of these dietary interventions prevent common impairments associated with the aging process. However, significantly altering macronutrient intake, which is required for a KD, may be unappealing to individuals and decrease compliance to dietary treatments. In contrast to a KD, TRF allows individuals to continue eating the foods they are used to, and only requires a change in the time of day at which they eat. Therefore, we investigated both a KD and a diet with a more Western-like macronutrient profile in the context of TRF, and compared both diets to animals allowed access to standard chow ad libitum in young adult and aged rats. While limited effects on cytokine levels were observed, both methods of microbiome analysis (16S sequencing and metagenomics) indicate that TRF and KDs significantly altered the gut microbiome in aged rats. These changes were largely dependent on changes to feeding paradigm (TRF vs. ad libitum) alone regardless of macronutrient content for many gut microbiota, but there were also macronutrient-specific changes. Specifically, functional analysis indicates significant differences in several pathways, including those involved in the tricarboxylic acid (TCA) cycle, carbohydrate metabolism and neurodegenerative disease. These data indicate that age- and disease-related gut dysbiosis may be ameliorated through the use of TRF with both standard diets and KDs.
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Affiliation(s)
- Abbi R. Hernandez
- Division of Gerontology, Geriatrics and Palliative Care, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (T.W.B.); (C.S.C.)
- UAB Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Nathan Shock Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Correspondence:
| | - Keri M. Kemp
- CardioRenal Physiology and Medicine Section, Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
| | - Sara N. Burke
- Center for Cognitive Aging and Memory, Department of Neuroscience and McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32611, USA;
| | - Thomas W. Buford
- Division of Gerontology, Geriatrics and Palliative Care, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (T.W.B.); (C.S.C.)
- UAB Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Nathan Shock Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Integrative Center for Aging Research, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Geriatric Research Education and Clinical Center, Birmingham VA Medical Center, Birmingham, AL 35294, USA
| | - Christy S. Carter
- Division of Gerontology, Geriatrics and Palliative Care, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (T.W.B.); (C.S.C.)
- UAB Center for Exercise Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Nathan Shock Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Integrative Center for Aging Research, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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209
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Lourenco JM, Krause TR, Welch CB, Callaway TR, Pringle TD. Longitudinal Changes of the Ruminal Microbiota in Angus Beef Steers. Animals (Basel) 2022; 12:ani12091066. [PMID: 35565493 PMCID: PMC9102304 DOI: 10.3390/ani12091066] [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: 03/07/2022] [Revised: 04/11/2022] [Accepted: 04/14/2022] [Indexed: 12/15/2022] Open
Abstract
The ruminal microbiota of Angus cows and steers were characterized using 16s rRNA gene sequencing, and the expression of their metabolic pathways was predicted. Samples were collected on weaning day from the steers and the cows, and subsequently on three other occasions from the steers. Results showed that microbial richness, evenness, and diversity decreased (p < 0.001) in the rumen of the steers as they were weaned and transitioned to a high-concentrate feedlot diet. However, on the day of weaning, microbial evenness was similar to that observed in the rumen of cows (p = 0.12). The abundance of archaea was similar (p = 0.59) between the cows and steers at weaning, but it decreased (p = 0.04) in the rumen of steers after weaning, and remained stable (p ≥ 0.44) for the remainder of their lives. Likewise, no difference (p = 0.51) in the abundance of Bacteroidetes was detected between the cows and the calves on the day they were weaned, but the abundance of this phylum increased (p = 0.001) and remained stable after that. These results suggest that cows may have a strong influence on the composition, and help modulate the ruminal microbiota of young calves; however, following weaning, their ruminal microbiotas tend to differentiate from that state observed at earlier ages.
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210
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Microbial Involvement in the Bioremediation of Total Petroleum Hydrocarbon Polluted Soils: Challenges and Perspectives. ENVIRONMENTS 2022. [DOI: 10.3390/environments9040052] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Nowadays, soil contamination by total petroleum hydrocarbons is still one of the most widespread forms of contamination. Intervention technologies are consolidated; however, full-scale interventions turn out to be not sustainable. Sustainability is essential not only in terms of costs, but also in terms of restoration of the soil resilience. Bioremediation has the possibility to fill the gap of sustainability with proper knowledge. Bioremediation should be optimized by the exploitation of the recent “omic” approaches to the study of hydrocarburoclastic microbiomes. To reach the goal, an extensive and deep knowledge in the study of bacterial and fungal degradative pathways, their interactions within microbiomes and of microbiomes with the soil matrix has to be gained. “Omic” approaches permits to study both the culturable and the unculturable soil microbial communities active in degradation processes, offering the instruments to identify the key organisms responsible for soil contaminant depletion and restoration of soil resilience. Tools for the investigation of both microbial communities, their degradation pathways and their interaction, will be discussed, describing the dedicated genomic and metagenomic approaches, as well as the interpretative tools of the deriving data, that are exploitable for both optimizing bio-based approaches for the treatment of total petroleum hydrocarbon contaminated soils and for the correct scaling up of the technologies at the industrial scale.
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211
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Bryanskaya AV, Shipova AA, Rozanov AS, Kolpakova OA, Lazareva EV, Uvarova YE, Efimov VM, Zhmodik SM, Taran OP, Goryachkovskaya TN, Peltek SE. Diversity and Metabolism of Microbial Communities in a Hypersaline Lake along a Geochemical Gradient. BIOLOGY 2022; 11:biology11040605. [PMID: 35453804 PMCID: PMC9031644 DOI: 10.3390/biology11040605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/13/2022] [Accepted: 04/14/2022] [Indexed: 11/16/2022]
Abstract
In the south of western Siberia (Russia), there are many unique and unexplored soda, saline, and freshwater lakes. In this study, the results are presented on microbial diversity, its metabolic potential, and their relation with a set of geochemical parameters for a hypersaline lake ecosystem in the Novosibirsk region (Oblast). The metagenomic approach used in this work allowed us to determine the composition and structure of a floating microbial community, the upper layer of silt, and the strata of bottom sediments in a natural saline lake via two bioinformatic approaches, whose results are in good agreement with each other. In the floating microbial community and in the upper layers of the bottom sediment, bacteria of the Proteobacteria (Gammaproteobacteria), Cyanobacteria, and Bacteroidetes phyla were found to predominate. The lower layers were dominated by Proteobacteria (mainly Deltaproteobacteria), Gemmatimonadetes, Firmicutes, and Archaea. Metabolic pathways were reconstructed to investigate the metabolic potential of the microbial communities and other hypothetical roles of the microbial communities in the biogeochemical cycle. Relations between different taxa of microorganisms were identified, as was their potential role in biogeochemical transformations of C, N, and S in a comparative structural analysis that included various ecological niches.
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Affiliation(s)
- Alla V. Bryanskaya
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Correspondence: or ; Tel.: +7-383-363-4963 (ext. 4120)
| | - Aleksandra A. Shipova
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Alexei S. Rozanov
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Oxana A. Kolpakova
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Elena V. Lazareva
- V.S. Sobolev Institute of Geology and Mineralogy SB RAS, 630090 Novosibirsk, Russia; (E.V.L.); (S.M.Z.)
| | - Yulia E. Uvarova
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Vadim M. Efimov
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Sergey M. Zhmodik
- V.S. Sobolev Institute of Geology and Mineralogy SB RAS, 630090 Novosibirsk, Russia; (E.V.L.); (S.M.Z.)
| | - Oxana P. Taran
- FRC Krasnoyarsk Science Center SB RAS, Institute of Chemistry and Chemical Technology SB RAS, 660036 Krasnoyarsk, Russia;
| | - Tatyana N. Goryachkovskaya
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Sergey E. Peltek
- Laboratory of Molecular Biotechnologies, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (A.A.S.); (A.S.R.); (O.A.K.); (Y.E.U.); efim (V.M.E.); (T.N.G.); (S.E.P.)
- Kurchatov Genomics Center, Federal Research Center Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
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212
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Passarini MRZ, Ottoni JR, Costa PEDS, Hissa DC, Falcão RM, Melo VMM, Balbino VQ, Mendonça LAR, Lima MGDS, Coutinho HDM, Verde LCL. Fungal community diversity of heavy metal contaminated soils revealed by metagenomics. Arch Microbiol 2022; 204:255. [PMID: 35412096 DOI: 10.1007/s00203-022-02860-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 03/17/2022] [Accepted: 03/20/2022] [Indexed: 11/29/2022]
Abstract
The inappropriate disposal of toxic compounds generated by industrial activity has been impacting the environment considerably. Microbial communities inhabiting contaminated sites may represent interesting ecological alternatives for the decontamination of environments. The present work aimed to investigate the fungal diversity and its functionality contained in stream sediments with industrial waste contaminated with heavy metals by using metagenomic approach. A total of 12 fungal orders were retrieved from datasets and, at phylum level, Ascomycota was the most abundant, followed by Basidiomycota, Chytridiomycota and Blastocladiomycota. Higher abundance of sequences was encountered within the less contaminated site, while the lower abundance was found in the sample with the higher contamination with lead. Gene sequences related to DNA repair and heavy metals biosorption processes were found in the four samples analyzed. The genera Aspergillus and Chaetomium, and Saccharomycetales order were highly present within all samples, showing their potential to be used for bioremediation studies. The present work demonstrated the importance of using the metagenomic approach to understand the dynamics and the possible metabolic pathways associated with fungal communities related to environmental samples containing heavy metals, as well as evidenced the importance of improving culturomics techniques for isolating strains with potential application in bioremediation processes of environments contaminated with heavy metals.
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Affiliation(s)
- Michel Rodrigo Zambrano Passarini
- UNILA-Universidade Federal da Integração Latino-Americana, Av. Tarquínio Joslin Dos Santos, 1000-Jd Universitário, Foz do Iguaçu, PR, 85870-650, Brazil.
| | - Júlia Ronzella Ottoni
- UNILA-Universidade Federal da Integração Latino-Americana, Av. Tarquínio Joslin Dos Santos, 1000-Jd Universitário, Foz do Iguaçu, PR, 85870-650, Brazil
| | | | | | - Raul Maia Falcão
- Department of Genetics, Federal University of Pernambuco, Recife, Brazil
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213
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Relationship between nitrifying microorganisms and other microorganisms residing in the maize rhizosphere. Arch Microbiol 2022; 204:246. [PMID: 35394234 DOI: 10.1007/s00203-022-02857-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 03/15/2022] [Accepted: 03/18/2022] [Indexed: 01/10/2023]
Abstract
The microbial network of rhizosphere is unique as a result of root exudate. Insights into the relationship that exists with the energy metabolic functional groups will help in biofertilizer production. We hypothesize that there exists a relationship between nitrifying microorganisms and other energy metabolic functional microbial groups in the maize rhizosphere across different growth stages. Nucleospin soil DNA extraction kit was used to extract DNA from soil samples collected from maize rhizosphere. The 16S metagenomics sequencing was carried out on Illumina Miseq. The sequence obtained was analyzed on MG-RAST. Nitrospira genera were the most abundant in the nitrifying community. Nitrifying microorganisms were more than each of the studied functional groups except for nitrogen-fixing bacteria. Also, majority of the microorganisms were noticed at the fruiting stage and there was variation in the microbial structure across different growth stages. The result showed that there exists a substantial amount of both negative and positive correlation within the nitrifying microorganisms, and between them and other energy metabolic functional groups. The knowledge obtained from this study will help improve the growth and development of maize through modification of the rhizosphere microbial community structure.
