scholarly journals Community structure follows simple assembly rules in microbial microcosms

2016 ◽  
Author(s):  
Jonathan Friedman ◽  
Logan M. Higgins ◽  
Jeff Gore
Keyword(s):  
Community Structure ◽  
Predictive Power ◽  
Bacterial Species ◽  
Additional Information ◽  
Interacting Species ◽  
Assembly Rule ◽  
Simple Assembly ◽  
Synthetic Microbial Communities ◽  
Tremendous Impact ◽  
Entire Planet

IntroductionMicrobes typically form diverse communities of interacting species, whose activities have tremendous impact on the plants, animals, and humans they associate with1–3, as well as on the biogeochemistry of the entire planet4. The ability to predict the structure of these complex communities is crucial to understanding, managing, and utilizing them5. Here, we propose a simple, qualitative assembly rule that predicts community structure from the outcomes of competitions between small sets of species, and experimentally assess its predictive power using synthetic microbial communities. The rule's accuracy was evaluated by competing combinations of up to eight soil bacterial species, and comparing the experimentally observed outcomes to the predicted ones. Nearly all competitions resulted in a unique, stable community, whose composition was independent of the initial species fractions. Survival in three-species competitions was predicted by the pairwise outcomes with an accuracy of ~90%. Obtaining a similar level of accuracy in competitions between sets of seven or all eight species required incorporating additional information regarding the outcomes of the three-species competitions. Our results demonstrate experimentally the ability of a simple bottom-up approach to predict community structure. Such an approach is key for anticipating the response of communities to changing environments, designing interventions to steer existing communities to more desirable states, and, ultimately, rationally designing communities de novo6,7.

scholarly journals Comparison of rhizosphere soil microbial diversity of different introduced alfalfa varieties

2020 ◽  
Author(s):  
Chunhui Ma ◽  
Jiangjiao Qi ◽  
Xue Yu ◽  
Lihe Su ◽  
Tingting He ◽  
...  
Keyword(s):  
Community Structure ◽  
Fungal Community ◽  
High Throughput Sequencing ◽  
Bacterial Species ◽  
Chemical Properties ◽  
Animal Husbandry ◽  
Desert Soil ◽  
High Yield ◽  
Soil Microbial Diversity ◽  
Fungal Community Structure

Abstract Alfalfa (Medicago sativa L.) is an important forage legume in farming and animal husbandry systems. In this study, MiSeq high-throughput sequencing was applied to assess the relationship between bacterial and fungal community structures and alfalfa growth characteristics and soil physical and chemical properties induced by different cultivars alfalfa (Victoria, Kangsai, Aohan) in the grey desert soil. The results showed that the diversity of bacterial and fungal in Victoria was higher, and the bacterial diversity was significantly lower for alfalfa with Aohan than for the others, and the fungal diversity was lower for alfalfa with Kangsai than for the others. Heatmap showed that total nitrogen, fresh weight, pH and organic have significantly affect fungal community structure, whereas pH and organic carbon also significant effects on bacterial community structure. LefSe analysis showed that the growth adaptability of introduced alfalfa is mainly related to fungal and bacterial species, and the beneficial microorganisms with significant differences and relative high abundance are significantly enriched in Victoria. Pathogens with high relative abundance are mainly concentrated in Aohan alfalfa soil. Based on our findings, Victoria is the high-yield alfalfa suitable for planting in gray desert soil, while planting Kangsai and Aohan alfalfa needs probiotic for adjuvant.

