Insights into the pan-microbiome: skin microbial communities of Chinese individuals differ from other racial groups

Abstract Many studies have characterized microbiomes of western individuals. However, studies involving non-westerners are scarce. This study characterizes the skin microbiomes of Chinese individuals. Skin-associated genera, including Propionibacterium, Corynebacterium, Staphylococcus and Enhydrobacter were prevalent. Extensive inter-individual microbiome variations were detected, with core genera present in all individuals constituting a minority of genera detected. Species-level analyses presented dominance of potential opportunistic pathogens in respective genera. Host properties including age, gender and household were associated with variations in community structure. For all sampled sites, skin microbiomes within an individual is more similar than that of different co-habiting individuals, which is in turn more similar than individuals living in different households. Network analyses highlighted general and skin-site specific relationships between genera. Comparison of microbiomes from different population groups revealed race-based clustering explained by community membership (Global R = 0.968) and structure (Global R = 0.589), contributing to enlargement of the skin pan-microbiome. This study provides the foundation for subsequent in-depth characterization and microbial interactive analyses on the skin and other parts of the human body in different racial groups and an appreciation that the human skin pan-microbiome can be much larger than that of a single population.

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Speciation and Antibiotic Susceptibilities of Coagulase Negative Staphylococci Isolated from Ocular Infections

Antibiotics ◽

10.3390/antibiotics10060721 ◽

2021 ◽

Vol 10 (6) ◽

pp. 721

Author(s):

John E. Romanowski ◽

Shannon V. Nayyar ◽

Eric G. Romanowski ◽

Vishal Jhanji ◽

Robert M. Q. Shanks ◽

...

Keyword(s):

Empiric Therapy ◽

Species Level ◽

Opportunistic Pathogens ◽

Coagulase Negative Staphylococci ◽

Biochemical System ◽

Ocular Infections ◽

Antibiotic Susceptibilities ◽

System 2 ◽

Intravitreal Treatment ◽

Susceptibility Profiles

Coagulase-negative staphylococci (CoNS) are frequently occurring ocular opportunistic pathogens that are not easily identifiable to the species level. The goal of this study was to speciate CoNS and document antibiotic susceptibilities from cases of endophthalmitis (n = 50), keratitis (n = 50), and conjunctivitis/blepharitis (n = 50) for empiric therapy. All 150 isolates of CoNS were speciated using (1) API Staph (biochemical system), (2) Biolog GEN III Microplates (phenotypic substrate system), and (3) DNA sequencing of the sodA gene. Disk diffusion antibiotic susceptibilities for topical and intravitreal treatment were determined based on serum standards. CoNS identification to the species level by all three methods indicated that S. epidermidis was the predominant species of CoNS isolated from cases of endophthalmitis (84–90%), keratitis (80–86%), and conjunctivitis/blepharitis (62–68%). Identifications indicated different distributions of CoNS species among endophthalmitis (6), keratitis (10), and conjunctivitis/blepharitis (13). Antibiotic susceptibility profiles support empiric treatment of endophthalmitis with vancomycin, and keratitis treatment with cefazolin or vancomycin. There was no clear antibiotic choice for conjunctivitis/blepharitis. S. epidermidis was the most frequently found CoNS ocular pathogen, and infection by other CoNS appears to be less specific and random. Antibiotic resistance does not appear to be a serious problem associated with CoNS.

