Long-term stability of the urogenital microbiota of asymptomatic European women

Abstract Background To date, information on healthy female urinary microbiota is available mostly at genus level and at one time point. However, profound species-level characterization of healthy urinary microbiome and its stability over time are essential for further correct interpretation of its role in healthy urogenital tract. In this study, we investigated female urogenital microbiome (FUM) at two timepoints (within 2.5-year interval) in young asymptomatic European women. We used culturomics with accurate isolates’ identification (MALDI-TOF MS and gene markers sequencing) to understand species stability within healthy FUM. Results Extended culturomics of voided midstream urine sample pairs revealed a mean Shannon diversity index of 1.25 and mean of 19 species/sample (range 5–39 species; total of 115 species; 1830 isolates). High overall species variability between individuals was captured by beta diversity and a variety of community structure types, with the largest cluster characterized by Lactobacillus crispatus, often in combination with Gardnerella vaginalis or Gardnerella genomospecies 3. Significant FUM composition differences, related to Finegoldia magna and Streptococcus anginosus, according to smoking status were found. A high species variability within individuals (Shannon index SD > 0.5 in 7 out of 10 sample pairs) with a mean of 29% of shared species (range 9.1–41.7%) was observed. Moreover, 4 out of 10 sample pairs clustered in the same community structure type. The stable FUM sample pairs presented high abundance of Lactobacillus crispatus, Streptococcus agalactiae or Lactobacillus paragasseri and Bifidobacterium spp.. Moreover, Gardnerella vaginalis, Gardnerella genomospecies 3 or Gardnerella swidsinskii were often maintained within individuals in high abundance. Conclusions Shift in species composition at two distant timepoints was frequently observed among urogenital microbiome of European asymptomatic women. This suggests possible interchange of particular species in healthy FUM and the existence of multiple health-associated FUM compositions in certain individuals. Additionally, we provided additional evidence on resilience of particular bacterial communities and identified certain species more prone to persist in urogenital tract. This study revealed important details on the FUM composition complexity relevant for studies aiming to understand microbiota role in the urogenital tract health and for identification of eubiotic and dysbiotic FUM.

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STRUKTUR KOMUNITAS MAKRO ALGA DI PESISIR PULAU KECAMATAN BULANG

SIMBIOSA ◽

10.33373/sim-bio.v3i2.282 ◽

2014 ◽

Vol 3 (2) ◽

Author(s):

Notowinarto Notowinarto ◽

Ramses Ramses ◽

Mulhairi Mulhairi

Keyword(s):

Community Structure ◽

Diversity Index ◽

Algal Species ◽

Algal Communities ◽

Marine Life ◽

Ph Values ◽

Abundance Patterns ◽

Coastal Marine ◽

Temperature Parameter ◽

Important Value Index

Bulang districts Batam Islands of Riau province (Riau Islands), its consists of many islands with as well as having the potential diversity of coastal marine life in particular kinds of macro algae or seaweed. Conducted research aimed to determine the structure of macro- algal communities in the intertidal zone islands. The results of the identification of algal species found 16 species are: the Order of Chlorophyceae as 6 spesies; Order Phaeophyceae as 2 spesies; and Order Rhodophyceae as 8 spesies. The community structure at the five stations showed the highest values were found in the island of dominance Cicir (D ' = 0.79) , uniformity index values on Tengah Island (E ' = 0.99) , while the island Balak had the highest diversity index (H ' = 0.88) , with the abundance patterns of population structure on the island is pretty good Central . Results of correlation analysis of regression between IVI types of algae with the conditions of environmental quality suggests that there is a significance (Fhit ˃ F table and the value of r = > 90 %) between IVI algae Halimeda sp and Cryptarachne polyglandulosa at each station with a temperature parameter surface (⁰C) , depth temperature (⁰C) and pH values. Keywords : Algae, Community Structure, Important Value Index.