Characterization of bacterial community structure dynamics in a rat burn wound model using 16S rRNA gene sequencing

2022 ◽  
Author(s):  
Chen Zheng-li ◽  
Peng Yu ◽  
Wu Guo-sheng ◽  
Hong Xu-Dong ◽  
Fan Hao ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Community Structure ◽  
Bacterial Species ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Sprague Dawley ◽  
Rrna Gene Sequencing

Abstract Burns destroy the skin barrier and alter the resident bacterial community, thereby facilitating bacterial infection. To treat a wound infection, it is necessary to understand the changes in the wound bacterial community structure. However, traditional bacterial cultures allow the identification of only readily growing or purposely cultured bacterial species and lack the capacity to detect changes in the bacterial community. In this study, 16S rRNA gene sequencing was used to detect alterations in the bacterial community structure in deep partial-thickness burn wounds on the back of Sprague-Dawley rats. These results were then compared with those obtained from the bacterial culture. Bacterial samples were collected prior to wounding and 1, 7, 14, and 21 days after wounding. The 16S rRNA gene sequence analysis showed that the number of resident bacterial species decreased after the burn. Both resident bacterial richness and diversity, which were significantly reduced after the burn, recovered following wound healing. The dominant resident strains also changed, but the inhibition of bacterial community structure was in a non-volatile equilibrium state, even in the early stage after healing. Furthermore, the correlation between wound and environmental bacteria increased with the occurrence of burns. Hence, the 16S rRNA gene sequence analysis reflected the bacterial condition of the wounds better than the bacterial culture. 16S rRNA sequencing in the Sprague-Dawley rat burn model can provide more information for the prevention and treatment of burn infections in clinical settings and promote further development in this field.

scholarly journals Effects of tobacco–peanut relay intercropping on soil bacteria community structure

2019 ◽  
Vol 69 (13) ◽  
pp. 1531-1536 ◽  
Author(s):  
Lin Gao ◽  
Xin-min Liu ◽  
Yong-mei Du ◽  
Hao Zong ◽  
Guo-ming Shen
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Soil Bacteria ◽  
Pathogenic Bacteria ◽  
Bacterial Species ◽  
Continuous Cropping ◽  
Soil Microbial ◽  
Relay Intercropping ◽  
Bacteria Community Structure

Abstract Purpose A reasonable cultivation pattern is beneficial to maintain soil microbial activity and optimize the structure of the soil microbial community. To determine the effect of tobacco−peanut (Nicotiana tabacum−Arachis hypogaea) relay intercropping on the microbial community structure in soil, we compared the effects of relay intercropping and continuous cropping on the soil bacteria community structure. Methods We collected soil samples from three different cropping patterns and analyzed microbial community structure and diversity using high-throughput sequencing technology. Result The number of operational taxonomic units (OTU) for bacterial species in the soil was maximal under continuous peanut cropping. At the phylum level, the main bacteria identified in soil were Proteobacteria, Actinobacteria, and Acidobacteria, which accounted for approximately 70% of the total. The proportions of Actinobacteria and Firmicutes increased, whereas the proportion of Proteobacteria decreased in soil with tobacco–peanut relay intercropping. Moreover, the proportions of Firmicutes and Proteobacteria among the soil bacteria further shifted over time with tobacco–peanut relay intercropping. At the genus level, the proportions of Bacillus and Lactococcus increased in soil with tobacco–peanut relay intercropping. Conclusion The community structure of soil bacteria differed considerably with tobacco–peanut relay intercropping from that detected under peanut continuous cropping, and the proportions of beneficial bacteria (the phyla Actinobacteria and Firmicutes, and the genera Bacillus and Lactococcus) increased while the proportion of potentially pathogenic bacteria (the genera Variibacter and Burkholderia) decreased. These results provide a basis for adopting tobacco–peanut relay intercropping to improve soil ecology and microorganisms, while making better use of limited cultivable land.

scholarly journals Characterization of the Vaginal DNA Virome in Health and Dysbiosis

Viruses ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 1143 ◽  
Author(s):  
Rasmus Riemer Jakobsen ◽  
Thor Haahr ◽  
Peter Humaidan ◽  
Jørgen Skov Jensen ◽  
Witold Piotr Kot ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Bacterial Species ◽  
Metagenomic Sequencing ◽  
Nugent Score ◽  
Double Stranded Dna ◽  
Viral Community ◽  
Atopobium Vaginae

