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Lundmark, A., Hu, Y. O. O., Huss, M., Johannsen, G., Andersson, A. F. & Yucel-Lindberg, T. (2019). Identification of Salivary Microbiota and Its Association With Host Inflammatory Mediators in Periodontitis. Frontiers in Cellular and Infection Microbiology, 9, Article ID 216.
Open this publication in new window or tab >>Identification of Salivary Microbiota and Its Association With Host Inflammatory Mediators in Periodontitis
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2019 (English)In: Frontiers in Cellular and Infection Microbiology, E-ISSN 2235-2988, Vol. 9, article id 216Article in journal (Refereed) Published
Abstract [en]

Periodontitis is a microbial-induced chronic inflammatory disease, which may not only result in tooth loss, but can also contribute to the development of various systemic diseases. The transition from healthy to diseased periodontium depends on microbial dysbiosis and impaired host immune response. Although periodontitis is a common disease as well as associated with various systemic inflammatory conditions, the taxonomic profiling of the salivary microbiota in periodontitis and its association with host immune and inflammatory mediators has not been reported. Therefore, the aim of this study was to identify key pathogens and their potential interaction with the host's inflammatory mediators in saliva samples for periodontitis risk assessment. The microbial 16S rRNA gene sequencing and the levels of inflammatory mediators were performed in saliva samples from patients with chronic periodontitis and periodontally healthy control subjects. The salivary microbial community composition differed significantly between patients with chronic periodontitis and healthy controls. Our analyses identified a number of microbes, including bacteria assigned to Eubacterium saphenum, Tannerella forsythia, Filifactor alocis, Streptococcus mitis/parasanguinis, Parvimonas micra, Prevotella sp., Phocaeicola sp., and Fretibacterium sp. as more abundant in periodontitis, compared to healthy controls. In samples from healthy individuals, we identified Campylobacter concisus, and Veillonella sp. as more abundant. Integrative analysis of the microbiota and inflammatory mediators/cytokines revealed associations that included positive correlations between the pathogens Treponema sp. and Selenomas sp. and the cytokines chitinase 3-like 1, sIL-6R alpha, sTNF-R1, and gp 130/sIL-6R beta. In addition, a negative correlation was identified between IL-10 and Filifactor alocis. Our results reveal distinct and disease-specific patterns of salivary microbial composition between patients with periodontitis and healthy controls, as well as significant correlations between microbiota and host-mediated inflammatory cytokines. The positive correlations between the pathogens Treponema sp. and Selenomas sp. and the cytokines chitinase 3-like 1, sIL-6R alpha, sTNF-R1, and gp 130/sIL-6R beta might have the future potential to serve as a combined bacteria-host salivary biomarker panel for diagnosis of the chronic infectious disease periodontitis. However, further studies are required to determine the capacity of these microbes and inflammatory mediators as a salivary biomarker panel for periodontitis.

Place, publisher, year, edition, pages
Frontiers Media S.A., 2019
Keywords
16S rRNA sequencing, cytokines, inflammatory mediators, microbiome, microbiota, periodontitis, saliva
National Category
Gastroenterology and Hepatology
Identifiers
urn:nbn:se:kth:diva-255316 (URN)10.3389/fcimb.2019.00216 (DOI)000472529100001 ()31281801 (PubMedID)2-s2.0-85068883187 (Scopus ID)
Note

QC 20190729

Available from: 2019-07-29 Created: 2019-07-29 Last updated: 2019-07-29Bibliographically approved
Hu, Y. O. O., Ndegwa, N., Alneberg, J., Johansson, S., Logue, J. B., Huss, M., . . . Andersson, A. F. (2018). Stationary and portable sequencing-based approaches for tracing wastewater contamination in urban stormwater systems. Scientific Reports, 8, Article ID 11907.
Open this publication in new window or tab >>Stationary and portable sequencing-based approaches for tracing wastewater contamination in urban stormwater systems
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2018 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 11907Article in journal (Refereed) Published
Abstract [en]