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214
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Zhang B, Ma L, Zhang Y, Qi K, Li C, Qi J. Impact of ozonated water disinfestation on soil fungal community composition in continuous ginger field. PLoS One 2022; 17:e0266619. [PMID: 35390087 PMCID: PMC8989316 DOI: 10.1371/journal.pone.0266619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 03/23/2022] [Indexed: 12/04/2022] Open
Abstract
This study aimed to explore the impact of ozonated water (OW) disinfestation on soil fungal community composition in continuous ginger field. All soil samples were collected in continuous ginger field. There were two groups and 5 time points (0, 1, 3, 5, 9 day) in our study, including OW disinfestation treatment group (O3 group) and control group (CK group). Via internal transcribed spacer (ITS) sequencing and further analysis, the changes of fungal community composition were determined. As a result, at 0 and 9 days after aeration, the operational taxonomic units (OTUs) in O3 group were significantly higher than that in CK group. Compared with the CK group, in O3 group: the ACE and Chao1 index significantly increased on day 1, and the Shannon index significantly decreased while Simpson index significantly increased on day 0 after aeration. In O3 group, there were dynamic changes of top 10 abundance fungi from the genus-level and the growth of Trichoderma and Rhodotorula had been promoted while Hannaella was inhibited. In conclusion, OW disinfestation had complicated impacts on fungal communities in continuous ginger fields. The growth of Trichoderma and Rhodotorula has been promoted during disinfestation, which provided more reference information for soil OW disinfestation research.
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Affiliation(s)
- Bo Zhang
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences/Shandong Province Key Laboratory of Plant Virology, Jinan, Shandong, P. R. China
| | - Liguo Ma
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences/Shandong Province Key Laboratory of Plant Virology, Jinan, Shandong, P. R. China
| | - Yueli Zhang
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences/Shandong Province Key Laboratory of Plant Virology, Jinan, Shandong, P. R. China
| | - Kai Qi
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences/Shandong Province Key Laboratory of Plant Virology, Jinan, Shandong, P. R. China
| | - Changsong Li
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences/Shandong Province Key Laboratory of Plant Virology, Jinan, Shandong, P. R. China
| | - Junshan Qi
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences/Shandong Province Key Laboratory of Plant Virology, Jinan, Shandong, P. R. China
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215
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Brugaletta G, De Cesare A, Laghi L, Manfreda G, Zampiga M, Oliveri C, Pérez-Calvo E, Litta G, Lolli S, Sirri F. A multi-omics approach to elucidate the mechanisms of action of a dietary muramidase administered to broiler chickens. Sci Rep 2022; 12:5559. [PMID: 35365750 PMCID: PMC8976025 DOI: 10.1038/s41598-022-09546-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/17/2022] [Indexed: 12/01/2022] Open
Abstract
A novel dietary muramidase has been shown to have positive effects on broiler chickens. However, very little is known about its mechanisms of action. The present multi-omics investigation sought to address this knowledge gap. A total of 2,340 day-old male broilers were assigned to 3 groups (12 replicates each) fed, from 0 to 42 d, a basal diet (control group—CON) or the basal diet supplemented with muramidase at 25,000 (low-dose group—MUL) or 45,000 LSU(F)/kg feed (high-dose group—MUH). MUH significantly outperformed CON in terms of cumulative feed intake (4,798 vs 4,705 g), body weight (2,906 vs 2,775 g), and feed conversion ratio (1.686 vs 1.729), while MUL exhibited intermediate performance. At caecal level, MUH showed the lowest alpha diversity, a significantly different beta diversity, a reduction in Firmicutes, and a rise in Bacteroidetes, especially compared with MUL. MUH also exhibited a considerable decrease in Clostridiaceae and an overrepresentation of Bacteroidaceae and Lactobacillaceae. At blood level, MUH had lower hypoxanthine—probably due to its drop at caecal level—histidine, and uracil, while greater pyruvate, 2-oxoglutarate, and glucose. This study sheds light on the mode of action of this muramidase and lays the groundwork for future investigations on its effects on the intestinal ecosystem and systemic metabolism of broiler chickens.
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Affiliation(s)
- Giorgio Brugaletta
- Department of Agricultural and Food Sciences, Alma Mater Studiorum - University of Bologna, Ozzano dell'Emilia, Bologna, 40064, Italy
| | - Alessandra De Cesare
- Department of Veterinary Medical Sciences, Alma Mater Studiorum - University of Bologna, Ozzano dell'Emilia, Bologna, 40064, Italy.
| | - Luca Laghi
- Department of Agricultural and Food Sciences, Alma Mater Studiorum - University of Bologna, Ozzano dell'Emilia, Bologna, 40064, Italy
| | - Gerardo Manfreda
- Department of Agricultural and Food Sciences, Alma Mater Studiorum - University of Bologna, Ozzano dell'Emilia, Bologna, 40064, Italy
| | - Marco Zampiga
- Department of Agricultural and Food Sciences, Alma Mater Studiorum - University of Bologna, Ozzano dell'Emilia, Bologna, 40064, Italy
| | - Chiara Oliveri
- Department of Agricultural and Food Sciences, Alma Mater Studiorum - University of Bologna, Ozzano dell'Emilia, Bologna, 40064, Italy
| | - Estefanía Pérez-Calvo
- Research Center for Animal Nutrition and Health, DSM Nutritional Products, Village-Neuf, Saint Louis, 68305, France
| | - Gilberto Litta
- DSM Nutritional Products, Animal Nutrition and Health, Segrate, Milano, 20054, Italy
| | - Susanna Lolli
- DSM Nutritional Products, Animal Nutrition and Health, Segrate, Milano, 20054, Italy
| | - Federico Sirri
- Department of Agricultural and Food Sciences, Alma Mater Studiorum - University of Bologna, Ozzano dell'Emilia, Bologna, 40064, Italy
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216
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Aljahdali N. The contribution of gastrointestinal microbiota in the existence of Type 2 diabetes in Saudi Arabia: Current information and perspectives. Saudi J Biol Sci 2022; 29:103286. [PMID: 35602871 PMCID: PMC9120060 DOI: 10.1016/j.sjbs.2022.103286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/10/2022] [Accepted: 04/17/2022] [Indexed: 11/30/2022] Open
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217
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Multidrug resistance from a one health perspective in Ethiopia: A systematic review and meta-analysis of literature (2015–2020). One Health 2022; 14:100390. [PMID: 35686143 PMCID: PMC9171526 DOI: 10.1016/j.onehlt.2022.100390] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 04/15/2022] [Accepted: 04/16/2022] [Indexed: 11/22/2022] Open
Abstract
Purpose The emergence of antimicrobial resistance is a major global health challenge and becoming an urgent priority for policymakers. There is a paucity of scientific studies presenting the multidrug resistance pattern from one health perspective in Ethiopia. Therefore, a systematic review and meta-analysis aimed to determine the pooled prevalence of multidrug resistance in bacteria from human, animal, food, and environmental sources. Methods In this systematic review and meta-analysis, an electronic search was made in PubMed & Google scholar using different keywords. The studies conducted in all areas of Ethiopia, published from 2015 to 2020 in peer-reviewed journals, English full-length papers were included. The meta-analysis was done on STATA version 14. The pooled prevalence of multidrug resistance for each bacterium was analysed using the random-effects model; Cochran Q statistics and the I2 statistic was used to analyse heterogeneity and considered significant at p < 0.01. Results 81 studies were included in the systematic review and meta-analysis; 53 human studies, eight animal studies, and 16 environments/food studies. The meta-analysis included six species from gram-positive bacteria and 13 from gram-negative bacteria. S. aureus 53% (95%CI: 42–64%), Coagulase negative Staphylococci 68%(95%CI:53–82), Pseudomonas spp. 73%(95%CI:48–93%), E. coli 70% (95%CI:61–78%), Citrobacter spp. 71%(95%CI:54–87%), Klebsiella spp. 68% (54–80%), Enterobacter spp. 67% (48–83%) and Salmonella spp. 65% (95%CI:48–81%) were the common multidrug-resistant species of bacteria from two or more sources. Conclusion In Ethiopia, the pooled prevalence of MDR is high in most bacterial species from humans, animals, food, and environmental sources. Staphylococcus, most members of the Enterobacteriaceae and Pseudomonas, are the standard MDR bacterial population involving all sources. Therefore, integrated policy and intervention measures should be implemented to reduce the emergence and spread of MDR bacteria for better animal and human health outcomes.
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218
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Yasir M, Khan R, Ullah R, Bibi F, Khan I, Mustafa Karim A, Al-Ghamdi AK, Azhar EI. Bacterial diversity and the antimicrobial resistome in the southwestern highlands of Saudi Arabia. Saudi J Biol Sci 2022; 29:2138-2147. [PMID: 35531257 PMCID: PMC9072880 DOI: 10.1016/j.sjbs.2021.11.047] [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: 08/20/2021] [Revised: 11/06/2021] [Accepted: 11/17/2021] [Indexed: 11/24/2022] Open
Abstract
Soil is a reservoir of microbial diversity and the most supportive habitat for acquiring and transmitting antimicrobial resistance. Resistance transfer usually occurs from animal to soil and vice versa, and it may ultimately appear in clinical pathogens. In this study, the southwestern highlands of Saudi Arabia were studied to assess the bacterial diversity and antimicrobial resistance that could be affected by the continuous development of tourism in the region. Such effects could have a long-lasting impact on the local environment and community. Culture-dependent, quantitative polymerase chain reaction (qPCR), and shotgun sequencing-based metagenomic approaches were used to evaluate the diversity, functional capabilities, and antimicrobial resistance of bacteria isolated from collected soil samples. Bacterial communities in the southwestern highlands were mainly composed of Proteobacteria, Bacteroidetes, and Actinobacteria. A total of 102 antimicrobial resistance genes (ARGs) and variants were identified in the soil microbiota and were mainly associated with multidrug resistance, followed by macrolide, tetracycline, glycopeptide, bacitracin, and beta-lactam antibiotic resistance. The mechanisms of resistance included efflux, antibiotic target alteration, and antibiotic inactivation. qPCR confirmed the detection of 18 clinically important ARGs. In addition, half of the 49 identified isolates were phenotypically resistant to at least one of the 15 antibiotics tested. Overall, ARGs and indicator genes of anthropogenic activities (human-mitochondrial [hmt] gene and integron-integrase [int1]) were found in relatively lower abundance. Along with a high diversity of bacterial communities, variation was observed in the relative abundance of bacterial taxa among sampling sites in the southwestern highlands of Saudi Arabia.
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Affiliation(s)
- Muhammad Yasir
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Raees Khan
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Riaz Ullah
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Fehmida Bibi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Imran Khan
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau S.A.R
| | - Asad Mustafa Karim
- Department of Bioscience and Biotechnology, The University of Suwon, Hwaseong City, Gyeonggi-do, Republic of Korea
| | - Ahmed K Al-Ghamdi
- Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Esam I Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia.,Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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219
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Naidoo Y, Valverde A, Pierneef RE, Cowan DA. Differences in Precipitation Regime Shape Microbial Community Composition and Functional Potential in Namib Desert Soils. MICROBIAL ECOLOGY 2022; 83:689-701. [PMID: 34105010 DOI: 10.1007/s00248-021-01785-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/27/2021] [Indexed: 06/12/2023]
Abstract
Precipitation is one of the major constraints influencing the diversity, structure, and activity of soil microbial communities in desert ecosystems. However, the effect of changes in precipitation on soil microbial communities in arid soil microbiomes remains unresolved. In this study, using 16S rRNA gene high-throughput sequencing and shotgun metagenome sequencing, we explored changes in taxonomic composition and functional potential across two zones in the Namib Desert with contrasting precipitation regime. We found that precipitation regime had no effect on taxonomic and functional alpha-diversity, but that microbial community composition and functional potential (beta-diversity) changed with increased precipitation. For instance, Acidobacteriota and 'resistance to antibiotics and toxic compounds' related genes were relatively more abundant in the high-rainfall zone. These changes were largely due to a small set of microbial taxa, some of which were present in low abundance (i.e. members of the rare biosphere). Overall, these results indicate that key climatic factors (i.e. precipitation) shape the taxonomic and functional attributes of the arid soil microbiome. This research provides insight into how changes in precipitation patterns associated with global climate change may impact microbial community structure and function in desert soils.
