| 1. |
- Berga, Mercè, et al.
(författare)
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Functional and Compositional Stability of Bacterial Metacommunities in Response to Salinity Changes
- 2017
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Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Disturbances and environmental change are important factors determining the diversity,composition, and functioning of communities. However, knowledge about how naturalbacterial communities are affected by such perturbations is still sparse. We performeda whole ecosystem manipulation experiment with freshwater rock pools where weapplied salinity disturbances of different intensities. The aim was to test how thecompositional and functional resistance and resilience of bacterial communities,alpha- and beta-diversity and the relative importance of stochastic and deterministiccommunity assembly processes changed along a disturbance intensity gradient.We found that bacterial communities were functionally resistant to all salinity levels (3, 6, and 12 psu) and compositionally resistant to a salinity increase to 3 psu andresilient to increases of 6 and 12 psu. Increasing salinities had no effect on local richnessand evenness, beta-diversity and the proportion of deterministically vs. stochasticallyassembled communities. Our results show a high functional and compositional stabilityof bacterial communities to salinity changes of different intensities both at localand regional scales, which possibly reflects long-term adaptation to environmentalconditions in the study system.
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| 2. |
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| 3. |
- Cheng, Liqin, et al.
(författare)
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Vaginal microbiota and human papillomavirus infection among young Swedish women
- 2020
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Ingår i: npj Biofilms and Microbiomes. - : Springer Science and Business Media LLC. - 2055-5008. ; 6:1
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Tidskriftsartikel (refereegranskat)abstract
- Human papillomavirus (HPV) infection is one of the most common sexually transmitted diseases. To define the HPV-associated microbial community among a high vaccination coverage population, we carried out a cross-sectional study with 345 young Swedish women. The microbial composition and its association with HPV infection, including 27 HPV types, were analyzed. Microbial alpha-diversity was found significantly higher in the HPV-infected group (especially with oncogenic HPV types and multiple HPV types), compared with the HPV negative group. The vaginal microbiota among HPV-infected women was characterized by a larger number of bacterial vaginosis-associated bacteria (BVAB), Sneathia, Prevotella, and Megasphaera. In addition, the correlation analysis demonstrated that twice as many women with non-Lactobacillus-dominant vaginal microbiota were infected with oncogenic HPV types, compared with L. crispatus-dominated vaginal microbiota. The data suggest that HPV infection, especially oncogenic HPV types, is strongly associated with a non-Lactobacillus-dominant vaginal microbiota, regardless of age and vaccination status.
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| 4. |
- Hugerth, Luisa W, et al.
(författare)
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Assessment of In Vitro and In Silico Protocols for Sequence-Based Characterization of the Human Vaginal Microbiome
- 2020
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Ingår i: mSphere. - : American Society for Microbiology. - 2379-5042. ; 5:6
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Tidskriftsartikel (refereegranskat)abstract
- The vaginal microbiome has been connected to a wide range of health outcomes. This has led to a thriving research environment but also to the use of conflicting methodologies to study its microbial composition. Here, we systematically assessed best practices for the sequencing-based characterization of the human vaginal microbiome. As far as 16S rRNA gene sequencing is concerned, the V1-V3 region performed best in silico, but limitations of current sequencing technologies meant that the V3-V4 region performed equally well. Both approaches presented very good agreement with qPCR quantification of key taxa, provided that an appropriate bioinformatic pipeline was used. Shotgun metagenomic sequencing presents an interesting alternative to 16S rRNA gene amplification and sequencing but requires deeper sequencing and more bioinformatic expertise and infrastructure. We assessed different tools for the removal of host reads and the taxonomic annotation of metagenomic reads, including a new, easy-to-build and -use reference database of vaginal taxa. This curated database performed as well as the best-performing previously published strategies. Despite the many advantages of shotgun sequencing, none of the shotgun approaches assessed here agreed with the qPCR data as well as the 16S rRNA gene sequencing.IMPORTANCE The vaginal microbiome has been connected to various aspects of host health, including susceptibility to sexually transmitted infections as well as gynecological cancers and pregnancy outcomes. This has led to a thriving research environment but also to conflicting available methodologies, including many studies that do not report their molecular biological and bioinformatic methods in sufficient detail to be considered reproducible. This can lead to conflicting messages and delay progress from descriptive to intervention studies. By systematically assessing best practices for the characterization of the human vaginal microbiome, this study will enable past studies to be assessed more critically and assist future studies in the selection of appropriate methods for their specific research questions.