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Effects of Plastic Debris on the Biofilm Bacterial Communities in Lake Water

Water ◽

10.3390/w13111465 ◽

2021 ◽

Vol 13 (11) ◽

pp. 1465

Author(s):

Chao Shen ◽

Liuyan Huang ◽

Guangwu Xie ◽

Yulai Wang ◽

Zongkai Ma ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

Diversity Index ◽

Plastic Substrate ◽

Simpson Index ◽

Plastic Debris ◽

Plastic Substrates ◽

Wiener Diversity Index

Increasing discharge of plastic debris into aquatic ecosystems and the worsening ecological risks have received growing attention. Once released, plastic debris could serve as a new substrate for microbes in waters. The complex relationship between plastics and biofilms has aroused great interest. To confirm the hypothesis that the presence of plastic in water affects the composition of biofilm in natural state, in situ biofilm culture experiments were conducted in a lake for 40 days. The diversity of biofilm attached on natural (cobble stones (CS) and wood) and plastic substrates (Polyethylene terephthalate (PET) and Polymethyl methacrylate (PMMA)) were compared, and the community structure and composition were also analyzed. Results from high-throughput sequencing of 16S rRNA showed that the diversity and species richness of biofilm bacterial communities on natural substrate (observed species of 1353~1945, Simpson index of 0.977~0.989 and Shannon–Wiener diversity index of 7.42~8.60) were much higher than those on plastic substrates (observed species of 900~1146, Simpson index of 0.914~0.975 and Shannon–Wiener diversity index of 5.47~6.99). The NMDS analyses were used to confirm the taxonomic significance between different samples, and Anosim (p = 0.001, R = 0.892) and Adonis (p = 0.001, R = 808, F = 11.19) demonstrated that this classification was statistically rigorous. Different dominant bacterial communities were found on plastic and natural substrates. Alphaproteobacterial, Betaproteobacteria and Synechococcophycideae dominated on the plastic substrate, while Gammaproteobacteria, Phycisphaerae and Planctomycetia played the main role on the natural substrates. The bacterial community structure of the two substrates also showed significant difference which is consistent with previous studies using other polymer types. Our results shed light on the fact that plastic debris can serve as a new habitat for biofilm colonization, unlike natural substrates, pathogens and plastic-degrading microorganisms selectively attached to plastic substrates, which affected the bacterial community structure and composition in aquatic environment. This study provided a new insight into understanding the potential impacts of plastics serving as a new habitat for microbial communities in freshwater environments. Future research should focus on the potential impacts of plastic-attached biofilms in various aquatic environments and the whole life cycle of plastics (i.e., from plastic fragments to microplastics) and also microbial flock characteristics using microbial plastics in the natural environment should also be addressed.

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Spatial and Temporal Variation in Microbial Diversity and Community Structure in a Contaminated Mangrove Wetland

Applied Sciences ◽

10.3390/app10175850 ◽

2020 ◽

Vol 10 (17) ◽

pp. 5850

Author(s):

Jiaojiao Ma ◽

Ting Zhou ◽

Chunyu Xu ◽

Dawen Shen ◽

Songjun Xu ◽

...

Keyword(s):

Community Structure ◽

Spatial Variation ◽

Temporal Variation ◽

Bacterial Diversity ◽

Diversity Index ◽

Total Carbon ◽

Spatial And Temporal Variation ◽

Rrna Gene ◽

Mangrove Wetland ◽

Mangrove Soils

Field and laboratory investigations were conducted to characterize bacterial diversity and community structure in a badly contaminated mangrove wetland adjacent to the metropolitan area of a megacity in subtropical China. Next-generation sequencing technique was used for sequencing the V4–V5 region of the 16s rRNA gene on the Illumina system. Collectively, Proteobacteria, Chloroflexi, Planctomycetes, Actinobacteria and Bacteroidetes were the predominant phyla identified in the investigated soils. A significant spatial variation in bacterial diversity and community structure was observed for the investigated mangrove soils. Heavy metal pollution played a key role in reducing the bacterial diversity. The spatial variation in soil-borne heavy metals shaped the spatial variation in bacterial diversity and community structure in the study area. Other environmental factors such as total carbon and total nitrogen in the soils that are affected by seasonal change in temperature could also influence the bacterial abundance, diversity and community structure though the temporal variation was relatively weaker, as compared to spatial variation. The bacterial diversity index was lower in the investigated site than in the comparable reference site with less contaminated status. The community structure in mangrove soils at the current study site was, to a remarkable extent, different from those in the tropical mangrove wetlands around the world.