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Affiliation(s)
- Yashini Naidoo
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa.
| | - Angel Valverde
- IRNASA-CSIC, C/Cordel de Merinas 40-52, 37008, Salamanca, Spain
| | - Rian E Pierneef
- Biotechnology Platform, Agricultural Research Council, Soutpan Road, Onderstepoort Campus, Pretoria, 0110, South Africa
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Lynnwood Road, Pretoria, 0002, South Africa
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220
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Clarification of the Dynamic Autothermal Thermophilic Aerobic Digestion Process Using Metagenomic Analysis. Microbiol Spectr 2022; 10:e0056122. [PMID: 35348372 PMCID: PMC9045309 DOI: 10.1128/spectrum.00561-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This study details a unique process of autothermal thermophilic aerobic digestion (ATAD) of human excreta useful in producing nitrogen-rich and pathogen-free organic fertilizer. The process was divided into initial, middle, and final phases, based on changes in temperature, dissolved oxygen (DO), and bacterial community structure. The aim of this study was to determine bacterial factors that would affect liquid fertilizer production in the process, using shotgun metagenomic analysis of each phase. Although the abundances of all 28 gene categories include 4 categories in SEED subsystems level 1 were similar to those in another type of wastewater treatment system, the abundances of 4 gene categories changed remarkably. Among them, a decrease in the abundance of the phage-related gene category and the presence of antibacterial substances in secondary metabolism may explain the change in bacterial community structure from the material to the initial phase. Increases in the abundances of two gene categories, phage-related and secondary metabolism, coincided with a decrease in alpha diversity from the material to the initial phase. A potential increase in the abundance of genes in the category of sporulation from the middle to the final phase was correlated with deterioration of growth conditions and stabilization processes. In addition, prompt consumption of short-chain fatty acids in the initial phase and unusually stable ammonia accumulation throughout the process could be explained by the presence/absence of related metabolic genes. In conclusion, the relationships between bacterial function and unique characteristics of ATAD were revealed; our findings support the enhancement of liquid fertilizer production from wastewater. IMPORTANCE Metagenome analysis was performed to determine the microbial dynamics of the unique autothermal thermophilic aerobic digestion process of human excreta, which includes initial, middle, and final phases. In this study, we revealed the details of functional genes related to physicochemical and bacterial characteristics in the ATAD process. Four gene categories showed increases and decreases during the digestion process. In addition, the unusual stable accumulation of ammonia and prompt consumption of short-chain fatty acids were explained by the absence or presence of related metabolic genes. In addition to revealing the relationships between bacteria and physicochemical properties, the results of this research may support improving wastewater management systems worldwide by using the ATAD process in liquid fertilizer production systems.
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221
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Elolimy A, Rosa F, Tripp P, Zeineldin M, Bowlin AK, Randolph C, Robeson MS, Yeruva L. Bacterial and Fungal Adaptations in Cecum and Distal Colon of Piglets Fed With Dairy-Based Milk Formula in Comparison With Human Milk. Front Microbiol 2022; 13:801854. [PMID: 35401465 PMCID: PMC8989072 DOI: 10.3389/fmicb.2022.801854] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 02/08/2022] [Indexed: 11/13/2022] Open
Abstract
Exclusive breastfeeding is recommended to newborns during the first 6 months of life, whereas dairy-based infant formula is an alternative nutrition source offered to infants. Several studies demonstrated that breastfed infants have a different gut bacterial composition relative to formula-fed infants. In addition, animal models have shown that human milk (HM)–fed piglets had a distinct intestinal bacterial composition compared with milk formula (MF)–fed piglets. However, the gut fungal composition and the interactions with the bacterial community in breastfed compared with formula-fed infants remain to be investigated. In an attempt to evaluate such differences, we used an animal model to perform a shotgun metagenomics analysis on the cecal and distal colon contents of neonatal piglets fed with pasteurized HM or a dairy-based infant formula (MF) during the first 21 days of life. At postnatal day 21 (PND 21), a subset of piglets from each diet group (n = 11 per group) was euthanized. The remaining piglets in each group were weaned to a solid diet and euthanized at PND 51 (n = 13 per group). Large intestine contents (i.e., cecum and distal colon) were subjected to shotgun metagenomics analysis. The differential taxonomic composition of bacteria and fungi and the predicted functional gene profiling were evaluated. Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria are the most abundant bacterial phyla observed in piglets at PND 21 and PND 51. In the large intestine at PND 21 and PND 51, Proteobacteria phylum was significantly higher in MF-fed group, and species Burkholderiales bacterium of phyla was significantly higher in MF group relative to HM group. In addition, in HM group, several Lactobacillus spp. and Bacteroides spp. were higher relative to MF group in the large intestine at PND 21 and PND 51. Fungal genus Aspergillus was higher in MF, whereas Malassezia was lower relative to HM group. Persistent effects of the neonatal diets were observed at PND 51, where alpha- and beta-diversity differences were detected for bacterial and fungal species in the large intestine. Overall, our findings indicate that neonatal diet affects the large intestinal microbial community during the exclusive milk-feeding period, as well as after the introduction of the complementary food.
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Affiliation(s)
- Ahmed Elolimy
- Arkansas Children’s Nutrition Center, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Little Rock, AR, United States
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Fernanda Rosa
- Arkansas Children’s Nutrition Center, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Little Rock, AR, United States
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
- School of Veterinary Medicine, Texas Tech University, Amarillo, TX, United States
| | - Patricia Tripp
- Arkansas Children’s Nutrition Center, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Little Rock, AR, United States
| | - Mohamed Zeineldin
- Department of Animal Medicine, College of Veterinary Medicine, Benha University, Banha, Egypt
| | - Anne K. Bowlin
- Arkansas Children’s Nutrition Center, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Little Rock, AR, United States
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Christopher Randolph
- Center for Translational Pediatric Research, Arkansas Children’s Research Institute, Little Rock, AR, United States
| | - Michael S. Robeson
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Laxmi Yeruva
- Arkansas Children’s Nutrition Center, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Little Rock, AR, United States
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
- *Correspondence: Laxmi Yeruva,
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Ibacache-Quiroga C, González-Pizarro K, Charifeh M, Canales C, Díaz-Viciedo R, Schmachtenberg O, Dinamarca MA. Metagenomic and Functional Characterization of Two Chilean Kefir Beverages Reveals a Dairy Beverage Containing Active Enzymes, Short-Chain Fatty Acids, Microbial β-Amyloids, and Bio-Film Inhibitors. Foods 2022; 11:foods11070900. [PMID: 35406987 PMCID: PMC8997647 DOI: 10.3390/foods11070900] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 02/05/2023] Open
Abstract
Kefir beverage is a probiotic food associated with health benefits, containing probiotic microorganisms and biomolecules produced during fermentation. The microbial composition of these beverages varies among countries, geographical regions, and the substrates, therefore, the characterization of kefir beverages is of great relevance in understanding their potential health-promoting and biotechnological applications. Therefore, this study presents the metagenomic and functional characterization of two Chilean kefir beverages, K02 and K03, through shotgun and amplicon-based metagenomic, microbiological, chemical, and biochemical studies. Results show that both beverages’ microbiota were mainly formed by Bacteria (>98%), while Eukarya represented less than 2%. Regarding Bacteria, the most abundant genera were Acetobacter (93.43% in K02 and 80.99% in K03) and Lactobacillus (5.72% in K02 and 16.75% in K03), while Kazachstania was the most abundant genus from Eukarya (42.55% and 36.08% in K02 and K03). Metagenomic analyses revealed metabolic pathways for lactose and casein assimilation, biosynthesis of health-promoting biomolecules, and clusters for antibiotic resistance, quorum sensing communication, and biofilm formation. Enzymatic activities, microbial β-amyloids, and short-chain fatty acids (acetic acid and propionic acid) were also detected in these beverages. Likewise, both kefir beverages inhibited biofilm formation of the opportunistic pathogen Pseudomonas aeruginosa.
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Affiliation(s)
- Claudia Ibacache-Quiroga
- Escuela de Nutrición y Dietética, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso 2360102, Chile
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Valparaíso 2360102, Chile; (K.G.-P.); (M.C.); (R.D.-V.)
- Correspondence: (C.I.-Q.); (M.A.D.); Tel.: +56-322-508-440 (C.I.-Q.); +56-322-508-442 (M.A.D.)
| | - Karoll González-Pizarro
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Valparaíso 2360102, Chile; (K.G.-P.); (M.C.); (R.D.-V.)
| | - Mariam Charifeh
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Valparaíso 2360102, Chile; (K.G.-P.); (M.C.); (R.D.-V.)
| | - Christian Canales
- Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Concepción 4080871, Chile;
| | - Rodrigo Díaz-Viciedo
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Valparaíso 2360102, Chile; (K.G.-P.); (M.C.); (R.D.-V.)
- Escuela de Química y Farmacia, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso 2360102, Chile
| | - Oliver Schmachtenberg
- Instituto de Biología, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso 2360102, Chile;
- Centro Interdisciplinario de Neurociencias (CINV), Universidad de Valparaíso, Valparaíso 2381850, Chile
| | - M. Alejandro Dinamarca
- Escuela de Nutrición y Dietética, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso 2360102, Chile
- Centro de Micro-Bioinnovación, Universidad de Valparaíso, Valparaíso 2360102, Chile; (K.G.-P.); (M.C.); (R.D.-V.)
- Correspondence: (C.I.-Q.); (M.A.D.); Tel.: +56-322-508-440 (C.I.-Q.); +56-322-508-442 (M.A.D.)
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Nóbrega MS, Silva BS, Tschoeke DA, Appolinario LR, Calegario G, Venas TM, Macedo L, Asp N, Cherene B, Marques JSJ, Seidel M, Dittmar T, Santos IR, de Rezende CE, Thompson CC, Thompson FL. Mangrove microbiome reveals importance of sulfur metabolism in tropical coastal waters. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 813:151889. [PMID: 34826491 DOI: 10.1016/j.scitotenv.2021.151889] [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: 10/20/2021] [Revised: 11/17/2021] [Accepted: 11/18/2021] [Indexed: 06/13/2023]
Abstract
Mangroves under macro-tidal regimes are global carbon sequestration hotspots but the microbial drivers of biogeochemical cycles remain poorly understood. Here, we investigate the drivers of mangrove microbial community composition across a porewater-creek-estuary-ocean continuum. Observations were performed on the Amazon region in one of the largest mangrove systems worldwide with effective sequestration of organic carbon buried in soils and dissolved carbon via outwelling to the ocean. The potential export to the adjacent oceanic region ranged from 57 to 380 kg of dissolved and particulate organic carbon per second (up to 33 thousand tons C per day). Macro tides modulated microbial communities and their metabolic processes, e.g., anoxygenic phototrophy, sulfur, and nitrogen cycling. Respiration, sulfur metabolism and dissolved organic carbon (DOC) levels were linked to functional groups and microbial cell counts. Total microbial counts decreased and cyanobacteria counts peaked in the spring tide. The microbial groups driving carbon, nitrogen, sulfur and methane cycles were consistent across all spatial scales. Taxonomic groups engaged in sulfur cycling (Allochromatium, Desulfovibrio, and Thibacillus) within mangroves were abundant at all scales. Tidally-driven porewater exchange within mangroves drove a progressive increase of sulfur cycle taxonomic groups and their functional genes both temporally (tidal cycles) and spatially (from mangrove porewater to continental shelf). Overall, we revealed a unified and consistent response of microbiomes at different spatial and temporal scales to tidally-driven mangrove porewater exchange.