Urban sewer systems consist of wastewater and stormwater sewers, of which only wastewater is processed before being discharged. Occasionally, misconnections or damages in the network occur, resulting in untreated wastewater entering natural water bodies via the stormwater system. Cultivation of faecal indicator bacteria (e.g. Escherichia coli; E. coli) is the current standard for tracing wastewater contamination. This method is cheap but has limited specificity and mobility. Here, we compared the E. coli culturing approach with two sequencing-based methodologies (Illumina MiSeq 16S rRNA gene amplicon sequencing and Oxford Nanopore MinION shotgun metagenomic sequencing), analysing 73 stormwater samples collected in Stockholm. High correlations were obtained between E. coli culturing counts and frequencies of human gut microbiome amplicon sequences, indicating E. coli is indeed a good indicator of faecal contamination. However, the amplicon data further holds information on contamination source or alternatively how much time has elapsed since the faecal matter has entered the system. Shotgun metagenomic sequencing on a subset of the samples using a portable real-time sequencer, MinION, correlated well with the amplicon sequencing data. This study demonstrates the use of DNA sequencing to detect human faecal contamination in stormwater systems and the potential of tracing faecal contamination directly in the field.

Place, publisher, year, edition, pages
NATURE PUBLISHING GROUP, 2018
National Category
Microbiology
Identifiers
urn:nbn:se:kth:diva-234183 (URN)10.1038/s41598-018-29920-7 (DOI)000441159800013 ()30093614 (PubMedID)2-s2.0-85051497618 (Scopus ID)
Note

QC 20181003

Available from: 2018-10-03 Created: 2018-10-03 Last updated: 2018-10-03Bibliographically approved
Lamei, S., Hu, Y. O. O., Olofsson, T. C., Andersson, A. F., Forsgren, E. & Vasquez, A. (2017). Improvement of identification methods for honeybee specific Lactic Acid Bacteria; future approaches. PLoS ONE, 12(3), Article ID e0174614.
Open this publication in new window or tab >>Improvement of identification methods for honeybee specific Lactic Acid Bacteria; future approaches
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2017 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 12, no 3, article id e0174614Article in journal (Refereed) Published
Abstract [en]

Honeybees face many parasites and pathogens and consequently rely on a diverse set of individual and group-level defenses to prevent disease. The crop microbiota of Apis mellifera, composed of 13 Lactic Acid Bacterial (LAB) species within the genera Lactobacillus and Bifidobacterium, form a beneficial symbiotic relationship with each other and the honeybee to protect their niche and their host. Possibly playing a vital role in honeybee health, it is important that these honeybee specific Lactic Acid Bacterial (hbs-LAB) symbionts can be correctly identified, isolated and cultured, to further investigate their health promoting properties. We have previously reported successful identification to the strain level by culture-dependent methods and we recently sequenced and annotated the genomes of the 13 hbs-LAB. However, the hitherto applied techniques are unfortunately very time consuming, expensive and not ideal when analyzing a vast quantity of samples. In addition, other researchers have constantly failed to identify the 13 hbs-LAB from honeybee samples by using inadequate media and/or molecular techniques based on 16S rRNA gene sequencing with insufficient discriminatory power. The aim of this study was to develop better and more suitable methods for the identification and cultivation of hbs-LAB. We compared currently used bacterial cultivation media and could for the first time demonstrate a significant variation in the hbs-LAB basic requirements for optimal growth. We also present a new bacterial identification approach based on amplicon sequencing of a region of the 16S rRNA gene using the Illumina platform and an error correction software that can be used to successfully differentiate and rapidly identify the 13 hbs-LAB to the strain level.

Place, publisher, year, edition, pages
PUBLIC LIBRARY SCIENCE, 2017
National Category
Biological Sciences
Identifiers
urn:nbn:se:kth:diva-206698 (URN)10.1371/journal.pone.0174614 (DOI)000399174300061 ()28346815 (PubMedID)2-s2.0-85016432762 (Scopus ID)
Note

QC 20170509

Available from: 2017-05-09 Created: 2017-05-09 Last updated: 2017-11-29Bibliographically approved
Lindh, M. V., Sjostedt, J., Ekstam, B., Casini, M., Lundin, D., Hugerth, L. W., . . . Pinhassi, J. (2017). Metapopulation theory identifies biogeographical patterns among core and satellite marine bacteria scaling from tens to thousands of kilometers. Environmental Microbiology, 19(3), 1222-1236
Open this publication in new window or tab >>Metapopulation theory identifies biogeographical patterns among core and satellite marine bacteria scaling from tens to thousands of kilometers
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2017 (English)In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 19, no 3, p. 1222-1236Article in journal (Refereed) Published
Abstract [en]

