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Kalanzi D, Mayanja-Kizza H, Nakanjako D, Semitala F, Mboowa G, Mbabali M, Kigozi E, Katabazi FA, Sserwadda I, Kateete DP, Achan B, Sewankambo NK, Muwonge A. Microbial characteristics of dental caries in HIV positive individuals. Front Oral Health 2022; 3:1004930. [PMID: 36211252 PMCID: PMC9533146 DOI: 10.3389/froh.2022.1004930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Background Dental caries is a multifactorial disease that affects many people. Even though microorganisms play a crucial role in causing dental caries, diagnosis is routinely macroscopic. In order to improve early detection especially in HIV patients who are disproportionately affected, there is need to reconcile the macroscopic and microscopic characteristics of dental caries. Therefore, the aim of this study was to characterize the oral microbiota profile along the decayed, missing, filled teeth (DMFT) index using amplicon sequencing data. Methods Amplicon sequencing of the V6-V8 region of the 16S rRNA gene was done on DNA recovered from whole unstimulated saliva of 59 HIV positive and 29 HIV negative individuals. The microbial structure, composition and co-occurrence networks were characterized using QIIME-2, Phyloseq, Microbiome-1.9.2 and Metacoder in R. Results We characterized the oral microbiota into 2,093 operational taxonomic units (OTUs), 21 phyla and 239 genera from 2.6 million high quality sequence reads. While oral microbiota did not cluster participants into distinct groups that track with the DMFT index, we observed the following: (a) The proportion of accessory microbiota was highest in the high DMFT category while the core size (∼50% of richness) remained relatively stable across all categories. (b) The abundance of core genera such as Stomatobaculum, Peptostreptococcus and Campylobacter was high at onset of dental caries, (c) A general difference in oral microbial biomass. (d) The onset of dental caries (low DMFT) was associated with significantly lower oral microbial entropy. Conclusions Although oral microbial shifts along the DMFT index were not distinct, we demonstrated the potential utility of microbiota dynamics to characterize oral disease. Therefore, we propose a microbial framework using the DMFT index to better understand dental caries among HIV positive people in resource limited settings.
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Affiliation(s)
- Dunstan Kalanzi
- Department of Dentistry, School of Health Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Harriet Mayanja-Kizza
- Department of Medicine, School of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - Damalie Nakanjako
- Department of Medicine, School of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - Fred Semitala
- Department of Medicine, School of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - Gerald Mboowa
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Muhammad Mbabali
- Department of Dentistry, School of Health Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Edgar Kigozi
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Fred Ashaba Katabazi
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Ivan Sserwadda
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - David P. Kateete
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Beatrice Achan
- Department of Medical Microbiology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Nelson K. Sewankambo
- Department of Medicine, School of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - Adrian Muwonge
- Division of Genetics and Genomics, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
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Kudjordjie EN, Hooshmand K, Sapkota R, Darbani B, Fomsgaard IS, Nicolaisen M. Fusarium oxysporum Disrupts Microbiome-Metabolome Networks in Arabidopsis thaliana Roots. Microbiol Spectr 2022; 10:e0122622. [PMID: 35766498 PMCID: PMC9430778 DOI: 10.1128/spectrum.01226-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/29/2022] [Indexed: 12/13/2022] Open
Abstract
While the plant host metabolome drives distinct enrichment of detrimental and beneficial members of the microbiome, the mechanistic interomics relationships remain poorly understood. Here, we studied microbiome and metabolome profiles of two Arabidopsis thaliana accessions after Fusarium oxysporum f.sp. mathioli (FOM) inoculation, Landsberg erecta (Ler-0) being susceptible and Col-0 being resistant against FOM. By using bacterial and fungal amplicon sequencing and targeted metabolite analysis, we observed highly dynamic microbiome and metabolome profiles across FOM host progression, while being markedly different between FOM-inoculated and noninoculated Col-0 and Ler-0. Co-occurrence network analysis revealed more robust microbial networks in the resistant Col-0 compared to Ler-0 during FOM infection. Correlation analysis revealed distinct metabolite-OTU correlations in Ler-0 compared with Col-0 which could possibly be explained by missense variants of the Rfo3 and Rlp2 genes in Ler-0. Remarkably, we observed positive correlations in Ler-0 between most of the analyzed metabolites and the bacterial phyla Proteobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, and Verrucomicrobia, and negative correlations with Actinobacteria, Firmicutes, and Chloroflexi. The glucosinolates 4-methyoxyglucobrassicin, glucoerucin and indole-3 carbinol, but also phenolic compounds were strongly correlating with the relative abundances of indicator and hub OTUs and thus could be active in structuring the A. thaliana root-associated microbiome. Our results highlight interactive effects of host plant defense and root-associated microbiota on Fusarium infection and progression. Our findings provide significant insights into plant interomic dynamics during pathogen invasion and could possibly facilitate future exploitation of microbiomes for plant disease control. IMPORTANCE Plant health and fitness are determined by plant-microbe interactions which are guided by host-synthesized metabolites. To understand the orchestration of this interaction, we analyzed the distinct interomic dynamics in resistant and susceptible Arabidopsis ecotypes across different time points after infection with Fusarium oxysporum (FOM). Our results revealed distinct microbial profiles and network resilience during FOM infection in the resistant Col-0 compared with the susceptible Ler-0 and further pinpointed specific microbe-metabolite associations in the Arabidopsis microbiome. These findings provide significant insights into plant interomics dynamics that are likely affecting fungal pathogen invasion and could possibly facilitate future exploitation of microbiomes for plant disease control.
