scholarly journals Metagenomic Exploration of Bacterial Community Structure of Earthworms’ Gut

2021 ◽  
Author(s):  
Samrendra Singh Thakur ◽  
Azhar Rashid Lone ◽  
Nalini Tiwari ◽  
Subodh Kumar Jain ◽  
Shweta Yadav
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Gut Microbiota ◽  
Bacterial Community Structure ◽  
Alpha Diversity ◽  
Eudrilus Eugeniae ◽  
Phenotypic Analysis ◽  
Perionyx Excavatus ◽  
Gram Negative ◽  
Earthworm Species

Living organisms are naturally bestowed with unique and imitable qualities for maintaining ecological balance and earthworms are no exceptions. These so-called keystone species of terrestrial ecosystems are equipped with wonderful machinery, allowing them to nurture soil beautifully. Earthworm gut represents a potential microbial reservoir, having a complex interdependence with the host. The study aimed to profile bacterial community structure of three earthworm species belonging to two different life forms; Perionyx excavatus and Eudrilus eugeniae (epigeic), Polypheretima elongata (endogeic) respectively. Diversity analysis using 16S amplicon sequencing revealed that the dominant phyla were Proteobacteria (34.17-77.88) followed by Actinobacteria (13.43-35.54%), Firmicutes (1.69-15.45%) and Bacteroidetes (0.51-8.12%). The alpha diversity indices explicit similar gut microbiota of Perionyx excavatus and Eudrilus eugeniae and while higher alpha diversity was recorded in comparison to Polypheretima elongata gut. The taxonomic to the phenotypic annotation of 16S rRNA metagenomes revealed that dominance of Gram-negative bacterial community in all earthworm species while, Polypheretima elongata comprises higher percentage (78%) of Gram-negative bacterial community to Perionyx excavatus (32.3%) and Eudrilus eugeniae (38.3%). The oxygen requirement phenotypic analysis showed that all earthworm species were abundant with aerobic followed by anaerobic bacterial groups. Furthermore, functional metabolism phenotypic analysis revealed that a high abundance of ammonia oxidizers (29.3-80.2%), the gut microbiomes showed the relative abundance of sulphate reducer (22.6-78.7%), nitrite reducer (19.8-73.2%), dehalogenators (12.6-25.1%), illustrating in the role of these microbial communities in various degradation and bioremediation processes. The present study signifies the intrinsic gut microbiota of earthworm species for intensified biodegradation.

scholarly journals Analysis of Microbial Community Structure Around Roots of Stipa Grandis

2021 ◽  
Author(s):  
Ai-Min Zhu ◽  
Guo-Dong Han ◽  
Hai-Li Liu ◽  
Yue-Hua Wang
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Rhizosphere Soil ◽  
Root Zone ◽  
Diversity Index ◽  
Alpha Diversity ◽  
Microbial Structure ◽  
Root Epidermis ◽  
16S Rna

Abstract The root zone microbial structure is particularly complex for plants with rhizosheaths, which may play an important role in the future agricultural sustainable development. However, one of the important reasons for restricting our study of rhizosheath microbial structure is that there is no definite method for rhizosheath separation. The aim of this study was to explore the isolation methods of rhizosheath and the diversity and functional characteristics of microorganisms around the rhizosphere. In this study, we isolated the rhizosheath of Stipa grandis, a dominant species in desert steppe, and the microorganisms in the roots, root epidermis, rhizosheath, rhizosphere soil were extracted and sequenced by 16s RNA and ITS. The bacterial alpha diversity index was in the order rhizosphere soil > rhizosheath > root epidermis > endophytic, and the fungal alpha diversity index was rhizosphere soil and rhizosheath > root epidermis and endophytic. There were significant differences in bacterial community structure between the root epidermis and endophytic, rhizosheath, rhizosphere soil, and the sum of relative abundance of the dominant bacterial populations Actinobacteria and Proteobacteria was 73.9% in the root epidermis. Different from bacterial community structure, the community structure of root epidermis fungi was similar to endophytic, but significantly different from rhizosheath and rhizosphere soil. We suggest that the root epidermis can act as the interface between the host plant root and the external soil environment. This study will provide theoretical and technical guidance for the isolation of plant rhizosheath and the study of microorganisms in it.

scholarly journals 16S rRNA gene amplicon-based metagenomic analysis of bacterial communities in the rhizospheres of selected mangrove species from Mida Creek and Gazi Bay, Kenya

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0248485
Author(s):  
Edith M. Muwawa ◽  
Chinedu C. Obieze ◽  
Huxley M. Makonde ◽  
Joyce M. Jefwa ◽  
James H. P. Kahindi ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Bacterial Community Composition ◽  
Geographical Location ◽  
Alpha Diversity ◽  
Rrna Gene ◽  
Chemical Parameters ◽  
Mangrove Species ◽  
Gazi Bay

Prokaryotic communities play key roles in biogeochemical transformation and cycling of nutrients in the productive mangrove ecosystem. In this study, the vertical distribution of rhizosphere bacteria was evaluated by profiling the bacterial diversity and community structure in the rhizospheres of four mangrove species (Sonneratia alba, Rhizophora mucronata, Ceriops tagal and Avicennia marina) from Mida Creek and Gazi Bay, Kenya, using DNA-metabarcoding. Alpha diversity was not significantly different between sites, but, significantly higher in the rhizospheres of S. alba and R. mucronata in Gazi Bay than in Mida Creek. Chemical parameters of the mangrove sediments significantly correlated inversely with alpha diversity metrics. The bacterial community structure was significantly differentiated by geographical location, mangrove species and sampling depth, however, differences in mangrove species and sediment chemical parameters explained more the variation in bacterial community structure. Proteobacteria (mainly Deltaproteobacteria and Gammaproteobacteria) was the dominant phylum while the families Desulfobacteraceae, Pirellulaceae and Syntrophobacteraceae were dominant in both study sites and across all mangrove species. Constrained redundancy analysis indicated that calcium, potassium, magnesium, electrical conductivity, pH, nitrogen, sodium, carbon and salinity contributed significantly to the species–environment relationship. Predicted functional profiling using PICRUSt2 revealed that pathways for sulfur and carbon metabolism were significantly enriched in Gazi Bay than Mida Creek. Overall, the results indicate that bacterial community composition and their potential function are influenced by mangrove species and a fluctuating influx of nutrients in the mangrove ecosystems of Gazi Bay and Mida Creek.