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Epiphyton of oligotrophic lakes of Leningrad region

Issues of modern algology (Вопросы современной альгологии) ◽

10.33624/2311-0147-2021-1(25)-71-79 ◽

2021 ◽

pp. 71-79

Author(s):

Elena V. Stanislavskaya

Keyword(s):

Community Structure ◽

Dominant Species ◽

Taxonomic Composition ◽

Species Level ◽

Taxonomic Structure ◽

Leningrad Region ◽

Oligotrophic Lakes ◽

Epiphytic Algae ◽

Lake Ecosystems ◽

Epiphytic Communities

Here are results of investigation of taxonomic composition, community structure and dominant species of epiphytic algae in 12 oligotrophic lakes located in different geomorphic regions of Leningrad region. In summer epiphytic communities there were 385 algal taxa, they belonged to 6 taxonomic divisions: Cyanophyta (Cyanoprokaryota) – 50 (13%), Bacillaryophyta – 175 (45%), Chlorophyta – 37 (10%), Charophyta – 118 (30%), Xanthophyta – 4 (1,55%), Rhodophyta – 1 (0,45%). The taxonomic structure of each lake was predominant diatoms and desmids, but the biomass was dominated by zygnems and green algae. In total, the taxonomic composition of the epiphyton in the studied lakes is similar, the differences are revealed at the species level. The structure of dominanting epiphyton complex was rather constant and composed by a small number of species. The greatest contribution to the epiphyton was made by Tabellaria flocculosa and species of the genus Bulbochaete. The structure of the epiphyton reflects the undisturbed nature of lake ecosystems, as well as their northern location.

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Enhancing link prediction by exploring community membership of nodes

International Journal of Modern Physics B ◽

10.1142/s021797921950382x ◽

2019 ◽

Vol 33 (31) ◽

pp. 1950382

Author(s):

Shenshen Bai ◽

Shiyu Fang ◽

Longjie Li ◽

Rui Liu ◽

Xiaoyun Chen

Keyword(s):

Community Structure ◽

Prediction Model ◽

Link Prediction ◽

Prediction Accuracy ◽

Network Data ◽

Data Link ◽

Structure Information ◽

Community Membership

With the proliferation of available network data, link prediction has become increasingly important and captured growing attention from various disciplines. To enhance the prediction accuracy by making full use of community structure information, this paper proposes a new link prediction model, namely CMS, in which different community memberships of nodes are investigated. In the opinion of CMS, different memberships can have different influence to link’s formation. To estimate the connection likelihood between two nodes, the CMS model weights the contribution of each shared neighbor according to the corresponding community membership. Three CMS-based methods are derived by introducing three forms of contribution that neighbors make. Extensive experiments on 12 networks are conducted to evaluate the performance of CMS-based methods. The results manifest that CMS-based methods are more effective and robust than baselines.

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Multivariate Analysis of Community Structure Over Ten Years Following the Exxon Valdez Oil Spill

International Oil Spill Conference Proceedings ◽

10.7901/2169-3358-2003-1-285 ◽

2003 ◽

Vol 2003 (1) ◽

pp. 285-289

Author(s):

E.S. Gilfillan ◽

D.S. Page ◽

K.R. Parker

Keyword(s):

Community Structure ◽

Oil Spill ◽

Exxon Valdez ◽

Worst Case ◽

Sediment Grain Size ◽

Site Specific ◽

Exxon Valdez Oil Spill ◽

Biological Communities ◽

Study Designs ◽

Animal Communities

ABSTRACT A 1990/1991 shoreline ecology program to assess the fate and effects of the Exxon Valdez oil spill in Prince William Sound was updated in 1998 and 1999. This update included a sediment sampling program for organisms at “worst case” sites and at randomly chosen reference sites. Correspondence analysis (CA), a statistical method that examines animal communities in terms of their similarity, was used to define community structure Statistical analysis of the degree of similarity between communities was used to assess effects of site-specific variables (sediment grain size, total organic carbon (TOC) and wave energy), interannual variation, and degree of oiling. Interannual variability had a significant effect on community structure, whereas site specific variables and degree of oiling did not. Differences in communities between 1998 and other years were particularly dramatic. The importance of interannual change demonstrates the importance of multi-year sampling and of appropriate study designs for separating impact effects from the natural occurring environmental factors which affect biological communities.