Bacterial vaginosis (BV) is characterized by a reduction in Lactobacillus (L.) spp. abundance and increased abundance of facultative anaerobes, such as Gardnerella spp. BV aetiology is not fully understood; however, bacteriophages could play a pivotal role in the perturbation of the vaginal bacterial community. We investigated the vaginal viral community, including bacteriophages and the association to the bacterial community and BV-status. Vaginal samples from 48 patients undergoing IVF treatment for non-female factor infertility were subjected to metagenomic sequencing of purified virus-like particles. The vaginal viral community was characterized and correlated with the BV-status by Nugent score, bacterial community, structure, and the presence of key vaginal bacterial species. The majority of identified vaginal viruses belonged to the class of double-stranded DNA bacteriophages, with eukaryotic viruses constituting 4% of the total reads. Clear links between the viral community composition and BV (q = 0.006, R = 0.26) as well as the presence of L. crispatus (q = 0.001, R = 0.43), L. iners, Gardnerella spp., and Atopobium vaginae were found (q < 0.002, R > 0.15). The eukaryotic viral community also correlated with BV-status (q = 0.018, R = 0.20). In conclusion, the vaginal virome was clearly linked with bacterial community structure and BV-status.

scholarly journals Analysis of Post-Mortem Changes in Human Microbiome

2021 ◽  
Vol 6 (1) ◽  
pp. 319-326
Author(s):  
A. M. Pohorielova ◽  
◽  
I. Ye. Sokolova ◽  
V. G. Gavrilyuk ◽  
K. O. Vinogradova ◽  
...  
Keyword(s):  
Causes Of Death ◽  
Bacterial Species ◽  
Human Microbiome ◽  
Post Mortem ◽  
Salmonella Spp ◽  
Additional Information ◽  
The Third ◽  
National University ◽  
Statistical Identification ◽  
Staphylococcus Spp

The article presents the results of the thanatomicrobiome study from 18 corpses. Biomaterial for the study was selected in the Department of forensic examination of corpses in "Dnipropetrovsk Regional Bureau of Forensic Medicine" of the Dnipropetrovsk Regional Council during September 2020. Microbiological investigation was conducted at the Department of Microbiology, Virology and Biotechnology of Oles Honchar Dnipro National University. The purpose of the study was to determine the composition of the human thanatomicrobiome and its characteristic marker microorganisms for using it in forensics. Therefore, the task of this research was to study the characteristics of the postmortem microflora depending on age, sex, causes of death, post-mortem time of objects. Material and methods. To solve the assigned tasks such methods were used: microbiological, biochemical, physicochemical, statistical. Identification of microorganisms was conducted with using of selective and differential-diagnostic nutrient medium. Results and discussion. Among the isolated microorganisms in the thanatomicrobiome, the most common were represented by bacteria of genera Staphylococcus, Streptococcus, Enterococcus and family Enterobacteriaceae. Determining of thanatomicrobiome characteristics depending on sex was shown that the highest frequency of isolation for most bacterial species was found in men. The highest frequency of detection of microorganisms was observed on the first day after death. Staphylococcus spp. and Streptococcus spp. were presented in the postmortem microflora during all three days of observation, but frequency of their detection after 48 hours was significantly reduced. Salmonella spp. and Pseudomonas spp. were detected in the thanatomicrobiome only on the third day after death. In the study of the dependence of the microbiota on the causes of death, it was found that the frequency of Streptococcus spp. was higher in subjects who died from hanging, and bacteria of the genera Staphylococcus, Enterococcus, and Klebsiella were predominantly isolated from those who died of cardiovascular disorders. Bacteria of genera Staphylococcus, Streptococcus, Enterococcus, which together make up the vast majority of microorganisms was 64% in the oral cavity and 82% in the armpits should be considered as biomarkers of thanatomicrobiome. An indicative biomarker is also the increase of certain species of enterobacteria in the process of corpses destruction. Yeast and clostridia were specific markers of oral thanatomicrobiome. Conclusion. The composition of the thanatomicrobiome and its features may provide additional information about the conditions of death

scholarly journals A Model for Traffic Accidents Prediction Based on Driver Personality Traits Assessment