Metapopulation theory developed in terrestrial ecology provides applicable frameworks for interpreting the role of local and regional processes in shaping species distribution patterns. Yet, empirical testing of metapopulation models on microbial communities is essentially lacking. We determined regional bacterioplankton dynamics from monthly transect sampling in the Baltic Sea Proper using 16S rRNA gene sequencing. A strong positive trend was found between local relative abundance and occupancy of populations. Notably, the occupancy-frequency distributions were significantly bimodal with a satellite mode of rare endemic populations and a core mode of abundant cosmopolitan populations (e.g. Synechococcus, SAR11 and SAR86 clade members). Temporal changes in population distributions supported several theoretical frameworks. Still, bimodality was found among bacterioplankton communities across the entire Baltic Sea, and was also frequent in globally distributed datasets. Datasets spanning waters with widely different physicochemical characteristics or environmental gradients typically lacked significant bimodal patterns. When such datasets were divided into subsets with coherent environmental conditions, bimodal patterns emerged, highlighting the importance of positive feedbacks between local abundance and occupancy within specific biomes. Thus, metapopulation theory applied to microbial biogeography can provide novel insights into the mechanisms governing shifts in biodiversity resulting from natural or anthropogenically induced changes in the environment.

Place, publisher, year, edition, pages
Wiley-VCH Verlagsgesellschaft, 2017
National Category
Ecology Evolutionary Biology
Identifiers
urn:nbn:se:kth:diva-205505 (URN)10.1111/1462-2920.13650 (DOI)000397525100031 ()28028880 (PubMedID)2-s2.0-85012069850 (Scopus ID)
Note

QC 20170510

Available from: 2017-05-10 Created: 2017-05-10 Last updated: 2017-05-10Bibliographically approved
Zhu, X., Shen, Y., Chen, X., Hu, Y. O. O., Xiang, H., Tao, J. & Ling, Y. (2016). Biodegradation mechanism of microcystin-LR by a novel isolate of Rhizobium sp. TH and the evolutionary origin of the mlrA gene. International Biodeterioration & Biodegradation, 115, 17-25
Open this publication in new window or tab >>Biodegradation mechanism of microcystin-LR by a novel isolate of Rhizobium sp. TH and the evolutionary origin of the mlrA gene
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2016 (English)In: International Biodeterioration & Biodegradation, ISSN 0964-8305, E-ISSN 1879-0208, Vol. 115, p. 17-25Article in journal (Refereed) Published
Abstract [en]

The frequent presence of microcystin (MC) in eutrophic water bodies worldwide poses a serious threat to ecosystems. Biodegradation has been extensively investigated as a main pathway for MC attenuation, and an mlr-dependent mechanism of MC degradation have been elucidated in detail. However, the evolutionary origin and the distribution of mlr genes in MC-degrading bacteria is poorly understood. In this study, a novel Rhizobium sp. TH, which is the first α-proteobacterial MC-degrading bacterium other than Sphingomonadales, was isolated. Strain TH degraded MC via the mlr-dependent mechanism with a first-order rate constant of 0.18–0.29 h−1 under near-natural conditions. The partial length mlr gene cluster was sequenced, and the function of its key gene, mlrA, was verified by heterologous expression in Escherichia coli. Phylogenetic analyses show that the mlrA gene initially arose in α-proteobacteria by vertical evolution, and the two strains from β- and γ-proteobacteria acquired it by horizontal gene transfer. Therefore, the mlrA gene mainly exists in α-proteobacteria but is seldom present in other bacteria. A pair of primers matching well with mlrA sequences reported so far were designed and could be used to determine the MC-degrading mechanism for novel isolates or to screen for MC-degrading ability among environmental samples.

Place, publisher, year, edition, pages
Elsevier, 2016
Keywords
Degradation, Evolutionary origin, Mechanism, Microcystin, mlrA gene, Rhizobium, Bacteria, Escherichia coli, Gene expression, Gene transfer, Genes, Mechanisms, Rate constants, Strain, Toxic materials, Environmental sample, First-order rate constants, Heterologous expression, Horizontal gene transfer, Microcystins, Phylogenetic analysis, Biodegradation, eutrophic environment, evolutionary biology, gene, phylogenetics, reaction kinetics, rhizobacterium, toxin, Alphaproteobacteria, Bacteria (microorganisms), Gammaproteobacteria, Proteobacteria, Rhizobium sp., Sphingomonadales
National Category
Biological Sciences
Identifiers
urn:nbn:se:kth:diva-195227 (URN)10.1016/j.ibiod.2016.07.011 (DOI)000388048700003 ()2-s2.0-84979710830 (Scopus ID)
Note

QC 20161117

Available from: 2016-11-17 Created: 2016-11-02 Last updated: 2019-02-08Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-2025-2198

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