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Affiliation(s)
- Maria S Nóbrega
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Bruno S Silva
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Diogo A Tschoeke
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Center of Technology-COPPE, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Luciana R Appolinario
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Gabriela Calegario
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Taina M Venas
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Larissa Macedo
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Nils Asp
- Universidade Federal do Pará (UFPA), Instituto de Estudos Costeiros (IECOS), Campus de Bragança, Pará, Brazil
| | - Braulio Cherene
- Laboratory of Environmental Sciences (LCA), Center of Biosciences and Biotechnology (CBB), State University of Northern of Rio de Janeiro Darcy Ribeiro (UENF), Campos dos goytacazes, Brazil
| | - Jomar S J Marques
- Laboratory of Environmental Sciences (LCA), Center of Biosciences and Biotechnology (CBB), State University of Northern of Rio de Janeiro Darcy Ribeiro (UENF), Campos dos goytacazes, Brazil
| | - Michael Seidel
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
| | - Thorsten Dittmar
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Oldenburg, Germany
| | - Isaac R Santos
- Department of Marine Sciences, University of Gothenburg, Sweden; National Marine Science Centre, Southern Cross University, Coffs Harbour, Australia
| | - Carlos Eduardo de Rezende
- Laboratory of Environmental Sciences (LCA), Center of Biosciences and Biotechnology (CBB), State University of Northern of Rio de Janeiro Darcy Ribeiro (UENF), Campos dos goytacazes, Brazil
| | - Cristiane C Thompson
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Center of Technology-COPPE, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| | - Fabiano L Thompson
- Laboratory of Microbiology, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Center of Technology-COPPE, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
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Hydrogen Sulfide Production with a Microbial Consortium Isolated from Marine Sediments Offshore. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10030436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Hydrogen, electric energy production, and metal toxic bioremediation are some of the biotechnological applications of sulfate-reducing organisms, which potentially depend on the sulfide produced. In this study, offshore of Yucatan, the capacity to produce hydrogen sulfide using microbial consortia from marine sediment (SC469, PD102, SD636) in batch reactors was evaluated. Kinetic tests were characterized by lactate oxidation to acetate, propionate, CO2 and methane. The inoculum SC469, located in open-ocean, differed strongly in microbial diversity and showed better performance in substrate utilization with the highest hydrogen sulfide production (246 mmolg−1 VSS) at a specific hydrogen sulfide rate of 113 mmol g−1 VSS d−1 with a 0.79 molar ratio of sulfate/lactate. Sulfate-reducing microbial consortia enriched in the laboratory from marine sediments collected offshore in Yucatan and with a moderate eutrophication index, differed strongly in microbial diversity with loss of microorganisms with greater capacity for degradation of organic macromolecules. The sulfate-reducing microorganisms were characterized using Illumina MiSeq technology and were mainly Desulfomicrobium, Clostridium and Desulfobacter.
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225
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Discovery and Biotechnological Exploitation of Glycoside-Phosphorylases. Int J Mol Sci 2022; 23:ijms23063043. [PMID: 35328479 PMCID: PMC8950772 DOI: 10.3390/ijms23063043] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 02/04/2023] Open
Abstract
Among carbohydrate active enzymes, glycoside phosphorylases (GPs) are valuable catalysts for white biotechnologies, due to their exquisite capacity to efficiently re-modulate oligo- and poly-saccharides, without the need for costly activated sugars as substrates. The reversibility of the phosphorolysis reaction, indeed, makes them attractive tools for glycodiversification. However, discovery of new GP functions is hindered by the difficulty in identifying them in sequence databases, and, rather, relies on extensive and tedious biochemical characterization studies. Nevertheless, recent advances in automated tools have led to major improvements in GP mining, activity predictions, and functional screening. Implementation of GPs into innovative in vitro and in cellulo bioproduction strategies has also made substantial advances. Herein, we propose to discuss the latest developments in the strategies employed to efficiently discover GPs and make the best use of their exceptional catalytic properties for glycoside bioproduction.
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226
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Bates KA, Sommer U, Hopkins KP, Shelton JMG, Wierzbicki C, Sergeant C, Tapley B, Michaels CJ, Schmeller DS, Loyau A, Bosch J, Viant MR, Harrison XA, Garner TWJ, Fisher MC. Microbiome function predicts amphibian chytridiomycosis disease dynamics. MICROBIOME 2022; 10:44. [PMID: 35272699 PMCID: PMC8908643 DOI: 10.1186/s40168-021-01215-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 12/10/2021] [Indexed: 05/07/2023]
Abstract
BACKGROUND The fungal pathogen Batrachochytrium dendrobatidis (Bd) threatens amphibian biodiversity and ecosystem stability worldwide. Amphibian skin microbial community structure has been linked to the clinical outcome of Bd infections, yet its overall functional importance is poorly understood. METHODS Microbiome taxonomic and functional profiles were assessed using high-throughput bacterial 16S rRNA and fungal ITS2 gene sequencing, bacterial shotgun metagenomics and skin mucosal metabolomics. We sampled 56 wild midwife toads (Alytes obstetricans) from montane populations exhibiting Bd epizootic or enzootic disease dynamics. In addition, to assess whether disease-specific microbiome profiles were linked to microbe-mediated protection or Bd-induced perturbation, we performed a laboratory Bd challenge experiment whereby 40 young adult A. obstetricans were exposed to Bd or a control sham infection. We measured temporal changes in the microbiome as well as functional profiles of Bd-exposed and control animals at peak infection. RESULTS Microbiome community structure and function differed in wild populations based on infection history and in experimental control versus Bd-exposed animals. Bd exposure in the laboratory resulted in dynamic changes in microbiome community structure and functional differences, with infection clearance in all but one infected animal. Sphingobacterium, Stenotrophomonas and an unclassified Commamonadaceae were associated with wild epizootic dynamics and also had reduced abundance in laboratory Bd-exposed animals that cleared infection, indicating a negative association with Bd resistance. This was further supported by microbe-metabolite integration which identified functionally relevant taxa driving disease outcome, of which Sphingobacterium and Bd were most influential in wild epizootic dynamics. The strong correlation between microbial taxonomic community composition and skin metabolome in the laboratory and field is inconsistent with microbial functional redundancy, indicating that differences in microbial taxonomy drive functional variation. Shotgun metagenomic analyses support these findings, with similar disease-associated patterns in beta diversity. Analysis of differentially abundant bacterial genes and pathways indicated that bacterial environmental sensing and Bd resource competition are likely to be important in driving infection outcomes. CONCLUSIONS Bd infection drives altered microbiome taxonomic and functional profiles across laboratory and field environments. Our application of multi-omics analyses in experimental and field settings robustly predicts Bd disease dynamics and identifies novel candidate biomarkers of infection. Video Abstract.
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Affiliation(s)
- Kieran A Bates
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK.
- MRC Centre for GlobaI Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, W2 1PG, UK.
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK.
| | - Ulf Sommer
- NERC Biomolecular Analysis Facility - Metabolomics Node (NBAF-B), School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Kevin P Hopkins
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Jennifer M G Shelton
- MRC Centre for GlobaI Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, W2 1PG, UK
| | - Claudia Wierzbicki
- MRC Centre for GlobaI Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, W2 1PG, UK
| | - Christopher Sergeant
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Benjamin Tapley
- ZSL London Zoo, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | | | - Dirk S Schmeller
- Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse INP, Université Toulouse 3 - Paul Sabatier (UPS), Toulouse, France
| | - Adeline Loyau
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Alte Fischerhütte 2, 16775, Stechlin, Germany
| | - Jaime Bosch
- IMIB Biodiversity Research Institute (CSIC-University of Oviedo), 33600, Mieres, Spain
| | - Mark R Viant
- NERC Biomolecular Analysis Facility - Metabolomics Node (NBAF-B), School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Xavier A Harrison
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4DQ, UK
| | - Trenton W J Garner
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Matthew C Fisher
- MRC Centre for GlobaI Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, W2 1PG, UK
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Likar M, Grašič M, Stres B, Regvar M, Gaberščik A. Original Leaf Colonisers Shape Fungal Decomposer Communities of Phragmites australis in Intermittent Habitats. J Fungi (Basel) 2022; 8:jof8030284. [PMID: 35330286 PMCID: PMC8951327 DOI: 10.3390/jof8030284] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 01/29/2023] Open
Abstract
Common reed (Phragmites australis) has high biomass production and is primarily subjected to decomposition processes affected by multiple factors. To predict litter decomposition dynamics in intermittent lakes, it is critical to understand how communities of fungi, as the primary decomposers, form under different habitat conditions. This study reports the shotgun metagenomic sequencing of the initial fungal communities on common reed leaves decomposing under different environmental conditions. We demonstrate that a complex network of fungi forms already on the plant persists into the decomposition phase. Phragmites australis leaves contained at least five fungal phyla, with abundant Ascomycota (95.7%) and Basidiomycota (4.1%), identified as saprotrophs (48.6%), pathotrophs (22.5%), and symbiotrophs (12.6%). Most of the correlations between fungi in fresh and decomposing leaves were identified as co-occurrences (positive correlations). The geographic source of litter and leaf age did not affect the structure and diversity of fungal communities. Keystone taxa were mostly moisture-sensitive. Our results suggest that habitat has a strong effect on the formation of the fungal communities through keystone taxa. Nevertheless, it can also alter the proportions of individual fungal groups in the community through indirect effects on competition between the fungal taxa and their exploitation of favourable conditions.
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Affiliation(s)
- Matevž Likar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (M.G.); (M.R.); (A.G.)
- Correspondence: ; Tel.: +386-1-320-3-418
| | - Mateja Grašič
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (M.G.); (M.R.); (A.G.)
| | - Blaž Stres
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia;
| | - Marjana Regvar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (M.G.); (M.R.); (A.G.)
| | - Alenka Gaberščik
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (M.G.); (M.R.); (A.G.)
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228
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Krasnopeev AY, Bukin YS, Potapov SA, Belykh OI. Data Filtering Algorithm for DNA Metabarcoding Studies of Ecological Communities. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422020089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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229
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D'Alò F, Baldrian P, Odriozola I, Morais D, Větrovský T, Zucconi L, Ripa C, Cannone N, Malfasi F, Onofri S. Composition and functioning of the soil microbiome in the highest altitudes of the Italian Alps and potential effects of climate change. FEMS Microbiol Ecol 2022; 98:6541846. [PMID: 35238906 DOI: 10.1093/femsec/fiac025] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 02/04/2022] [Accepted: 03/01/2022] [Indexed: 11/14/2022] Open
Abstract
As the European Alps are experiencing a strong climate warming; this study analyzed the soil microbiome at different altitudes and among different vegetation types at the Stelvio Pass (Italian Alps), aiming to i) characterize the composition and functional potential of the microbiome of soils and their gene expression during the peak vegetative stage; ii) explore the potential short-term (using open top chambers) and long-term (space-for-time substitutions) effects of increasing temperature on the alpine soil microbiome. We found that the functional potential of the soil microbiome and its expression differed among vegetation types. Microbial α-diversity increased along the altitudinal gradient. At lower altitude, shrubland had the highest proportion of fungi, which was correlated with higher amounts of CAZymes, specific for degrading fungal biomass and recalcitrant plant biopolymers. Subalpine upward vegetation shift could lead a possible loss of species of alpine soils. Shrub encroachment may accelerate higher recalcitrant C decomposition and reduce total ecosystem C storage, increasing the efflux of CO2 to the atmosphere with a positive feedback to warming. Five years of warming had no effect on the composition and functioning of microbial communities, indicating that longer-term warming experiments are needed to investigate the effects of temperature increases on the soil microbiome.
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Affiliation(s)
- Federica D'Alò
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università, 01100 Viterbo, Italy
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Iñaki Odriozola
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Daniel Morais
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220 Praha 4, Czech Republic
| | - Laura Zucconi
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università, 01100 Viterbo, Italy
| | - Caterina Ripa
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università, 01100 Viterbo, Italy
| | - Nicoletta Cannone
- Department of Science and High Technology, Insubria University, Via Valleggio, 11, 21100 Como (CO), Italy
| | - Francesco Malfasi
- Department of Science and High Technology, Insubria University, Via Valleggio, 11, 21100 Como (CO), Italy
| | - Silvano Onofri
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università, 01100 Viterbo, Italy
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Yamada E, Martin CG, Moreno-Huizar N, Fouquier J, Neff CP, Coleman SL, Schneider JM, Huber J, Nusbacher NM, McCarter M, Campbell TB, Lozupone CA, Palmer BE. Intestinal microbial communities and Holdemanella isolated from HIV+/- men who have sex with men increase frequencies of lamina propria CCR5 + CD4 + T cells. Gut Microbes 2022; 13:1997292. [PMID: 34818131 PMCID: PMC8632320 DOI: 10.1080/19490976.2021.1997292] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Men who have sex with men (MSM), regardless of HIV infection status, have an intestinal microbiome that is compositionally distinct from men who have sex with women (MSW) and women. We recently showed HIV-negative MSM have elevated levels of intestinal CD4+ T cells expressing CCR5, a critical co-receptor for HIV. Whether elevated expression of CCR5 is driven by the altered gut microbiome composition in MSM has not been explored. Here we used in vitro stimulation of gut Lamina Propria Mononuclear Cells (LPMCs) with whole intact microbial cells isolated from stool to demonstrate that fecal bacterial communities (FBCs) from HIV-positive/negative MSM induced higher frequencies of CCR5+ CD4+ T cells compared to FBCs from HIV-negative MSW and women. To identify potential microbial drivers, we related the frequency of CCR5+ CD4+ T cells to the abundance of individual microbial taxa in rectal biopsy of HIV-positive/negative MSM and controls, and Holdemanella biformis was strongly associated with increased frequency of CCR5+ CD4+ T cells. We used in vitro stimulation of gut LPMCs with the type strain of H. biformis, a second strain of H.biformis and an isolate of the closely related Holdemanella porci , cultured from either a HIV-positive or a HIV-negative MSM stool. H. porci elevated the frequency of both CCR5+ CD4+ T cells and the ratio of TNF-α/IL-10 Genomic comparisons of the 3 Holdemanella isolates revealed unique cell wall and capsular components, which may be responsible for their differences in immunogenicity. These findings describe a novel mechanism potentially linking intestinal dysbiosis in MSM to HIV transmission and mucosal pathogenesis.