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| 5. |
- Langenheder, Silke, et al.
(författare)
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Remnants of marine bacterial communities can be retrieved from deep sediments in lakes of marine origin
- 2016
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Ingår i: Environmental Microbiology Reports. - : Wiley. - 1758-2229. ; 8:4, s. 479-485
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Tidskriftsartikel (refereegranskat)abstract
- Some bacteria can be preserved over time in deep sediments where they persist either in dormant or slow-growing vegetative stages. Here, we hypothesized that such cells can be revived when exposed to environmental conditions similar to those before they were buried in the sediments. To test this hypothesis, we collected bacteria from sediment samples of different ages (140–8500 calibrated years before present, cal BP) from three lakes that differed in the timing of their physical isolation from the Baltic Sea following postglacial uplift. After these bacterial communities were grown in sterile water from the Baltic Sea, we determined the proportion of 16S rRNA sequence reads associated with marine habitats by extracting the environment descriptive terms of homologous sequences retrieved from public databases. We found that the proportion of reads associated with marine descriptive term was significantly higher in cultures inoculated with sediment layers formed under Baltic conditions and where salinities were expected to be similar to current levels. Moreover, a similar pattern was found in the original sediment layers. Our study, therefore, suggests that remnants of marine bacterial communities can be preserved in sediments over thousands of years and can be revived from deep sediments in lakes of marine origin.
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| 6. |
- Marklund, Maria H. K., et al.
(författare)
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Asymmetrical habitat coupling of an aquatic predator : The importance of individual specialization
- 2019
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Ingår i: Ecology and Evolution. - : Wiley. - 2045-7758. ; 9:6, s. 3405-3415
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Tidskriftsartikel (refereegranskat)abstract
- Predators should stabilize food webs because they can move between spatially separate habitats. However, predators adapted to forage on local resources may have a reduced ability to couple habitats. Here, we show clear asymmetry in the ability to couple habitats by Eurasian perch—a common polymorphic predator in European lakes. We sampled perch from two spatially separate habitats—pelagic and littoral zones—in Lake Erken, Sweden. Littoral perch showed stronger individual specialization, but they also used resources from the pelagic zone, indicating their ability to couple habitats. In contrast, pelagic perch showed weaker individual specialization but near complete reliance on pelagic resources, indicating their preference to one habitat. This asymmetry in the habitat coupling ability of perch challenges the expectation that, in general, predators should stabilize spatially separated food webs. Our results suggest that habitat coupling might be constrained by morphological adaptations, which in this case were not related to genetic differentiation but were more likely related to differences in individual specialization.
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| 7. |
- Marklund, Maria H. K., et al.
(författare)
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The influence of habitat accessibility on the dietary and morphological specialisation of an aquatic predator
- 2018
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Ingår i: Oikos. - : John Wiley & Sons. - 0030-1299 .- 1600-0706. ; 127:1, s. 160-169
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Tidskriftsartikel (refereegranskat)abstract
- Individual diet and habitat specialisation are widespread in animal taxa and often related to levels of predation and competition. Mobile consumers such as predatory fish can stabilise lake food webs by ranging over a larger area than their prey, thereby switching between habitats. Although, this switching assumes that the predator has equal preference for the available prey, individual diet specialisation and morphological adaptations to different habitats could potentially prevent individuals from switching between habitats. In this study, we assessed the niche width and individual specialisation in Eurasian perch Perca fluviatilis in response to a shift in habitat use by manipulating the ability for this top predator to couple habitats. We ran an eight weeks pond experiment, to test the effect of habitat switching on diet and morphological specialisations. We show that habitat coupling influenced individual diet specialisation and niche use in expected directions where specialisation increased with decreasing habitat switching. In contrast to expectations, the morphological variation decreased with increasing diet specialisation. Our results expand on previous work and suggest that individual specialisation and niche width can impact the ability of mobile predators to couple habitats. Furthermore, it shows the importance of individual specialisations in relation to habitat coupling.
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| 8. |
- Sterpu, Irene, et al.