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Effects of Ecological Restoration Using Non-Native Mangrove Kandelia obovata to Replace Invasive Spartina alterniflora on Intertidal Macrobenthos Community in Maoyan Island (Zhejiang, China)

Journal of Marine Science and Engineering ◽

10.3390/jmse9080788 ◽

2021 ◽

Vol 9 (8) ◽

pp. 788

Author(s):

Qiuxuan Wang ◽

Carlos Duarte ◽

Li Song ◽

George Christakos ◽

Susana Agusti ◽

...

Keyword(s):

Community Structure ◽

Ecological Restoration ◽

Spartina Alterniflora ◽

Diversity Index ◽

Invasion History ◽

Kandelia Obovata ◽

Wiener Diversity Index ◽

Significant Difference ◽

Spatial Differences ◽

Average Biomass

Spartina alterniflora has extensively invaded the coastline of China, including in Maoyan Island of Zhejiang Province. Ecological restoration has been conducted using non-native mangrove Kandelia obovata to replace S. alterniflora in an attempt to restore the impacted intertidal zones. To illustrate the ecological effectiveness of the restoration projects, macrobenthos communities were studied among different habitats within the restored areas, including one non-restored S. alterniflora marsh (SA) and three differently-aged restored K. obovata stands planted in 2003, 2009, and 2011 respectively (KF14, KF8, and KF6). Besides, one unvegetated mudflat (MF) adjacent to the non-restored S. alterniflora marsh and one K. obovata forest transplanted in 2006 (RKF) at a previously barren mudflat without invasion history of S. alterniflora were set as reference sites. A total of 69 species of macrobenthos were collected from Maoyan Island, and the species richness was dominated by gastropoda (23 species), polychaeta (18 species), and malacostraca (16 species). There was no significant difference between the six sites in terms of the abundance of macrobenthos, with the average values of abundance peaking in KF6 (734.7 ind m−2) and being lowest in RKF (341.3 ind m−2). The six sites had significant differences in terms of the biomass of macrobenthos. The KF8 site contained the highest average biomass (168.3 g m−2), whereas the MF site had the lowest (54.3 g m−2). The Shannon-Wiener diversity index and Pielou’s evenness index of the macrobenthos did not exhibit significant differences among the six sites. However, the results of permutational multivariate analysis of variance (PERMANOVA) revealed significant spatial differences in the macrobenthos community structure between the sites. Since KF14 shared a similar macrobenthos community structure with RKF, while representing a strikingly different structure from SA, we infer that ecological restoration using K. obovata can restore the macrobenthos community to resemble to a normally planted K. obovata forest about 15 years after restoration.

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Bird community structure in natural and urbanized habitats along an altitudinal gradient in Pauri district (Garhwal Himalaya) of Uttarakhand state, India

Biologia ◽

10.2478/s11756-012-0068-z ◽

2012 ◽

Vol 67 (4) ◽

Cited By ~ 8

Author(s):

Archana Naithani ◽

Dinesh Bhatt

Keyword(s):

Community Structure ◽

Altitudinal Gradient ◽

Diversity Index ◽

Bird Species ◽

Bird Community ◽

High Elevation ◽

Base Line ◽

Natural Habitats ◽

Forest Habitat ◽

Rarefaction Analysis

AbstractIn the Indian subcontinent there is hardly any study that compares the bird community structure of urban/suburban areas with those of forest habitat. The present survey identified diverse assemblages of birds in the Pauri district at different elevations. A total of 125 bird species belonging to 40 families including two least count species (Lophura leucomelanos and Pucrasia marcolopha) were recorded during this survey in the forest and urbanized habitats of Pauri District (Garhwal Hiamalaya) of Uttarakhand state, India. The high elevation (Pauri 1600–2100 m a.s.l.), mid elevation (Srikot-Khanda 900–1300 m a.s.l.) and low elevation (Srinagar 500–900 m a.s.l.) contributed 88.8%, 63.2% and 58.4% of the total species respectively. Rarefaction analysis and Shannon diversity index showed that the high elevation forest habitat had highest bird species richness (BSR) and bird species diversity (BSD) followed by the mid and then the low elevation forests. BSR and BSD fluctuated across seasons at all elevations but not across habitat types. Present study provides a base line data about avian community composition in urbanized and natural habitats along altitudinal gradient in the study area. This information may be useful to the conservation biologists for the better management and conservation of the avifauna in the Western Himalaya, a part of one of the hot biodiversity spots of the world.

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Temporal and spatial variability in the community structure of the fauna of four sandy beaches in south-eastern New South Wales.