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Affiliation(s)
- Eiko Yamada
- Division of Allergy and Clinical Immunology, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, USA
| | - Casey G. Martin
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, USA
| | - Nancy Moreno-Huizar
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, USA
| | - Jennifer Fouquier
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, USA
| | - C. Preston Neff
- Division of Allergy and Clinical Immunology, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, USA
| | | | - Jennifer M. Schneider
- Division of Allergy and Clinical Immunology, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, USA
| | - Jonathan Huber
- Division of Allergy and Clinical Immunology, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, USA
| | - Nichole M. Nusbacher
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, USA
| | - Martin McCarter
- Department of Surgery, University of Colorado Anschutz, Aurora, Colorado, USA
| | - Thomas B. Campbell
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, USA
| | - Catherine A. Lozupone
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, USA
| | - Brent E. Palmer
- Division of Allergy and Clinical Immunology, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, USA,CONTACT Brent E. Palmer Division of Allergy and Clinical Immunology, Department of Medicine, University of Colorado Anschutz, Aurora, Colorado, USA
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Liu L, Fu Q, Li T, Shao K, Zhu X, Cong Y, Zhao X. Gut microbiota and butyrate contribute to nonalcoholic fatty liver disease in premenopause due to estrogen deficiency. PLoS One 2022; 17:e0262855. [PMID: 35108315 PMCID: PMC8809533 DOI: 10.1371/journal.pone.0262855] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 01/06/2022] [Indexed: 02/06/2023] Open
Abstract
The incidence of nonalcoholic fatty liver disease (NAFLD) in postmenopausal women has increased significantly. Estrogen plays a very important role in NAFLD, but whether NAFLD in premenopausal women was caused by estrogen deficiency was unknown. Thus, it is of great clinical significance to explore the mechanism of NAFLD in premenopausal women. Gut microbiota and its metabolites short chain fatty acids (SCFA) have been shown to play important roles in the development of NAFLD. In this study, we investigated the impact of gut microbiota and SCFA in NAFLD patients and mice caused by estrogen deficiency. We showed that premenopause NAFLD patients had much lower estrogen levels. Estrogen deficient mice, due to ovariectomy (OVX), suffered more severe liver steatosis with an elevated body weight, abdominal fat weight, serum triglycerides and deterioration in hepatic steatosis. Altered gut microbiota composition and decreased butyrate content were found in NAFLD patients and in OVX mice. Furthermore, fecal microbiota transplantation (FMT) or supplementing with butyrate alleviated NAFLD in OVX mice. The production of antimicrobial peptides (AMP) Reg3ɣ, β-defensins and the expression of intestinal epithelial tight junction, including ZO-1 and Occluding-5, were decreased in the OVX mice compared to control mice. Upregulation of PPAR-ɣ and VLDLR, downregulation of PPAR-ɑ indicated that OVX mice suffered from abnormal lipid metabolism. These data indicate that changes in the gut microbiota and SCFA caused by estrogen reduction, together with a disorder in AMP production and lipid metabolism, promote NAFLD, thus provide SCFAs derived from microbiota as new therapeutic targets for the clinical prevention and treatment of NAFLD.
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Affiliation(s)
- Limin Liu
- Department of Medical Experiment Center, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, China
- Department of Qingdao Key Lab of Mitochondrial Medicine, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, China
| | - Qingsong Fu
- Department of Medical Experiment Center, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, China
- Department of Qingdao Key Lab of Mitochondrial Medicine, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, China
- * E-mail: (XZ); (QF)
| | - Tiantian Li
- Department of Medical Experiment Center, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, China
- Department of Qingdao Key Lab of Mitochondrial Medicine, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, China
| | - Kai Shao
- Department of Medical Experiment Center, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, China
- Department of Qingdao Key Lab of Mitochondrial Medicine, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, China
| | - Xing Zhu
- Department of Pathology, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, China
| | - Yingzi Cong
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States of America
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States of America
| | - Xiaoyun Zhao
- Department of Medical Experiment Center, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, China
- Department of Qingdao Key Lab of Mitochondrial Medicine, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, China
- * E-mail: (XZ); (QF)
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Malik G, Arora R, Chaturvedi R, Paul MS. Implementation of Genetic Engineering and Novel Omics Approaches to Enhance Bioremediation: A Focused Review. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2022; 108:443-450. [PMID: 33837794 DOI: 10.1007/s00128-021-03218-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 03/25/2021] [Indexed: 06/12/2023]
Abstract
Bioremediation itself is considered to be a cost effective soil clean-up technique and preferred over invasive physical and chemical treatments. Besides increasing efficiency, application of genetic engineering has led to reduction in the time duration required to achieve remediation, overcoming the so called 'Achilles heel' of Bioremediation. Omics technologies, namely genomics, transcriptomics, proteomics, and metabolomics, are being employed extensively to gain insights at genetic level. A wise synchronised application of these approaches can help scrutinize complex metabolic pathways, and molecular changes in response to heavy metal stress, and also its fate i.e., uptake, transport, sequestration and detoxification. In the present review, an account of some latest achievements made in the field is presented.
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Affiliation(s)
| | - Rahul Arora
- The Francis Crick Institute, London, United Kingdom
- Division of Biosciences, University College London, London, United Kingdom
| | | | - Manoj S Paul
- Department of Botany, St. John's College, Agra, U.P, India
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Bocatti CR, Ferreira E, Ribeiro RA, de Oliveira Chueire LM, Delamuta JRM, Kobayashi RKT, Hungria M, Nogueira MA. Microbiological quality analysis of inoculants based on Bradyrhizobium spp. and Azospirillum brasilense produced "on farm" reveals high contamination with non-target microorganisms. Braz J Microbiol 2022; 53:267-280. [PMID: 34984661 PMCID: PMC8882540 DOI: 10.1007/s42770-021-00649-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 11/01/2021] [Indexed: 11/24/2022] Open
Abstract
The use of inoculants carrying diazotrophic and other plant growth-promoting bacteria plays an essential role in the Brazilian agriculture, with a growing use of microorganism-based bioproducts. However, in the last few years, some farmers have multiplied microorganisms in the farm, known as "on farm" production, including inoculants of Bradyrhizobium spp. for soybean (Glycine max L. Merrill.) and Azospirillum brasilense for corn (Zea mays L.) or co-inoculation in soybean. The objective was to assess the microbiological quality of such inoculants concerning the target microorganisms and contaminants. In the laboratory, 18 samples taken in five states were serial diluted and spread on culture media for obtaining pure and morphologically distinct colonies of bacteria, totaling 85 isolates. Molecular analysis based on partial sequencing of the 16S rRNA gene revealed 25 genera of which 44% harbor species potentially pathogenic to humans; only one of the isolates was identified as Azospirillum brasilense, whereas no isolate was identified as Bradyrhizobium. Among 34 isolates belonging to genera harboring species potentially pathogenic to humans, 12 had no resistance to antibiotics, six presented intrinsic resistance, and 18 presented non-intrinsic resistance to at least one antibiotic. One of the samples analyzed with a shotgun-based metagenomics approach to check for the microbial diversity showed several genera of microorganisms, mainly Acetobacter (~ 32% of sequences) but not the target microorganism. The samples of inoculants produced on farm were highly contaminated with non-target microorganisms, some of them carrying multiple resistances to antibiotics.
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Affiliation(s)
- Camila Rafaeli Bocatti
- Department of Microbiology, Universidade Estadual de Londrina, C. Postal 10.011, Londrina, PR, 86057-970, Brazil
| | - Eduara Ferreira
- Embrapa Soja, C. Postal 4006, Londrina, PR, 86081-981, Brazil
| | - Renan Augusto Ribeiro
- Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Brasília, DF, Brazil
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234
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Prevalence of Actinobacteria in the production of 2-methylisoborneol and geosmin, over Cyanobacteria in a temperate eutrophic reservoir. CHEMICAL ENGINEERING JOURNAL ADVANCES 2022. [DOI: 10.1016/j.ceja.2021.100226] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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235
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Zhang Q, Tang J, Angel R, Wang D, Hu X, Gao S, Zhang L, Tang Y, Zhang X, Koide RT, Yang H, Sun Q. Soil Properties Interacting With Microbial Metagenome in Decreasing CH 4 Emission From Seasonally Flooded Marshland Following Different Stages of Afforestation. Front Microbiol 2022; 13:830019. [PMID: 35283824 PMCID: PMC8905362 DOI: 10.3389/fmicb.2022.830019] [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: 12/06/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
Wetlands are the largest natural source of terrestrial CH4 emissions. Afforestation can enhance soil CH4 oxidation and decrease methanogenesis, yet the driving mechanisms leading to these effects remain unclear. We analyzed the structures of communities of methanogenic and methanotrophic microbes, quantification of mcrA and pmoA genes, the soil microbial metagenome, soil properties and CH4 fluxes in afforested and non-afforested areas in the marshland of the Yangtze River. Compared to the non-afforested land use types, net CH4 emission decreased from bare land, natural vegetation and 5-year forest plantation and transitioned to net CH4 sinks in the 10- and 20-year forest plantations. Both abundances of mcrA and pmoA genes decreased significantly with increasing plantation age. By combining random forest analysis and structural equation modeling, our results provide evidence for an important role of the abundance of functional genes related to methane production in explaining the net CH4 flux in this ecosystem. The structures of methanogenic and methanotrophic microbial communities were of lower importance as explanatory factors than functional genes in terms of in situ CH4 flux. We also found a substantial interaction between functional genes and soil properties in the control of CH4 flux, particularly soil particle size. Our study provides empirical evidence that microbial community function has more explanatory power than taxonomic microbial community structure with respect to in situ CH4 fluxes. This suggests that focusing on gene abundances obtained, e.g., through metagenomics or quantitative/digital PCR could be more effective than community profiling in predicting CH4 fluxes, and such data should be considered for ecosystem modeling.