(författare)
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No evidence for a placental microbiome in human pregnancies at term
- 2021
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Ingår i: American Journal of Obstetrics and Gynecology. - : Elsevier. - 0002-9378 .- 1097-6868. ; 224:3, s. 296.e1-296.e23
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Tidskriftsartikel (refereegranskat)abstract
- Background: The placenta plays an important role in the modulation of pregnancy immunity; however, there is no consensus regarding the existence of a placental microbiome in healthy full-term pregnancies.Objective: This study aimed to investigate the existence and origin of a placental microbiome.Study Design: A cross-sectional study comparing samples (3 layers of placental tissue, amniotic fluid, vernix caseosa, and saliva, vaginal, and rectal samples) from 2 groups of full-term births: 50 women not in labor with elective cesarean deliveries and 26 with vaginal deliveries. The comparisons were performed using polymerase chain reaction amplification and DNA sequencing techniques and bacterial culture experiments.Result: There were no significant differences regarding background characteristics between women who delivered by elective cesarean and those who delivered vaginally. Quantitative measurements of bacterial content in all 3 placental layers (quantitative polymerase chain reaction of the 16S ribosomal RNA gene) did not show any significant difference among any of the sample types and the negative controls. Here, 16S ribosomal RNA gene sequencing of the maternal side of the placenta could not differentiate between bacteria in the placental tissue and contamination of the laboratory reagents with bacterial DNA. Probe-specific quantitative polymerase chain reaction for bacterial taxa suspected to be present in the placenta could not detect any statistically significant difference between the 2 groups. In bacterial cultures, substantially more bacteria were observed in the placenta layers from vaginal deliveries than those from cesarean deliveries. In addition, 16S ribosomal RNA gene sequencing of bacterial colonies revealed that most of the bacteria that grew on the plates were genera typically found in human skin; moreover, it revealed that placentas delivered vaginally contained a high prevalence of common vaginal bacteria. Bacterial growth inhibition experiments indicated that placental tissue may facilitate the inhibition of bacterial growth.Conclusion: We found no evidence to support the existence of a placental microbiome in our study of 76 term pregnancies, which used polymerase chain reaction amplification and sequencing techniques and bacterial culture experiments. Incidental findings of bacterial species could be due to contamination or to low-grade bacterial presence in some locations; such bacteria do not represent a placental microbiome per se.
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| 9. |
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| 10. |
- Svanbäck, Richard, et al.
(författare)
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The interaction between predation risk and food ration on behavior and morphology of Eurasian perch
- 2017
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Ingår i: Ecology and Evolution. - : Wiley. - 2045-7758. ; 7:20, s. 8567-8577
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Tidskriftsartikel (refereegranskat)abstract
- The risk of both predation and food level has been shown to affect phenotypic development of organisms. However, these two factors also influence animal behavior that in turn may influence phenotypic development. Hence, it might be difficult to disentangle the behavioral effect from the predator or resource-level effects. This is because the presence of predators and high resource levels usually results in a lower activity, which in turn affects energy expenditure that is used for development and growth. It is therefore necessary to study how behavior interacts with changes in body shape with regard to resource density and predators. Here, we use the classic predator-induced morphological defense in fish to study the interaction between predator cues, resource availability, and behavioral activity with the aim to determine their relative contribution to changes in body shape. We show that all three variables, the presence of a predator, food level, and activity, both additively and interactively, affected the body shape of perch. In general, the presence of predators, lower swimming activity, and higher food levels induced a deep body shape, with predation and behavior having similar effect and food treatment the smallest effect. The shape changes seemed to be mediated by changes in growth rate as body condition showed a similar effect as shape with regard to food-level and predator treatments. Our results suggests that shape changes in animals to one environmental factor, for example, predation risk, can be context dependent, and depend on food levels or behavioral responses. Theoretical and empirical studies should further explore how this context dependence affects fitness components such as resource gain and mortality and their implications for population dynamics.
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| 11. |
- Wu, Shengru, et al.