2017 ◽  
Vol 29 (6) ◽  
pp. 631-642 ◽  
Author(s):  
Marjana Čubranić-Dobrodolac ◽  
Krsto Lipovac ◽  
Svetlana Čičević ◽  
Boris Antić
Keyword(s):  
Personality Traits ◽  
Structural Equation ◽  
Traffic Accidents ◽  
Predictive Power ◽  
Correlation Coefficients ◽  
Binary Logistic Regression ◽  
Driving Ability ◽  
Hierarchical Regression ◽  
Driver Behaviour ◽  
Additional Information

The model proposed in this paper uses four psychological instruments for assessing driver behaviour and personality traits aiming to find a relationship between the considered constructs and the occurrence of traffic accidents. A Barratt Impulsiveness Scale (BIS-11) was used for the assessment of impulsivity, Aggressive Driving Behaviour Questionnaire (ADBQ) for assessing the aggressiveness while driving, Manchester Driver Attitude Questionnaire (DAQ) and the Questionnaire for self-assessment of driving ability. Besides these instruments, the participants filled out an extensive demographic survey. Within the statistical analysis, in addition to the descriptive indicators, correlation coefficients were calculated and four hierarchical regression analyses were performed to determine the predictive power of personality traits on the occurrence of traffic accidents. Further, to confirm the results and to obtain additional information about the relationship between the considered variables, the structural equation modelling and binary logistic regression have been implemented. A sample of this research covered 305 drivers, of which there were 100 bus drivers and 102 truck drivers, as well as 103 drivers of privately owned vehicles. The results indicate that BIS-11 and ADBQ questionnaires show the best predictive power which means that impulsivity and aggressiveness as personality traits have the greatest influence on the occurrence of traffic accidents. This research could be useful in many fields, such as the design of selection procedures for professional drivers, development of programs for the prevention of traffic accidents and violations of law, rehabilitation of drivers who have been deprived of the driving license, etc.

scholarly journals Comparison of carcinogenicity predictions by the Oncologic expert system with NTP 2-year rodent study tumorigenicity results

2018 ◽  
Vol 2 ◽  
pp. 239784731877112
Author(s):  
Carr J Smith ◽  
Thomas A Perfetti
Keyword(s):  
Expert System ◽  
Liver Cancer ◽  
Predictive Power ◽  
Historical Data ◽  
Liver Tumors ◽  
Additional Information ◽  
Ordinal Ranking ◽  
National Toxicology Program ◽  
Toxicological Research ◽  
Actual Formation

The degree of correlation between tumors predicted by OncoLogic™ (Oncologic) and the actual formation of tumors as observed in the National Toxicology Program (NTP) 2-year rodent studies is lower for “justification reports” that incorporate historical data than for “data reports” that do not. The correlation between the ordinal ranking of the observed carcinogenicity of parent NTP chemicals and the predicted “level of carcinogenicity concern” from the justification reports obtained from Oncologic is poor ( r = 0.56). Similarly, the correlation between the ordinal ranking of the carcinogenicity of metabolites from parent NTP chemicals and the predicted “level of carcinogenicity concern” from the justification report obtained from Oncologic is also poor ( r = 0.43). In contrast, the correlation between the ordinal ranking of the observed carcinogenicity of parent NTP chemicals and the predicted level of carcinogenicity concern from the data reports obtained from Oncologic is comparatively better ( r = 0.75). The correlation between the ordinal ranking of the carcinogenicity of metabolites from parent NTP chemicals and the predicted “level of carcinogenicity concern” from the data reports generated from Oncologic is also comparatively good ( r = 0.68). The level of correlation between the ordinal tumorigenicity ranks of parent chemicals and between the ordinal tumorigenicity ranks of chemicals reported to induce liver tumors in the National Center for Toxicological Research liver cancer database was also investigated. There was a higher degree of correlation seen for Oncologic “data reports” as compared with Oncologic “justification reports.” Incorporation of additional information via “justification reports” weakens the predictive power of Oncologic.