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Affiliation(s)
- Qian Zhang
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Jie Tang
- Hunan Academy of Forestry, Changsha, China
| | - Roey Angel
- Soil and Water Research Infrastructure and Institute of Soil Biology, Biology Centre, Czech Academy of Sciences (CAS), České Budějovice, Czechia
| | - Dong Wang
- Institute of Forest Ecology, Environment and Nature Conservation, Chinese Academy of Forestry, Beijing, China
| | - Xingyi Hu
- Hubei Academy of Forestry, Wuhan, China
| | - Shenghua Gao
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Lei Zhang
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yuxi Tang
- Hunan Academy of Forestry, Changsha, China
| | - Xudong Zhang
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Roger T. Koide
- Department of Biology, Brigham Young University, Provo, UT, United States
| | - Haishui Yang
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Qixiang Sun
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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Abstract
Modern sequencing technologies have provided insight into the genetic diversity of numerous species, including the human pathogen Pseudomonas aeruginosa. Bacterial genomes often harbor bacteriophage genomes (prophages), which can account for upwards of 20% of the genome. Prior studies have found P. aeruginosa prophages that contribute to their host’s pathogenicity and fitness. These advantages come in many different forms, including the production of toxins, promotion of biofilm formation, and displacement of other P. aeruginosa strains. While several different genera and species of P. aeruginosa prophages have been studied, there has not been a comprehensive study of the overall diversity of P. aeruginosa-infecting prophages. Here, we present the results of just such an analysis. A total of 6,852 high-confidence prophages were identified from 5,383 P. aeruginosa genomes from strains isolated from the human body and other environments. In total, 3,201 unique prophage sequences were identified. While 53.1% of these prophage sequences displayed sequence similarity to publicly available phage genomes, novel and highly mosaic prophages were discovered. Among these prophages, there is extensive diversity, including diversity within the functionally conserved integrase and C repressor coding regions, two genes responsible for prophage entering and persisting through the lysogenic life cycle. Analysis of integrase, C repressor, and terminase coding regions revealed extensive reassortment among P. aeruginosa prophages. This catalog of P. aeruginosa prophages provides a resource for future studies into the evolution of the species. IMPORTANCE Prophages play a critical role in the evolution of their host species and can also contribute to the virulence and fitness of pathogenic species. Here, we conducted a comprehensive investigation of prophage sequences from 5,383 publicly available Pseudomonas aeruginosa genomes from human as well as environmental isolates. We identified a diverse population of prophages, including tailed phages, inoviruses, and microviruses; 46.9% of the prophage sequences found share no significant sequence similarity with characterized phages, representing a vast array of novel P. aeruginosa-infecting phages. Our investigation into these prophages found substantial evidence of reassortment. In producing this, the first catalog of P. aeruginosa prophages, we uncovered both novel prophages as well as genetic content that have yet to be explored.
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237
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Xue MY, Xie YY, Zhong Y, Ma XJ, Sun HZ, Liu JX. Integrated meta-omics reveals new ruminal microbial features associated with feed efficiency in dairy cattle. MICROBIOME 2022; 10:32. [PMID: 35172905 PMCID: PMC8849036 DOI: 10.1186/s40168-022-01228-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 01/07/2022] [Indexed: 05/23/2023]
Abstract
BACKGROUND As the global population continues to grow, competition for resources between humans and livestock has been intensifying. Increasing milk protein production and improving feed efficiency are becoming increasingly important to meet the demand for high-quality dairy protein. In a previous study, we found that milk protein yield in dairy cows was associated with the rumen microbiome. The objective of this study was to elucidate the potential microbial features that underpins feed efficiency in dairy cows using metagenomics, metatranscriptomics, and metabolomics. RESULTS Comparison of metagenomic and metatranscriptomic data revealed that the latter was a better approach to uncover the associations between rumen microbial functions and host performance. Co-occurrence network analysis of the rumen microbiome revealed differential microbial interaction patterns between the animals with different feed efficiency, with high-efficiency animals having more and stronger associations than low-efficiency animals. In the rumen of high-efficiency animals, Selenomonas and members of the Succinivibrionaceae family positively interacted with each other, functioning as keystone members due to their essential ecological functions and active carbohydrate metabolic functions. At the metabolic level, analysis using random forest machine learning suggested that six ruminal metabolites (all derived from carbohydrates) could be used as metabolic markers that can potentially differentiate efficient and inefficient microbiomes, with an accuracy of prediction of 95.06%. CONCLUSIONS The results of the current study provided new insights into the new ruminal microbial features associated with feed efficiency in dairy cows, which may improve the ability to select animals for better performance in the dairy industry. The fundamental knowledge will also inform future interventions to improve feed efficiency in dairy cows. Video Abstract.
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Affiliation(s)
- Ming-Yuan Xue
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
- Ministry of Education Key Laboratory of Molecular Animal Nutrition, Zhejiang University, Hangzhou, 310058, China
- Ministry of Education Innovation Team of Development and Function of Animal Digestive System, Zhejiang University, Hangzhou, 310058, China
| | - Yun-Yi Xie
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
- Ministry of Education Key Laboratory of Molecular Animal Nutrition, Zhejiang University, Hangzhou, 310058, China
| | - Yifan Zhong
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
- Ministry of Education Key Laboratory of Molecular Animal Nutrition, Zhejiang University, Hangzhou, 310058, China
| | - Xiao-Jiao Ma
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
- Ministry of Education Key Laboratory of Molecular Animal Nutrition, Zhejiang University, Hangzhou, 310058, China
| | - Hui-Zeng Sun
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
- Ministry of Education Key Laboratory of Molecular Animal Nutrition, Zhejiang University, Hangzhou, 310058, China.
- Ministry of Education Innovation Team of Development and Function of Animal Digestive System, Zhejiang University, Hangzhou, 310058, China.
| | - Jian-Xin Liu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
- Ministry of Education Key Laboratory of Molecular Animal Nutrition, Zhejiang University, Hangzhou, 310058, China.
- Ministry of Education Innovation Team of Development and Function of Animal Digestive System, Zhejiang University, Hangzhou, 310058, China.
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238
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Warnasekara J, Srimantha S, Senavirathna I, Kappagoda C, Farika N, Nawinna A, Agampodi S. The variable presence of Leptospira in the environment; an epidemiological explanation based on serial analysis of water samples. PLoS One 2022; 17:e0263719. [PMID: 35167605 PMCID: PMC8846531 DOI: 10.1371/journal.pone.0263719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 01/25/2022] [Indexed: 11/19/2022] Open
Abstract
Human leptospirosis involves the classic epidemiological triad (agent, host and environment); hence the investigations should include the knowledge on Leptospira within the animals and the environment. The objectives of this study are to explore the abundance of Leptospira in different climate zones of Sri Lanka and to describe the presence of Leptospira in the same water source at serial time points. First, water and soil samples were collected from different parts of Sri Lanka (Component-1); second, water sampling continued only in the dry zone (Component-2). Finally, serial water sampling from ten open wells was performed at five different time points (Component-3). Quantitative PCR of water and metagenomic sequencing of soil were performed to detect Leptospira. Three replicates for each sample were used for PCR testing, and positive result of two or more replicates was defined as 'strongly positive,' and one positive replicate was defined as positive. In the water and soil sample analysis in the whole country (Component-1), two out of 12 water sites were positive, and both were situated in the wet zone. Very small quantities of the genus Leptospira were detected by 16 amplicon analysis of soil in all 11 sites. In the dry zone water sample analysis (Component-2), only samples from 6 out of 26 sites were positive, of which one site was strongly positive. In the serial sample analysis (Component-3), Six, five, four, five, and six wells were positive in serial measurements. All wells were positive for at least one time point, while only one well was positive for all five time points. Proximity to the tank and greater distances from the main road were associated with strong positive results for Leptospira (P<0.05). The presence of Leptospira was not consistent, indicating the variable abundance of Leptospira in the natural environment. This intermittent nature of positivity could be explained by the repetitive contamination by animal urine.
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Affiliation(s)
- Janith Warnasekara
- Faculty of Medicine and Allied Sciences, Department of Community Medicine, Rajarata University of Sri Lanka, Saliyapura, Sri Lanka
| | - Shalka Srimantha
- Faculty of Medicine and Allied Sciences, Department of Community Medicine, Rajarata University of Sri Lanka, Saliyapura, Sri Lanka
| | - Indika Senavirathna
- Faculty of Medicine and Allied Sciences, Department of Community Medicine, Rajarata University of Sri Lanka, Saliyapura, Sri Lanka
- Faculty of Medicine and Allied Sciences, Department of Biochemistry, Rajarata University of Sri Lanka, Saliyapura, Sri Lanka
| | - Chamila Kappagoda
- Faculty of Medicine and Allied Sciences, Department of Community Medicine, Rajarata University of Sri Lanka, Saliyapura, Sri Lanka
| | - Nirmani Farika
- Faculty of Medicine and Allied Sciences, Department of Community Medicine, Rajarata University of Sri Lanka, Saliyapura, Sri Lanka
| | - Achala Nawinna
- Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka, Saliyapura, Sri Lanka
| | - Suneth Agampodi
- Faculty of Medicine and Allied Sciences, Department of Community Medicine, Rajarata University of Sri Lanka, Saliyapura, Sri Lanka
- Department of Internal Medicine, Section of Infectious Diseases, School of Medicine, Yale University, New Haven, Connecticut, United States of America
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239
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VanMensel D, Droppo IG, Weisener CG. Identifying chemolithotrophic and pathogenic-related gene expression within suspended sediment flocs in freshwater environments: A metatranscriptomic assessment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:150996. [PMID: 34656597 DOI: 10.1016/j.scitotenv.2021.150996] [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: 06/08/2021] [Revised: 09/27/2021] [Accepted: 10/11/2021] [Indexed: 06/13/2023]
Abstract
The introduction and proliferation of pathogenic organisms in aquatic systems is a serious global issue that consequently leads to economic, financial, and health concerns. Health and safety related to recreational water use is typically monitored through water quality assessments that are outdated and can be misleading. These traditional methods focus on broad taxa groups, provide no insight into the active community or source of contamination, and the sediment compartments (bed and suspended) are often overlooked. To bridge this knowledge gap, our study aimed to 1) examine the metatranscriptome of the microbial community associated with suspended sediment (SS) in freshwater systems; 2) explore the influence of SS in tributaries to the littoral zone of the receiving lake; and 3) compare the SS fraction with previously reported nearshore bed sediment data. Samples were collected seasonally from Lake St. Clair and Lake Erie. Beaches in this region are influenced by both agriculture runoff and continued urban expansion. Results show that both adjacent tributary and beach SS have similar microbial functional diversity and are strongly correlated by site and season. We identified expression of transcripts encoding sequences with similarities to genes involved in nine bacterial infectious disease pathways, including legionellosis (sdhA) and Vibrio cholerae pathogenesis. According to MG-RAST gene categories, lake samples typically showed higher overall expression (p < 0.05) of transcripts with similarities to genes involved in infectious disease pathways compared to the tributaries, with summer upregulated (p < 0.05) compared to fall. Our data suggests SS acts as a strong vector for pathogen transport, making this facet an important area for further research as it pertains to human health regarding recreational water use. To our knowledge, this work is the first to investigate SS in aquatic microbial communities using metatranscriptomic analyses and has significant potential to help address growing issues of microbial contamination impacting freshwater security.
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Affiliation(s)
- Danielle VanMensel
- Great Lakes Institute for Environmental Research, University of Windsor, 401 Sunset Ave, Windsor, Ontario N9B 3P4, Canada.
| | - Ian G Droppo
- Canada Centre for Inland Waters, Environment and Climate Change Canada, 867 Lakeshore Rd, Burlington, Ontario L7R 4A6, Canada
| | - Christopher G Weisener
- Great Lakes Institute for Environmental Research, University of Windsor, 401 Sunset Ave, Windsor, Ontario N9B 3P4, Canada
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240
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Freudenthal J, Ju F, Bürgmann H, Dumack K. Microeukaryotic gut parasites in wastewater treatment plants: diversity, activity, and removal. MICROBIOME 2022; 10:27. [PMID: 35139924 PMCID: PMC8827150 DOI: 10.1186/s40168-022-01225-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/30/2021] [Indexed: 05/05/2023]
Abstract
BACKGROUND During wastewater treatment, the wastewater microbiome facilitates the degradation of organic matter, reduction of nutrients, and removal of gut parasites. While the latter function is essential to minimize public health risks, the range of parasites involved and how they are removed is still poorly understood. RESULTS Using shotgun metagenomic (DNA) and metatranscriptomic (RNA) sequencing data from ten wastewater treatment plants in Switzerland, we were able to assess the entire wastewater microbiome, including the often neglected microeukaryotes (protists). In the latter group, we found a surprising richness and relative abundance of active parasites, particularly in the inflow. Using network analysis, we tracked these taxa across the various treatment compartments and linked their removal to trophic interactions. CONCLUSIONS Our results indicate that the combination of DNA and RNA data is essential for assessing the full spectrum of taxa present in wastewater. In particular, we shed light on an important but poorly understood function of wastewater treatment - parasite removal. Video Abstract.