(författare)
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Tonsillar microbiota : A cross-sectional study of patients with chronic tonsillitis or tonsillar hypertrophy
- 2021
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Ingår i: mSystems. - 2379-5077. ; 6:2
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Tidskriftsartikel (refereegranskat)abstract
- Chronic tonsillitis (CT) and tonsillar hypertrophy (TH) are common tonsillar diseases that are related to infection and inflammation. Little is known about tonsillar microbiota and its role in CT and TH. This study aims to identify palatine tonsillar microbiota both on the surface and in the core tissues of CT and TH patients. In total, 22 palatine tonsils were removed and collected from CT and TH patients who underwent surgery. The surface and core microbiota in the tonsils of CT and TH patients were compared using 16S rRNA gene sequencing of V3-V4 regions. Differential tonsillar microbiotas were found in the CT versus TH patients and surface versus core tissues. Further, a higher relative abundance of bacterial genera, including Haemophilus, Streptococcus, Neisseria, Capnocytophaga, Kingella, Moraxella, and Lachnospiraceae [G-2] in patients with TH and Dialister, Parvimonas, Bacteroidales [G-2], Aggregatibacter, and Atopobium in patients with CT, was observed. Of these, the differential genera of Dialister, Parvimonas, and Neisseria served as key factors in the tonsillar microbiota network. Notably, four representable tonsillar microbial types were identified, with one, consisting of a higher abundance of Haemophilus and Neisseria, exclusively detected in the TH patients. This study analyzed the different tonsillar microbiota from the surface and core tissues of CT and TH patients. Several bacteria and various microbial types related to CT and TH were identified, along with potential bacterial networks and related immune pathways.IMPORTANCE: The human microbiota has been shown to be functionally connected to infectious and inflammation-related diseases. So far, only limited studies had been performed on tonsillar microbiota, although tonsils play an essential role in the human immune defense system and encountered numerous microorganisms. Our work presented different tonsillar microbiota from surface and core tissues of chronic tonsillitis (CT) and tonsillar hypertrophy (TH) patients. Notably, one tonsillar microbiota type, which contains a higher abundance of Haemophilus and Neisseria, was only detected in the TH patients. Furthermore, certain bacteria, such as Haemophilus, Neisseria, Dialister, and Parvimonas, may serve as microbial biomarkers to discriminate CT patients from TH patients. These data provide important microbiota data in the tonsillar research area and are highly useful for researchers both in the oral microbiome field and clinical field.
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| 12. |
- Zha, Yinghua, 1987-
(författare)
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Assembly of Gut Microbial Communities in Freshwater Fish and Their Roles in Fish Condition
- 2017
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Animal hosts provide associated microorganisms with suitable ecological niches in their intestines. Microbes help their hosts to digest food, protect against pathogens, and influence the host’s metabolisms. Compositional variation of gut microbial communities is common among hosts, and may affect the health status of hosts. Diet and genetic factors are well known to influence the assembly of gut microbial communities. This thesis focuses on disentangling the contributions of factors including host genetics (sex), diet, environment, and other ecological processes to the assembly of gut microbial communities in freshwater fish. The association between gut microbial communities and fish condition is also evaluated in this thesis.Applying metacommunity theory, we found environmental factors including fish habitat, fish species, their diet, dispersal factors including microbes from fish diet, and ecological drift contributed to the assembly of fish gut microbial communities. The proportion of their contribution varied between fish species, where ecological drift explained more in perch than in roach.Under natural conditions fish populations face the risk of predation, which can induce competition and impose predation stress within prey individuals. This can therefore lead to changes in their diet qualities and quantities. In this thesis, it was shown that fish diet in terms of qualities and quantities significantly influenced the overall gut microbial composition, and this influence was dependent on fish sex, a host genetic factor. Predation stress was also suggested to significantly decrease the species richness. Furthermore, when fish were experiencing a diet shift, we showed that different bacterial phyla from novel food had different colonization success in the intestine, and this colonization success was positively influenced by predation stress. Fish condition was suggested in this thesis to be affected by gut microbial composition, especially by the contributions of the bacterial phyla Tenericutes and Actinobacteria.
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| 13. |
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| 14. |
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| 15. |
- Zha, Yinghua, et al.