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Affiliation(s)
- Enoch Narh Kudjordjie
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Slagelse, Denmark
| | - Kourosh Hooshmand
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Slagelse, Denmark
| | - Rumakanta Sapkota
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Slagelse, Denmark
| | - Behrooz Darbani
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Slagelse, Denmark
| | - Inge S. Fomsgaard
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Slagelse, Denmark
| | - Mogens Nicolaisen
- Department of Agroecology, Faculty of Technical Sciences, Aarhus University, Slagelse, Denmark
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Dietrich A, Matchado MS, Zwiebel M, Ölke B, Lauber M, Lagkouvardos I, Baumbach J, Haller D, Brandl B, Skurk T, Hauner H, Reitmeier S, List M. Namco: a microbiome explorer. Microb Genom 2022; 8. [PMID: 35917163 PMCID: PMC9484756 DOI: 10.1099/mgen.0.000852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
16S rRNA gene profiling is currently the most widely used technique in microbiome research and allows the study of microbial diversity, taxonomic profiling, phylogenetics, functional and network analysis. While a plethora of tools have been developed for the analysis of 16S rRNA gene data, only a few platforms offer a user-friendly interface and none comprehensively covers the whole analysis pipeline from raw data processing down to complex analysis. We introduce Namco, an R shiny application that offers a streamlined interface and serves as a one-stop solution for microbiome analysis. We demonstrate Namco's capabilities by studying the association between a rich fibre diet and the gut microbiota composition. Namco helped to prove the hypothesis that butyrate-producing bacteria are prompted by fibre-enriched intervention. Namco provides a broad range of features from raw data processing and basic statistics down to machine learning and network analysis, thus covering complex data analysis tasks that are not comprehensively covered elsewhere. Namco is freely available at https://exbio.wzw.tum.de/namco/.
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Affiliation(s)
- Alexander Dietrich
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Monica Steffi Matchado
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany.,Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
| | - Maximilian Zwiebel
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Benjamin Ölke
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Michael Lauber
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Ilias Lagkouvardos
- ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany
| | - Jan Baumbach
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany.,Institute of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | - Dirk Haller
- ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany.,Chair of Nutrition and Immunology, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Beate Brandl
- ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany
| | - Thomas Skurk
- ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany
| | - Hans Hauner
- ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany.,Institute of Nutritional Medicine, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Sandra Reitmeier
- ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany.,Chair of Nutrition and Immunology, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Markus List
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
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Hou Y, Zhang X, Zhou Q, Hong W, Wang Y. Hierarchical Microbial Functions Prediction by Graph Aggregated Embedding. Front Genet 2021; 11:608512. [PMID: 33584804 PMCID: PMC7874084 DOI: 10.3389/fgene.2020.608512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/20/2020] [Indexed: 02/01/2023] Open
Abstract
Matching 16S rRNA gene sequencing data to a metabolic reference database is a meaningful way to predict the metabolic function of bacteria and archaea, bringing greater insight to the working of the microbial community. However, some operational taxonomy units (OTUs) cannot be functionally profiled, especially for microbial communities from non-human samples cultured in defective media. Therefore, we herein report the development of Hierarchical micrObial functions Prediction by graph aggregated Embedding (HOPE), which utilizes co-occurring patterns and nucleotide sequences to predict microbial functions. HOPE integrates topological structures of microbial co-occurrence networks with k-mer compositions of OTU sequences and embeds them into a lower-dimensional continuous latent space, while maximally preserving topological relationships among OTUs. The high imbalance among KEGG Orthology (KO) functions of microbes is recognized in our framework that usually yields poor performance. A hierarchical multitask learning module is used in HOPE to alleviate the challenge brought by the long-tailed distribution among classes. To test the performance of HOPE, we compare it with HOPE-one, HOPE-seq, and GraphSAGE, respectively, in three microbial metagenomic 16s rRNA sequencing datasets, including abalone gut, human gut, and gut of Penaeus monodon. Experiments demonstrate that HOPE outperforms baselines on almost all indexes in all experiments. Furthermore, HOPE reveals significant generalization ability. HOPE's basic idea is suitable for other related scenarios, such as the prediction of gene function based on gene co-expression networks. The source code of HOPE is freely available at https://github.com/adrift00/HOPE.