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Affiliation(s)
- Jule Freudenthal
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Zülpicher Str. 47b, 50674 Köln, Germany
| | - Feng Ju
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, 310024 China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, 310024 China
| | - Helmut Bürgmann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
| | - Kenneth Dumack
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Zülpicher Str. 47b, 50674 Köln, Germany
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241
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Metagenomic Survey of Tomato Rhizosphere Microbiome Using the Shotgun Approach. Microbiol Resour Announc 2022; 11:e0113121. [PMID: 35112900 PMCID: PMC8812306 DOI: 10.1128/mra.01131-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Food sustainability, e.g., fruit and vegetables, is a major agricultural problem that requires monitoring. Rhizosphere microbiomes' abundance and functionality are essential in promoting tomato plants' growth and health. We selected farms in South Africa's North West Province and present the metagenomes of their tomato rhizospheres and associated functional potentials.
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242
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Song JG, Yu MS, Lee B, Lee J, Hwang SH, Na D, Kim HW. Analysis methods for the gut microbiome in neuropsychiatric and neurodegenerative disorders. Comput Struct Biotechnol J 2022; 20:1097-1110. [PMID: 35317228 PMCID: PMC8902474 DOI: 10.1016/j.csbj.2022.02.024] [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: 11/06/2021] [Revised: 02/24/2022] [Accepted: 02/24/2022] [Indexed: 12/14/2022] Open
Abstract
For a long time, the central nervous system was believed to be the only regulator of cognitive functions. However, accumulating evidence suggests that the composition of the microbiome is strongly associated with brain functions and diseases. Indeed, the gut microbiome is involved in neuropsychiatric diseases (e.g., depression, autism spectrum disorder, and anxiety) and neurodegenerative diseases (e.g., Parkinson’s disease and Alzheimer’s disease). In this review, we provide an overview of the link between the gut microbiome and neuropsychiatric or neurodegenerative disorders. We also introduce analytical methods used to assess the connection between the gut microbiome and the brain. The limitations of the methods used at present are also discussed. The accurate translation of the microbiome information to brain disorder could promote better understanding of neuronal diseases and aid in finding alternative and novel therapies.
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Affiliation(s)
- Jae Gwang Song
- Department of Bio-integrated Science and Technology, College of Life Sciences, Sejong University, Seoul 05006, Republic of Korea
| | - Myeong-Sang Yu
- Department of Biomedical Engineering, Department of Biomedical Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Bomi Lee
- Department of Bio-integrated Science and Technology, College of Life Sciences, Sejong University, Seoul 05006, Republic of Korea
| | - Jingyu Lee
- Department of Biomedical Engineering, Department of Biomedical Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Su-Hee Hwang
- Department of Biomedical Engineering, Department of Biomedical Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Dokyun Na
- Department of Biomedical Engineering, Department of Biomedical Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
- Corresponding authors.
| | - Hyung Wook Kim
- Department of Bio-integrated Science and Technology, College of Life Sciences, Sejong University, Seoul 05006, Republic of Korea
- Corresponding authors.
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243
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Loreille O, Tillmar A, Brandhagen MD, Otterstatter L, Irwin JA. Improved DNA Extraction and Illumina Sequencing of DNA Recovered from Aged Rootless Hair Shafts Found in Relics Associated with the Romanov Family. Genes (Basel) 2022; 13:genes13020202. [PMID: 35205247 PMCID: PMC8872530 DOI: 10.3390/genes13020202] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/18/2022] [Accepted: 01/20/2022] [Indexed: 12/04/2022] Open
Abstract
This study describes an optimized DNA extraction protocol targeting ultrashort DNA molecules from single rootless hairs. It was applied to the oldest samples available to us: locks of hairs that were found in relics associated with the Romanov family. Published mitochondrial DNA genome sequences of Tsar Nicholas II and his wife, Tsarina Alexandra, made these samples ideal to assess this DNA extraction protocol and evaluate the types of genetic information that can be recovered by sequencing ultrashort fragments. Using this method, the mtGenome of the Tsarina’s lineage was identified in hairs that were concealed in a pendant made by Karl Fabergé for Alexandra Feodorovna Romanov. In addition, to determine if the lock originated from more than one individual, two hairs from the lock were extracted independently and converted into Illumina libraries for shotgun sequencing on a NextSeq 500 platform. From these data, autosomal SNPs were analyzed to assess relatedness. The results indicated that the two hairs came from a single individual. Genetic testing of hairs that were found in the second artifact, a framed photograph of Louise of Hesse-Kassel, Queen of Denmark and maternal grandmother of Tsar Nicholas II, revealed that the hair belonged to a woman who shared Tsar Nicholas’ maternal lineage, including the well-known point heteroplasmy at position 16169.
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Affiliation(s)
- Odile Loreille
- Federal Bureau of Investigation Laboratory, DNA Support Unit, Quantico, VA 22135, USA; (M.D.B.); (J.A.I.)
- Correspondence:
| | - Andreas Tillmar
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, SE-587 58 Linkoping, Sweden;
- Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, SE-582 25 Linkoping, Sweden
| | - Michael D. Brandhagen
- Federal Bureau of Investigation Laboratory, DNA Support Unit, Quantico, VA 22135, USA; (M.D.B.); (J.A.I.)
| | - Linda Otterstatter
- Federal Bureau of Investigation Laboratory, Trace Evidence Unit, Quantico, VA 22135, USA;
| | - Jodi A. Irwin
- Federal Bureau of Investigation Laboratory, DNA Support Unit, Quantico, VA 22135, USA; (M.D.B.); (J.A.I.)
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244
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Costa SS, Lago LAB, Silva A, Graças DAD, Lameira J, Baraúna RA. Diversity of bacteriocins in the microbiome of the Tucuruí Hydroelectric Power Plant water reservoir and three-dimensional structure prediction of a zoocin. Genet Mol Biol 2022; 45:e20210204. [PMID: 35037933 PMCID: PMC8762718 DOI: 10.1590/1678-4685-gmb-2021-0204] [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: 07/15/2021] [Accepted: 11/05/2021] [Indexed: 11/22/2022] Open
Abstract
Bacteriocins are antimicrobial peptides expressed by bacteria through ribosomal activity. In this study, we analyzed the diversity of bacteriocin-like genes in the Tucuruí-HPP using a whole-metagenome shotgun sequencing approach. Three layers of the water column were analyzed (photic, aphotic and sediment). Detection of bacteriocin-like genes was performed with blastx using the BAGEL4 database as subject sequences. In order to calculate the abundance of bacteriocin-like genes we also determined the number of 16S rRNA genes using blastn. Taxonomic analysis was performed using RAST server and the metagenome was assembled using IDBA-UD in order to recover the full sequence of a zoocin which had its three-dimensional structure determined. The photic zone presented the highest number of reads affiliated to bacteriocins. The most abundant bacteriocins were sonorensin, Klebicin D , pyocin and colicin. The zoocin model was composed of eight anti-parallel β-sheets and two α-helices with a Zn2+ ion in the active site. This model was considerably stable during 10 ns of molecular dynamics simulation. We observed a high diversity of bacteriocins in the Tucuruí-HPP, demonstrating that the environment is an inexhaustible source for prospecting these molecules. Finally, the zoocin model can be used for further studies of substrate binding and molecular mechanisms involving peptidoglycan degradation.
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Affiliation(s)
- Sávio S Costa
- Parque de Ciência e Tecnologia Guamá, Laboratório de Engenharia Biológica, Belém, PA, Brazil
| | - Leticia A B Lago
- Parque de Ciência e Tecnologia Guamá, Laboratório de Engenharia Biológica, Belém, PA, Brazil
| | - Artur Silva
- Parque de Ciência e Tecnologia Guamá, Laboratório de Engenharia Biológica, Belém, PA, Brazil
| | - Diego A das Graças
- Parque de Ciência e Tecnologia Guamá, Laboratório de Engenharia Biológica, Belém, PA, Brazil
| | - Jerônimo Lameira
- Universidade Federal do Pará, Instituto de Ciências Exatas e Naturais, Laboratório de Planejamento e Desenvolvimento de Fármacos, Belém, PA, Brazil
| | - Rafael A Baraúna
- Parque de Ciência e Tecnologia Guamá, Laboratório de Engenharia Biológica, Belém, PA, Brazil
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Díaz-García L, Chaparro D, Jiménez H, Gómez-Ramírez LF, Bernal AJ, Burbano-Erazo E, Jiménez DJ. Top-Down Enrichment Strategy to Co-cultivate Lactic Acid and Lignocellulolytic Bacteria From the Megathyrsus maximus Phyllosphere. Front Microbiol 2022; 12:744075. [PMID: 35035382 PMCID: PMC8753987 DOI: 10.3389/fmicb.2021.744075] [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: 07/19/2021] [Accepted: 10/11/2021] [Indexed: 12/15/2022] Open
Abstract
Traditionally, starting inoculants have been applied to improve ensiling of forage used for livestock feed. Here, we aimed to build up a bioinoculant composed of lactic acid-producing and lignocellulolytic bacteria (LB) derived from the Megathyrsus maximus (guinea grass) phyllosphere. For this, the dilution-to-stimulation approach was used, including a sequential modification of the starting culture medium [Man, Rogosa, and Sharpe (MRS) broth] by addition of plant biomass (PB) and elimination of labile carbon sources. Along 10 growth-dilution steps (T1–T10), slight differences were observed in terms of bacterial diversity and composition. After the sixth subculture, the consortium started to degrade PB, decreasing its growth rate. The co-existence of Enterobacteriales (fast growers and highly abundance), Actinomycetales, Bacillales, and Lactobacillales species was observed at the end of the selection process. However, a significant structural change was noticed when the mixed consortium was cultivated in higher volume (500ml) for 8days, mainly increasing the proportion of Paenibacillaceae populations. Interestingly, Actinomycetales, Bacillales, and Lactobacillales respond positively to a pH decrease (4–5), suggesting a relevant role within a further silage process. Moreover, gene-centric metagenomic analysis showed an increase of (hemi)cellulose-degrading enzymes (HDEs) during the enrichment strategy. Reconstruction of metagenome-assembled genomes (MAGs) revealed that Paenibacillus, Cellulosimicrobium, and Sphingomonas appear as key (hemi)cellulolytic members (harboring endo-glucanases/xylanases, arabinofuranosidases, and esterases), whereas Enterococcus and Cellulosimicrobium have the potential to degrade oligosaccharides, metabolize xylose and might produce lactic acid through the phosphoketolase (PK) pathway. Based on this evidence, we conclude that our innovative top-down strategy enriched a unique bacterial consortium that could be useful in biotechnological applications, including the development/design of a synthetic bioinoculant to improve silage processes.