(författare)
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Different Roles of Environmental Selection, Dispersal, and Drift in the Assembly of Intestinal Microbial Communities of Freshwater Fish With and Without a Stomach
- 2020
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Ingår i: Frontiers in Ecology and Evolution. - : Frontiers Media SA. - 2296-701X. ; 8, s. 1-15
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Tidskriftsartikel (refereegranskat)abstract
- The composition of intestinal microbiota commonly varies among animal hosts and may affect host health. However, we have limited knowledge about the different relative roles of assembly processes, such as drift, dispersal and environmental selection, for the composition of gut microbiota. Here, we conducted a field study analyzing intestinal microbial communities of two fish species that either have (perch) or lack (roach) a stomach. We used a suite of statistical tools to evaluate the role of different assembly processes for intestine microbiota, including null model analysis (Chase et al., 2011; Fine and Kembel, 2011; Stegen et al., 2013), SourceTracker analysis (Knights et al., 2011) and several multivariate analyses, such as pRDA and PLS analysis. Drift, dispersal (i.e., microbes associated with food sources) and environmental factors (i.e., diet, host habitats), appeared to be of equal importance for the assembly of intestinal microbial communities in roach, while drift appeared most important in perch, followed by dispersal and environmental selection. Furthermore, we found that microbes associated with macroinvertebrates had a positive association to fish body condition (weight/length3) whereas microbes associated with zooplankton had a negative association to fish body condition. These results emphasize the important combined roles of drift, dispersal and environmental selection in shaping the host-associated microbial communities. We conclude that general conclusions about fish as a whole are not justified since different species differ in the relative roles of these important drivers of community assembly.
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| 16. |
- Zha, Yinghua, et al.
(författare)
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Effects of Dispersal and Initial Diversity on the Composition and Functional Performance of Bacterial Communities
- 2016
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 11:5
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Tidskriftsartikel (refereegranskat)abstract
- Natural communities are open systems and consequently dispersal can play an important role for the diversity, composition and functioning of communities at the local scale. It is, however, still unclear how effects of dispersal differ depending on the initial diversity of local communities. Here we implemented an experiment where we manipulated the initial diversity of natural freshwater bacterioplankton communities using a dilution-to-extinction approach as well as dispersal from a regional species pool. The aim was further to test whether dispersal effects on bacterial abundance and functional parameters (average community growth rates, respiration rates, substrate utilisation ability) differ in dependence of the initial diversity of the communities. First of all, we found that both initial diversity and dispersal rates had an effect on the recruitment of taxa from a regional source, which was higher in communities with low initial diversity and at higher rates of dispersal. Higher initial diversity and dispersal also promoted higher levels of richness and evenness in local communities and affected, both, separately or interactively, the functional performance of communities. Our study therefore suggests that dispersal can influence the diversity, composition and functioning of bacterial communities and that this effect may be enhanced if the initial diversity of communities is depleted.
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| 17. |
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| 18. |
- Zha, Yinghua, et al.
(författare)
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Effects of predation stress and food ration on perch gut microbiota
- 2018
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Ingår i: Microbiome. - : Springer Science and Business Media LLC. - 2049-2618. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Background: Gut microbiota provide functions of importance to influence hosts' food digestion, metabolism, and protection against pathogens. Factors that affect the composition and functions of gut microbial communities are well studied in humans and other animals; however, we have limited knowledge of how natural food web factors such as stress from predators and food resource rations could affect hosts' gut microbiota and how it interacts with host sex. In this study, we designed a two-factorial experiment exposing perch (Perca fluviatilis) to a predator (pike, Esox lucius), and different food ratios, to examine the compositional and functional changes of perch gut microbiota based on 16S rRNA amplicon sequencing. We also investigated if those changes are host sex dependent. Results: We showed that overall gut microbiota composition among individual perch significantly responded to food ration and predator presence. We found that species richness decreased with predator presence, and we identified 23 taxa from a diverse set of phyla that were over-represented when a predator was present. For example, Fusobacteria increased both at the lowest food ration and at predation stress conditions, suggesting that Fusobacteria are favored by stressful situations for the host. In concordance, both food ration and predation stress seemed to influence the metabolic repertoire of the gut microbiota, such as biosynthesis of other secondary metabolites, metabolism of cofactors, and vitamins. In addition, the identified interaction between food ration and sex emphasizes sex-specific responses to diet quantity in gut microbiota. Conclusions: Collectively, our findings emphasize an alternative state in gut microbiota with responses to changes in natural food webs depending on host sex. The obtained knowledge from this study provided us with an important perspective on gut microbiota in a food web context. RAHAMS MV, 1989, ECOLOGY, V70, P999
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