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Additive and site-specific effects of two foundation species on invertebrate community structure

Marine Ecology Progress Series ◽

10.3354/meps10867 ◽

2014 ◽

Vol 508 ◽

pp. 129-138 ◽

Cited By ~ 15

Author(s):

AR Hughes ◽

PE Gribben ◽

DL Kimbro ◽

MJ Bishop

Keyword(s):

Community Structure ◽

Foundation Species ◽

Invertebrate Community ◽

Site Specific ◽

Specific Effects ◽

Invertebrate Community Structure

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Comparative co-occurrence network analyses of the cichlid fish gut microbiota: community conservation and diet-associated shifts

10.1101/2020.05.26.118232 ◽

2020 ◽

Author(s):

Joan Lluís Riera ◽

Laura Baldo

Keyword(s):

Community Structure ◽

Gut Microbiota ◽

Positive Interactions ◽

Fish Family ◽

Comparative Analyses ◽

Cichlid Fishes ◽

Network Analyses ◽

Primary Model ◽

Microbial Associations ◽

Microbiota Structure

AbstractCo-occurrence networks of bacteria associations are a powerful approach to explore ecologically relevant aspects of the gut microbiota structure, beyond community composition alone. Here we exploit the remarkable diversity of cichlid fishes and their multiple lake assemblages to investigate a) network features and patterns of microbial associations that were robust to major phylogeographical variables, and b) community structure changes along cichlid dietary shifts. We tackled these objectives using the large gut microbiota sequencing dataset available (nine lakes from Africa and America), building geographical and diet-specific networks and performing comparative analyses. Major findings indicated that lake and continental networks were highly resembling in global topology and node taxonomic composition, suggesting important constraints in the cichlid gut community assembling. A small fraction of the observed co-occurrence pairwises was conserved across all lake assemblages; while the origin and ecological relevance of these core associations remains unclear, their persistence suggests a potential functional role in the cichlid gut. Comparison of carnivores and herbivores-specific networks as well as mapping of diet-specific values on the African Lake Tanganyika network revealed a clear community shift as a function of diet, with an increase in complexity and node taxonomic diversity from carnivores-omnivores-plantkivores to herbivores. More importantly, diet-associated nodes in herbivores formed complex modules of positive interactions. By intersecting results from association patterns and experimental trials, future studies will be directed to test the strength of these microbial associations and predict the outcome of community alterations driven by diet.ImportanceThe gut microbiota is a complex community of interacting bacteria. Predicting patterns of co-occurrence among microbes can help understanding key ecological aspects driving community structure, maintenance and dynamics. Here we showed a powerful application of co-occurrence networks to explore gut bacteria interactions in a primary model system to study animal diversification, the cichlid fishes. Taking advantage of the large scale of phylogeographical and ecological diversity of this fish family, we built gut microbiota networks from distinct lake and continental fish assemblages and performed extensive comparative analyses to retrieve conserved and trait-specific patterns of bacteria associations. Our results identified network features that were independent from the fish biogeography and that indicated an important host selection effect on gut community assembling. Focusing on a single lake assemblage, and therefore excluding the major geographical effect, we observed that the gut microbiota structure dramatically shifted from carnivore to herbivore fishes, with a substantial increase in the number and complexity of microbial interactions.

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COMMUNITY STRUCTURE OF GROUPER FISH (Serranidae) LANDED IN PEUKAN BADA SUBDISTRICT, ACEH PROVINCE

Jurnal Ilmu dan Teknologi Kelautan Tropis ◽

10.28930/jitkt.v8i1.12497 ◽

2016 ◽

Vol 8 (1) ◽

Author(s):

Rika Astuti ◽

. Yonvitner ◽

M. Mukhlis Kamal

Keyword(s):