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Affiliation(s)
- Laura Díaz-García
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Dayanne Chaparro
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Hugo Jiménez
- Colombian Corporation for Agricultural Research (Agrosavia), Mosquera, Colombia
| | | | - Adriana J Bernal
- Laboratory of Molecular Interactions of Agricultural Microbes, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | | | - Diego Javier Jiménez
- Microbiomes and Bioenergy Research Group, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
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Jankowski P, Gan J, Le T, McKennitt M, Garcia A, Yanaç K, Yuan Q, Uyaguari-Diaz M. Metagenomic community composition and resistome analysis in a full-scale cold climate wastewater treatment plant. ENVIRONMENTAL MICROBIOME 2022; 17:3. [PMID: 35033203 PMCID: PMC8760730 DOI: 10.1186/s40793-022-00398-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 01/05/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Wastewater treatment plants are an essential part of maintaining the health and safety of the general public. However, they are also an anthropogenic source of antibiotic resistance genes. In this study, we characterized the resistome, the distribution of classes 1-3 integron-integrase genes (intI1, intI2, and intI3) as mobile genetic element biomarkers, and the bacterial and phage community compositions in the North End Sewage Treatment Plant in Winnipeg, Manitoba. Samples were collected from raw sewage, returned activated sludge, final effluent, and dewatered sludge. A total of 28 bacterial and viral metagenomes were sequenced over two seasons, fall and winter. Integron-integrase genes, the 16S rRNA gene, and the coliform beta-glucuronidase gene were also quantified during this time period. RESULTS Bacterial classes observed above 1% relative abundance in all treatments were Actinobacteria (39.24% ± 0.25%), Beta-proteobacteria (23.99% ± 0.16%), Gamma-proteobacteria (11.06% ± 0.09%), and Alpha-proteobacteria (9.18 ± 0.04%). Families within the Caudovirales order: Siphoviridae (48.69% ± 0.10%), Podoviridae (23.99% ± 0.07%), and Myoviridae (19.94% ± 0.09%) were the dominant phage observed throughout the NESTP. The most abundant bacterial genera (in terms of average percent relative abundance) in influent, returned activated sludge, final effluent, and sludge, respectively, includes Mycobacterium (37.4%, 18.3%, 46.1%, and 7.7%), Acidovorax (8.9%, 10.8%, 5.4%, and 1.3%), and Polaromonas (2.5%, 3.3%, 1.4%, and 0.4%). The most abundant class of antibiotic resistance in bacterial samples was tetracycline resistance (17.86% ± 0.03%) followed by peptide antibiotics (14.24% ± 0.03%), and macrolides (10.63% ± 0.02%). Similarly, the phage samples contained a higher prevalence of macrolide (30.12% ± 0.30%), peptide antibiotic (10.78% ± 0.13%), and tetracycline (8.69% ± 0.11%) resistance. In addition, intI1 was the most abundant integron-integrase gene throughout treatment (1.14 × 104 gene copies/mL) followed by intI3 (4.97 × 103 gene copies/mL) while intI2 abundance remained low (6.4 × 101 gene copies/mL). CONCLUSIONS Wastewater treatment successfully reduced the abundance of bacteria, DNA phage and antibiotic resistance genes although many antibiotic resistance genes remained in effluent and biosolids. The presence of integron-integrase genes throughout treatment and in effluent suggests that antibiotic resistance genes could be actively disseminating resistance between both environmental and pathogenic bacteria.
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Affiliation(s)
- Paul Jankowski
- Department of Microbiology, University of Manitoba, 45 Chancellors Circle, Buller Building, Winnipeg, MB, R3T 2N2, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Jaydon Gan
- Department of Microbiology, University of Manitoba, 45 Chancellors Circle, Buller Building, Winnipeg, MB, R3T 2N2, Canada
| | - Tri Le
- Department of Microbiology, University of Manitoba, 45 Chancellors Circle, Buller Building, Winnipeg, MB, R3T 2N2, Canada
| | - Michaela McKennitt
- Clayton H. Riddell Faculty of Environment, Earth, and Resources, University of Manitoba, Winnipeg, MB, Canada
- Institute of the Environment, University of Ottawa, Ottawa, ON, Canada
| | - Audrey Garcia
- Department of Microbiology, University of Manitoba, 45 Chancellors Circle, Buller Building, Winnipeg, MB, R3T 2N2, Canada
| | - Kadir Yanaç
- Department of Civil Engineering, University of Manitoba, Winnipeg, MB, Canada
| | - Qiuyan Yuan
- Department of Civil Engineering, University of Manitoba, Winnipeg, MB, Canada
| | - Miguel Uyaguari-Diaz
- Department of Microbiology, University of Manitoba, 45 Chancellors Circle, Buller Building, Winnipeg, MB, R3T 2N2, Canada.
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247
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Senn S, Pangell K, Bowerman AL. Metagenomic Insights into the Composition and Function of Microbes Associated with the Rootzone of Datura inoxia. BIOTECH 2022; 11:biotech11010001. [PMID: 35822810 PMCID: PMC9245906 DOI: 10.3390/biotech11010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/20/2021] [Accepted: 12/30/2021] [Indexed: 11/16/2022] Open
Abstract
The purpose of this paper is to elucidate the roles that microbes may be playing in the rootzone of the medicinal plant Daturainoxia. We hypothesized that the microbes associated with the Datura rootzone would be significantly different than the similar surrounding fields in composition and function. We also hypothesized that rhizospheric and endophytic microbes would be associated with similar metabolic functions to the plant rootzone they inhabited. The methods employed were microbial barcoding, tests of essential oils against antibiotic resistant bacteria and other soil bacterial isolates, 16S Next Generation Sequencing (NGS) metabarcoding, and Whole Genome Shotgun (WGS) taxonomic and functional analyses. A few of the main bacterial genera of interest that were differentially abundant in the Datura root microbiome were Flavobacterium (p = 0.007), Chitinophaga (p = 0.0007), Pedobacter (p = 6 × 10−5), Bradyhizobium (p = 1 × 10−8), and Paenibacillus (p = 1.46 × 10−6). There was significant evidence that the microbes associated with the Datura rootzone had elevated function related to bacterial chalcone synthase (p = 1.49 × 10−3) and permease genes (p < 0.003). There was some evidence that microbial functions in the Datura rootzone provided precursors to important plant bioactive molecules or were beneficial to plant growth. This is important because these compounds are phyto-protective antioxidants and are precursors to many aromatic bioactive compounds that are relevant to human health. In the context of known interactions, and current results, plants and microbes influence the flavonoid biosynthetic pathways of one other, in terms of the regulation of the phenylpropanoid pathway. This is the first study to focus on the microbial ecology of the Datura rootzone. There are possible biopharmaceutical and agricultural applications of the natural interplay that was discovered during this study of the Datura inoxia rhizosphere.
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Affiliation(s)
- Savanah Senn
- Agriculture Sciences Department, Los Angeles Pierce College, 6201 Winnetka Avenue, PMB 553, Woodland Hills, CA 91304, USA; (K.P.); (A.L.B.)
- Environmental Sciences Graduate Program, Oregon State University, Corvallis, OR 97331, USA
- Correspondence:
| | - Kelly Pangell
- Agriculture Sciences Department, Los Angeles Pierce College, 6201 Winnetka Avenue, PMB 553, Woodland Hills, CA 91304, USA; (K.P.); (A.L.B.)
| | - Adrianna L. Bowerman
- Agriculture Sciences Department, Los Angeles Pierce College, 6201 Winnetka Avenue, PMB 553, Woodland Hills, CA 91304, USA; (K.P.); (A.L.B.)
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248
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Tadmor AD, Phillips R. MCRL: using a reference library to compress a metagenome into a non-redundant list of sequences, considering viruses as a case study. Bioinformatics 2022; 38:631-647. [PMID: 34636854 PMCID: PMC10060711 DOI: 10.1093/bioinformatics/btab703] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 10/03/2021] [Accepted: 10/07/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Metagenomes offer a glimpse into the total genomic diversity contained within a sample. Currently, however, there is no straightforward way to obtain a non-redundant list of all putative homologs of a set of reference sequences present in a metagenome. RESULTS To address this problem, we developed a novel clustering approach called 'metagenomic clustering by reference library' (MCRL), where a reference library containing a set of reference genes is clustered with respect to an assembled metagenome. According to our proposed approach, reference genes homologous to similar sets of metagenomic sequences, termed 'signatures', are iteratively clustered in a greedy fashion, retaining at each step the reference genes yielding the lowest E values, and terminating when signatures of remaining reference genes have a minimal overlap. The outcome of this computation is a non-redundant list of reference genes homologous to minimally overlapping sets of contigs, representing potential candidates for gene families present in the metagenome. Unlike metagenomic clustering methods, there is no need for contigs to overlap to be associated with a cluster, enabling MCRL to draw on more information encoded in the metagenome when computing tentative gene families. We demonstrate how MCRL can be used to extract candidate viral gene families from an oral metagenome and an oral virome that otherwise could not be determined using standard approaches. We evaluate the sensitivity, accuracy and robustness of our proposed method for the viral case study and compare it with existing analysis approaches. AVAILABILITY AND IMPLEMENTATION https://github.com/a-tadmor/MCRL. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Arbel D Tadmor
- TRON - Translational Oncology at the University Medical Center of Johannes Gutenberg University, 55131 Mainz, Germany
- Department of Biochemistry and Molecular Biophysics, California Institute of Technology, Pasadena, CA 91125, USA
| | - Rob Phillips
- Department of Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
- Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA
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Abstract
Multiomic analyses reported here involved two lines of chickens, from a common founder population, that had undergone long-term selection for high (HWS) or low (LWS) 56-day body weight. In these lines that differ by around 15-fold in body weight, we observed different compositions of intestinal microbiota in the holobionts and variation in DNA methylation, mRNA expression, and microRNA profiles in the ceca. Insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) was the most upregulated gene in HWS ceca with its expression likely affected by the upregulation of expression of gga-miR-2128 and a methylated region near its transcription start site (388 bp). Correlation analysis showed that IGF2BP1 expression was associated with an abundance of microbes, such as Lactobacillus and Methanocorpusculum. These findings suggest that IGF2BP1 was regulated in the hologenome in adapting to long-term artificial selection for body weight. Our study provides evidence that adaptation of the holobiont can occur in the microbiome as well as in the epigenetic profile of the host. IMPORTANCE The hologenome concept has broadened our perspectives for studying host-microbe coevolution. The multiomic analyses reported here involved two lines of chickens, from a common founder population, that had undergone long-term selection for high (HWS) or low (LWS) 56-day body weight. In these lines that differ by around 15-fold in body weight, we observed different compositions of intestinal microbiota in the holobionts, and variation in DNA methylation, mRNA expression, and microRNA profiles in ceca. The insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) was the most upregulated gene in HWS ceca with its expression likely affected by a methylated region near its transcription start site and the upregulation of expression of gga-miR-2128. Correlation analysis also showed that IGF2BP1 expression was associated with the abundance of microbes, such as Lactobacillus and Methanocorpusculum. These findings suggest that IGF2BP1 was regulated in the hologenome in response to long-term artificial selection for body weight. Our study shows that the holobiont may adapt in both the microbiome and the host's epigenetic profile.
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250
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Nguyen QV, Chong LC, Hor YY, Lew LC, Rather IA, Choi SB. Role of Probiotics in the Management of COVID-19: A Computational Perspective. Nutrients 2022; 14:nu14020274. [PMID: 35057455 PMCID: PMC8781206 DOI: 10.3390/nu14020274] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 02/01/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) was declared a pandemic at the beginning of 2020, causing millions of deaths worldwide. Millions of vaccine doses have been administered worldwide; however, outbreaks continue. Probiotics are known to restore a stable gut microbiota by regulating innate and adaptive immunity within the gut, demonstrating the possibility that they may be used to combat COVID-19 because of several pieces of evidence suggesting that COVID-19 has an adverse impact on gut microbiota dysbiosis. Thus, probiotics and their metabolites with known antiviral properties may be used as an adjunctive treatment to combat COVID-19. Several clinical trials have revealed the efficacy of probiotics and their metabolites in treating patients with SARS-CoV-2. However, its molecular mechanism has not been unraveled. The availability of abundant data resources and computational methods has significantly changed research finding molecular insights between probiotics and COVID-19. This review highlights computational approaches involving microbiome-based approaches and ensemble-driven docking approaches, as well as a case study proving the effects of probiotic metabolites on SARS-CoV-2.
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Affiliation(s)
- Quang Vo Nguyen
- Centre for Bioinformatics, School of Data Sciences, Perdana University, Suite 9.2, 9th Floor, Wisma Chase Perdana, Changkat Semantan, Wilayah Persekutuan, Kuala Lumpur 50490, Malaysia;
| | - Li Chuin Chong
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Beykoz, Istanbul 34820, Turkey;
| | - Yan-Yan Hor
- Department of Biotechnology, Yeungnam University, 280 Daehak-Ro, Gyeongsan 38541, Gyeongbuk, Korea;
| | - Lee-Ching Lew
- Probionic Corporation, Jeonbuk Institute for Food-Bioindustry, Jeonju 54810, Korea;
| | - Irfan A. Rather
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
- Center of Excellence in Bionanoscience Research, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
- Correspondence: (I.A.R.); (S.-B.C.)
| | - Sy-Bing Choi
- Centre for Bioinformatics, School of Data Sciences, Perdana University, Suite 9.2, 9th Floor, Wisma Chase Perdana, Changkat Semantan, Wilayah Persekutuan, Kuala Lumpur 50490, Malaysia;
- Correspondence: (I.A.R.); (S.-B.C.)
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