scholarly journals Worldwide exploration of the microbiome harbored by the cnidarian model,Exaiptasia pallida(Agassiz in Verrill, 1864) indicates a lack of bacterial association specificity at a lower taxonomic rank

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3235 ◽  
Author(s):  
Tanya Brown ◽  
Christopher Otero ◽  
Alejandro Grajales ◽  
Estefania Rodriguez ◽  
Mauricio Rodriguez-Lanetty
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Bacterial Community ◽  
Bacterial Species ◽  
Sea Anemone ◽  
Microbial Consortia ◽  
Rrna Gene ◽  
Core Microbiome ◽  
Wide Range ◽  
Exaiptasia Pallida

Examination of host-microbe interactions in early diverging metazoans, such as cnidarians, is of great interest from an evolutionary perspective to understand how host-microbial consortia have evolved. To address this problem, we analyzed whether the bacterial community associated with the cosmopolitan and model sea anemoneExaiptasia pallidashows specific patterns across worldwide populations ranging from the Caribbean Sea, and the Atlantic and Pacific oceans. By comparing sequences of the V1–V3 hypervariable regions of the bacterial 16S rRNA gene, we revealed that anemones host a complex and diverse microbial community. When examined at the phylum level, bacterial diversity and abundance associated withE. pallidaare broadly conserved across geographic space with samples, containing largelyProteobacteriaandBacteroides.However, the species-level makeup within these phyla differs drastically across space suggesting a high-level core microbiome with local adaptation of the constituents. Indeed, no bacterial OTU was ubiquitously found in all anemones samples. We also revealed changes in the microbial community structure after rearing anemone specimens in captivity within a period of four months. Furthermore, the variation in bacterial community assemblages across geographical locations did not correlate with the composition of microalgalSymbiodiniumsymbionts. Our findings contrast with the postulation that cnidarian hosts might actively select and maintain species-specific microbial communities that could have resulted from an intimate co-evolution process. The fact thatE. pallidais likely an introduced species in most sampled localities suggests that this microbial turnover is a relatively rapid process. Our findings suggest that environmental settings, not host specificity, seem to dictate bacterial community structure associated with this sea anemone. More than maintaining a specific composition of bacterial species some cnidarians associate with a wide range of bacterial species as long as they provide the same physiological benefits towards the maintenance of a healthy host. The examination of the previously uncharacterized bacterial community associated with the cnidarian sea anemone modelE. pallidais the first global-scale study of its kind.

scholarly journals Long-Term Combined Effects of Crude Oil and Dispersant on Sediment Bacterial Community

2020 ◽  
Vol 9 (1) ◽  
pp. 259-263
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Crude Oil ◽  
Bacterial Community Structure ◽  
Oil Spills ◽  
Bacterial Species ◽  
Combined Effects ◽  
Set Up ◽  
Sediment Bacterial Community

To better understand long-term combined effects of crude oil and dispersant on bacterial community, sediments microcosms were set up in triplicates and treated with dispersant (Corexit 9500A), crude oil, and Corexit 9500A plus crude oil. After 60 days exposure, there was a significant change in the bacterial community structure in all treatments. The shift in the bacterial community structure in Corexit 9500A plus crude oil treatment was considerably different from those by either Corexit 9500A or crude oil. DNA sequence analysis showed that Hydrocarboniphaga effuse, Parvibaculum lavamentivorans,and Alicyclobacillus ferrooxydans were the major bacterial species in crude oil treatment. Pandoraea thiooxydans, Janthinobacterium sp. and Hyphomicrobium nitrativorans were the most dominant species in Corexit 9500A treatment. The species Janthinobacterium sp., Parvibaculum lavamentivorans, and Dyella sp. were enriched in Corexit 9500A plus crude oil treatment. The majority of the detected species were hydrocarbons degraders. The study showed that Corexit 9500A addition enhanced the biodegradation rate by increasing the diversity and richness of hydrocarbons degrading species. Corexit A9500 application should be considered during crude oil spills to evaluate environmental impacts.

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