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Affiliation(s)
- Yujie Hou
- Department of Automation, Xiamen University, Xiamen, China.,Department of Automation, University of Science and Technology of China, Hefei, China
| | - Xiong Zhang
- Department of Automation, Xiamen University, Xiamen, China.,School of Automation Science and Engineering, South China University of Technology, Guangzhou, China
| | - Qinyan Zhou
- Department of Automation, Xiamen University, Xiamen, China.,Institute of AI and Robotics, Fudan University, Shanghai, China
| | - Wenxing Hong
- Department of Automation, Xiamen University, Xiamen, China.,Xiamen Key Laboratory of Big Data Intelligent Analysis and Decision, Xiamen, China
| | - Ying Wang
- Department of Automation, Xiamen University, Xiamen, China.,Xiamen Key Laboratory of Big Data Intelligent Analysis and Decision, Xiamen, China.,Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, Xiamen, China
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Liu Z, Wei H, Zhang J, Saleem M, He Y, Zhong J, Ma R. Higher Sensitivity of Microbial Network Than Community Structure under Acid Rain. Microorganisms 2021; 9:microorganisms9010118. [PMID: 33419116 PMCID: PMC7825572 DOI: 10.3390/microorganisms9010118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 12/24/2020] [Accepted: 12/26/2020] [Indexed: 12/17/2022] Open
Abstract
Acid rain (AR), as a global environmental threat, has profoundly adverse effects on natural soil ecosystems. Microorganisms involved in the nitrogen (N) cycle regulate the global N balance and climate stabilization, but little is known whether and how AR influences the structure and complexity of these microbial communities. Herein, we conducted an intact soil core experiment by manipulating the acidity of simulated rain (pH 7.5 (control, CK) vs. pH 4.0 (AR)) in subtropical agricultural soil, to reveal the differences in the structure and complexity of soil nitrifying and denitrifying microbiota using Illumina amplicon sequencing of functional genes (amoA, nirS, and nosZ). Networks of ammonia-oxidizing archaea (AOA) and nirS-carrying denitrifiers in AR treatment were less complex with fewer nodes and lower connectivity, while network of nosZ-carrying denitrifiers in AR treatment had higher complexity and connectivity relative to CK. Supporting this, AR reduced the abundance of keystone taxa in networks of AOA and nirS-carrying denitrifiers, but increased the abundance of keystone taxa in nosZ-carrying denitrifiers network. However, AR did not alter the community structure of AOA, ammonia-oxidizing bacteria (AOB), nirS-, and nosZ-carrying denitrifiers. Moreover, AR did not change soil N2O emissions during the experimental period. AOB community structure significantly correlated with content of soil available phosphorus (P), while the community structures of nirS- and nosZ-carrying denitrifiers both correlated with soil pH and available P content. Soil N2O emission was mainly driven by the nirS-carrying denitrifiers. Our results present new perspective on the impacts of AR on soil N-cycle microbial network complexity and keystone taxa in the context of global changes.
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Affiliation(s)
- Ziqiang Liu
- Guangdong Provincial Key Laboratory of Eco-circular Agriculture, South China Agricultural University, Guangzhou 510642, China; (Z.L.); (Y.H.); (J.Z.); (R.M.)
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Hui Wei
- Guangdong Provincial Key Laboratory of Eco-circular Agriculture, South China Agricultural University, Guangzhou 510642, China; (Z.L.); (Y.H.); (J.Z.); (R.M.)
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
- Guangdong Engineering Technology Research Centre of Modern Eco-agriculture and Circular Agriculture, Guangzhou 510642, China
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Correspondence: (H.W.); (J.Z.); Tel.: +86-20-8528-0211 (H.W.); +86-20-8528-5505 (J.Z.)
| | - Jiaen Zhang
- Guangdong Provincial Key Laboratory of Eco-circular Agriculture, South China Agricultural University, Guangzhou 510642, China; (Z.L.); (Y.H.); (J.Z.); (R.M.)
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
- Guangdong Engineering Technology Research Centre of Modern Eco-agriculture and Circular Agriculture, Guangzhou 510642, China
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Correspondence: (H.W.); (J.Z.); Tel.: +86-20-8528-0211 (H.W.); +86-20-8528-5505 (J.Z.)
| | - Muhammad Saleem
- Department of Biological Sciences, Alabama State University, Montgomery, AL 36104, USA;
| | - Yanan He
- Guangdong Provincial Key Laboratory of Eco-circular Agriculture, South China Agricultural University, Guangzhou 510642, China; (Z.L.); (Y.H.); (J.Z.); (R.M.)
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Jiawen Zhong
- Guangdong Provincial Key Laboratory of Eco-circular Agriculture, South China Agricultural University, Guangzhou 510642, China; (Z.L.); (Y.H.); (J.Z.); (R.M.)
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Rui Ma
- Guangdong Provincial Key Laboratory of Eco-circular Agriculture, South China Agricultural University, Guangzhou 510642, China; (Z.L.); (Y.H.); (J.Z.); (R.M.)
- Department of Ecology, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
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