Marine and Freshwater Research ◽

10.1071/mf9840663 ◽

1984 ◽

Vol 35 (6) ◽

pp. 663 ◽

Cited By ~ 46

Author(s):

DM Dexter

Keyword(s):

Community Structure ◽

Diversity Index ◽

Abundant Species ◽

Sandy Beaches ◽

Sampling Procedure ◽

Wave Action ◽

Physical Factors ◽

Faunal Composition ◽

South Wales ◽

Temporal And Spatial

Four intertidal sandy beaches with different exposures, La Perouse, Ocean Beach, Dolls Point, and Towra Point, were studied for temporal and spatial changes in faunal composition and community structure. Each of these beaches was sampled from 6 to 12 times between July 1980 and July 1981 using a 500 �m sieve. A stratified random sampling procedure across the intertidal zone isolated 40 660 individuals representing 85 species. Distribution and abundance of species were strongly influenced by tidal level. Densities changed during the year but no seasonal changes in intertidal zonation patterns were found. Changes in density were correlated with the reproductive activities of the abundant species, especially Pseudolana concinna and Exoediceros maculosus at La Perouse, and Spio pacifica at Dolls Point and Towra Point. The number of species increased from high to low tide, and also increased with decreasing exposure to wave action. Crustaceans dominated the fauna in the most exposed site and decreased in abundance with increasing protection. Ocean Beach experienced the least fluctuation in physical factors such as wave action, salinity, and temperature, and its fauna exhibited the highest diversity index (H') and evenness (J'), the most stable density, and the greatest stability in faunal composition through time. The highest densities and the most species were found at Towra Point, which also was the most protected site.

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Heterotrophic Bacterial Community Structure of Multistage Biofilters in a Commercial Pufferfish Takifugu rubripes RAS

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.726-731.1621 ◽

2013 ◽

Vol 726-731 ◽

pp. 1621-1627 ◽

Cited By ~ 2

Author(s):

Zhu Chen ◽

Ying Liu ◽

Liang Zi Liu ◽

Xiao Jing Wang ◽

Zhi Pei Liu ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Bacterial Community ◽

Bacterial Community Structure ◽

Heterotrophic Bacteria ◽

Diversity Index ◽

Community Diversity ◽

Takifugu Rubripes ◽

Recirculating Aquaculture ◽

Microbial Resources

The success of a recirculating aquaculture system (RAS) greatly depends on the structure, dynamics and activities of microbial community. Heterotrophic bacteria as the major members play various roles. The heterotrophic bacterial community structure in threestaged biofilters was studied using four different media. 228 isolates belonging to 77species were obtained and affiliated toGammaproteobacteria,Alphaproteobacteria,Bacteroidetes,Firmicutes,ActinobacteriaandBetaproteobacteria.Gammaproteobacteriawas the predominant group. The concurrence was found between potential pathogens (VibrioandShewanella) and probiotics (BacillusandPseudomonas). On the basis of community diversity index, we could infer that differences existed between stages, and the diversity index increased along the biofilters. A comprehensive understanding of microbial community in RAS will be in favor of utilization of microbial resources and optimizing the culture systems' operation.

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Struktur Komunitas Fitoplankton di Perairan Pesisir Pulau Siantan Kabupaten Kepulauan Anambas Provinsi Kepulauan Riau

CAHAYA PENDIDIKAN ◽

10.33373/chypend.v1i1.375 ◽

2016 ◽

Vol 1 (1) ◽

Author(s):

Lani Puspita ◽

Notowinarto Notowinarto ◽

Rudi Gunawan

Keyword(s):