Community Structure ◽

Species Composition ◽

Species Level ◽

Survey Method ◽

Taxonomic Information ◽

Individual Number ◽

Landing Sites ◽

Aceh Province

ABSTRACTInformation on important and economic grouper fish (Serranidae family) in Peukan Bada waters, Province of Aceh is very limited. This objecives of this research were to determine spatial and temporal variabilities in species composition and community structure of grouper landed in Peukan Bada, Aceh Besar District. The research was conducted using survey method during February to June 2015 on three fish landing sites i.e., Ujong Pancu, Lamtengoh, and Lamteh. The groupers were caught by using handline. The landed fishes were therefore counted and identified up to species level. The data were also analyzed based on taxonomic information and individual number of each species, community structure using the diversity index (H’), eveness (E), and dominance (D). The results obtained 835 individual, 21 species of grouper belong to 4 genera (Aethaloperca, Cephalopholis, Epinephelus dan Variola). Based on species, Epinephelus fasciatus and Cephalopholis sonnerati were the most grouper fishes in the region. Based on community structure, diversity value (H’) in Lam-tengoh was higher than that in Ujong Pancu and Lamteh. Total grouper fish catches were not significantly different (P>0,05) among the three region. Meanwhile, total grouper fish cacthes were significantly different between seasons (p<0,05). The diversity species variation during five months of observation was affected by the differences in catches area, the condition of aquatic enviroment, and oceanographic condition.Keywords: Groupers, Peukan Bada, species composition, community structure

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Molecular Ecological Network Analyses: An Effective Conservation Tool for the Assessment of Biodiversity, Trophic Interactions, and Community Structure

Frontiers in Ecology and Evolution ◽

10.3389/fevo.2020.588430 ◽

2020 ◽

Vol 8 ◽

Author(s):

Jordana M. Meyer ◽

Kevin Leempoel ◽

Gianalberto Losapio ◽

Elizabeth A. Hadly

Keyword(s):

Community Structure ◽

Trophic Interactions ◽

Ecological Network ◽

Network Analyses ◽

Effective Conservation ◽

Molecular Ecological Network

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Community Structure and Co-Occurrence Network Analysis of Bacteria and Fungi in Wheat Fields vs Fruit Orchards

10.21203/rs.3.rs-1142341/v1 ◽

2021 ◽

Author(s):

Xinyu Cui ◽

Huan He ◽

Fengxiao Zhu ◽

Xiaobo Liu ◽

You Ma ◽

...

Keyword(s):

Community Structure ◽

Amplicon Sequencing ◽

Yangtze River Delta ◽

Vital Role ◽

Fungal Communities ◽

Rrna Gene ◽

Network Analyses ◽

Planting Methods ◽

Bacteria And Fungi ◽

Occurrence Patterns

Abstract Soil microorganisms play a vital role in biogeochemical processes and nutrient turnover in agricultural ecosystems. However, the information on how the structure and co-occurrence patterns of microbial communities respond to the change of planting methods is still limited. In this study, a total of 34 soil samples were collected from 17 different fields of two planting types (wheat and orchards) along the Taige Canal in Yangtze River Delta. The distribution and diversity of bacterial and fungal communities in soil were determined using amplicon sequencing targeting the 16S rRNA gene and ITS gene, respectively. The dominated bacteria were Proteobacteria, Acidobacteriota, Actinobacteriota, Chloroflexi, Bacteroidota, and Firmicutes. The relative abundance of Actinobacteriota and Firmicutes was higher in the orchards, while Chloroflexi and Nitrospirota were more abundant in wheat fields. Ascomycota, Mortierellomycota, and Basidiomycota were the predominant fungi in both types of soils. The diversity of bacterial and fungal communities was greater in the wheat fields than in the orchards. The statistical analyses showed that pH was the main factor shaping the community structure. Moreover, high co-occurrence patterns of bacteria and fungi were confirmed in both wheat fields and orchards. Network analyses showed that both the wheat fields and orchards occurred modular structure, which mainly contained nodes of Acidobacteriota, Chloroflexi, Gemmatimonadota, Nitrospirota and Ascomycota. In summary, our work showed the co-occurrence network and the convergence/divergence of microbial community structure in wheat fields and orchards, giving a comprehensive understanding of the microbe-microbe interaction during planting methods changes.

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