Community Structure ◽

Coastal Area ◽

Diversity Index ◽

Natural Food ◽

Species Dominance ◽

Sampling Locations ◽

Level Data ◽

Dominance Level ◽

Index Value ◽

Sampling Times

Phytoplankton as a producers and natural food for fish have an important role in aquatic ecosystems, thus indirectly affecting the availability of fish catches. The research was conducted at Siantan Island Coastal Area Anambas Islands District Riau Islands Province. This coastal area is one of the fishing grounds in Anambas Island. This study aims to analyze the community structure of phytoplankton at Siantan Island Coastal Area Anambas Islands District Riau Islands Province. Sampling was conducted during March and April 2012. Community structure parameters analyzed include Species Diversity Level, Species Uniformity Level, and Species Dominance Level. Data were analyzed spatially and temporally. Similarity between the sampling locations was conduted by Multivariate Analysis - Cluster. Results of data analysis showed that the phytoplankton of Bacillariophyceae Class found in the most abundant amount. Diversity Index Value indicates that the level of phytoplankton plankton community in a state of moderate. Species Uniformity Index Value and Species Dominance Index Value indicates that phytoplankton in the three sampling locations are generally in a state of uniform and no one dominates. All three sampling locations have relatively the same condition and between sampling times (morning, afternoon, and evening) are also not very different condition. Keywords: phytoplankton, coastal, Anambas Islands

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Struktur Komunitas Fitoplankton di Kolam Bekas Pertambangan Batubara Desa Kampung Baru Kecamatan Cempaka

BIOSCIENTIAE ◽

10.20527/b.v17i2.3451 ◽

2021 ◽

Vol 17 (2) ◽

pp. 37

Author(s):

Sukoco Sukoco ◽

Gunawan Gunawan ◽

Muhamat Muhamat

Keyword(s):

Community Structure ◽

Coal Mining ◽

Sampling Method ◽

Diversity Index ◽

Pool Analysis ◽

Fertility Rate ◽

The State ◽

Purposive Sampling ◽

Phytoplankton Communities ◽

Average Abundance

This study aims to determine the structure of phytoplankton communities in the pool are former coal mining Desa Kampung Baru Kecamatan Cempaka which include abundance, diversity, uniformity and dominance. Phytoplankton samples taken in two pools with a purposive sampling method with a three-point shooting at each pond. Sampling was performed three times. Phylum of phytoplankton were identified in both pools as much as 2 phylum (Chloropyta and Chrysopita) with 17 genera. Average abundance of phytoplankton in the first pool of 7174 ind / liter and 6873 ind / liter in the second pool. The average diversity index of phytoplankton in the first pool of 1.540 and 1.621 in the second pool. Average uniformity index of phytoplankton in the first pool of 0622 and 0.623 in the second pool. The average index of phytoplankton dominance in the first pool of 0271 and 0250 in the second pool. Analysis of community structure (abundance, diversity, uniformity and dominance) shows the condition of the two ponds in the state is quite stable and capable of supporting life inside the phytoplankton. Where the pool in the fertility rate is the level of contamination is, the conditions included in the category of individuals spread more evenly and there are no species that dominate other species in the extreme.

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THE ANALYSIS OF OIL CONTENT IN SEDIMENT AND COMMUNITY STRUCTURE OF MACROZOOBENTHOS IN BELAWAN WATERS OF MEDAN CITY, NORTH SUMATERA PROVINCE

Asian Journal of Aquatic Sciences ◽

10.31258/ajoas.3.2.167-178 ◽

2020 ◽

Vol 3 (2) ◽

pp. 167-178

Author(s):

Doli Juna Setia Tanjung ◽

Bintal Amin ◽

Syafruddin Nasution

Keyword(s):

Community Structure ◽

Linear Regression ◽

Oil Content ◽

Diversity Index ◽

The Other ◽

Regression Analyses ◽

Simple Linear Regression ◽

Dominance Index ◽

Ocypode Quadrata ◽

Evenness Index

This research was conducted in March 2019 to determine the oil content in sediment, it’s community structure of macrozoobenthos and it’s a relationship in Belawan Waters of Medan City, North Sumatera. Four sampling stations with five replications in each station were surveyed. The results showed that the average oil content in sediments exceeded the threshold had set by the National Academy of Science. Macrozoobenthos found consists of Ocypode quadrata, Scyla serrate, Rotun dicauda, Penaeus sp, Murex tribulus, and Nassarius olivaccus. The highest abundance was in Station 3 and the lowest was in Station 2. The diversity index in each station was generally very low. Dominance Index in Station 4 was medium, whilst the other stations were high. Evenness index showed in Station 3 and 4 were in high population, Station 1 was in medium population and Station 2 was in low population. Simple linear regression analyses between oil content in sediment with community structure of macrozoobenthos indicated negative correlation ( Y = 10,5-0,0001x , R2 = 0,0004 and r = 0,02 ) which indicated that the higher the oil content, the lower the macrozoobenthos abundance in sediment.

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