scholarly journals Divergence in Gut Bacterial Community Structure between Male and Female Stag Beetles Odontolabis fallaciosa (Coleoptera, Lucanidae)

Animals ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 2352
Author(s):  
Xia Wan ◽  
Yu Jiang ◽  
Yuyan Cao ◽  
Binghua Sun ◽  
Xingjia Xiang
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
High Throughput Sequencing ◽  
Alpha Diversity ◽  
Illumina Miseq ◽  
Bacterial Interactions ◽  
Intestinal Bacterial Community ◽  
Males And Females ◽  
Stag Beetles

Odontolabis fallaciosa (Coleoptera: Lucanidae) is a giant and popular stag beetle with striking sexual dimorphism and male trimorphism. However, little is known about their intestinal microbiota, which might play an indispensable role in shaping the health of their hosts. The aim of this study was to investigate the intestinal bacterial community structure between the two sexes and among three male morphs of O. fallaciosa from China using high-throughput sequencing (Illumina MiSeq). The gut bacterial community structure was significantly different between males and females, suggesting that sex appeared to be the crucial factor shaping the intestinal bacterial community. Females had higher bacterial alpha-diversity than males. There was little difference in gut bacterial community structure among the three male morphs. However, compared to medium and small males, large individuals were associated with the higher relative abundance of Firmicutes and Firmicutes/Bacteroides (F/B) ratio, which might contribute to nutritional efficiency. Overall, these results might help to further our understanding of beetle–bacterial interactions of O. fallaciosa between the two sexes, and among the three male morphs.

scholarly journals Gut microbiota relationships to lung function and adult asthma phenotype: a pilot study

2018 ◽  
Vol 5 (1) ◽  
pp. e000324 ◽  
Author(s):  
Lesa Begley ◽  
Siddharth Madapoosi ◽  
Kristopher Opron ◽  
Ogechukwu Ndum ◽  
Alan Baptist ◽  
...  
Keyword(s):  
Community Structure ◽  
Pilot Study ◽  
Lung Function ◽  
Bacterial Community ◽  
Gut Microbiota ◽  
Bacterial Community Structure ◽  
Forced Expiratory Volume ◽  
Asthma Phenotype ◽  
Paired Samples ◽  
Compositional Stability

IntroductionDespite strong evidence that maturation patterns of the gut microbiome in early life influence the risk for childhood asthma, very little is known about gut microbiota patterns in adults with established asthma, and of greater interest relationships to phenotypic features that characterise asthma heterogeneity.MethodsFifty-eight faecal samples from 32 adults with (n=24) and without (n=8) asthma were analysed using 16S ribosomal RNA gene sequencing methods to characterise intestinal bacterial composition. Compositional stability of paired samples was evaluated and features of gut bacterial community structure analysed in relation to extensive clinical characterisation data collected from subjects, who were enrolled in a prospective observational cohort study at the University of Michigan.ResultsDifferences in gut bacterial community structure were associated with aeroallergen sensitisation and lung function as assessed by forced expiratory volume in 1 s (FEV1) %predicted. Associations with FEV1 were consistently observed across independent analytic approaches. k-means clustering of the gut microbiota data in subjects with asthma revealed three different clusters, distinguished most strongly by FEV1 (p<0.05) and trends in differences in other clinical and inflammatory features.ConclusionIn this pilot study of asthmatic and non-asthmatic subjects, significant relationships between gut microbiota composition, aeroallergen sensitisation and lung function were observed. These preliminary findings merit further study in larger cohorts to explore possible mechanistic links to asthma phenotype.

scholarly journals Isolation of Rhizosheath and Analysis of Microbial Community Structure Around Roots of Stipa Grandis

2021 ◽  
Author(s):  
Ai-Min Zhu ◽  
Qian Wu ◽  
Hai-Li Liu ◽  
Hai-lian Sun ◽  
Guo-Dong Han
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Rhizosphere Soil ◽  
Root Zone ◽  
Diversity Index ◽  
Plant Root ◽  
Alpha Diversity ◽  
Microbial Structure ◽  
Root Epidermis

Abstract Background：The root zone microbial structure is particularly complex for plants with rhizosheaths, which may play an important role in the future agricultural sustainable development. However, one of the important reasons for restricting our study of rhizosheath microbial structure is that there is no definite method for rhizosheath separation. The aim of this study was to explore the isolation methods of rhizosheath and the diversity characteristics of microorganisms around the rhizosphere. In this study, we isolated the rhizosheath of Stipa grandis, a dominant species in desert steppe, and the microorganisms in the roots, root epidermis, rhizosheath, rhizosphere soil were extracted and sequenced by 16SrRNA and ITS.Results:The bacterial alpha diversity index was in the order rhizosphere soil > rhizosheath>root epidermis>endophytic, and the fungal alpha diversity index wasrhizosphere soil and rhizosheath> root epidermisand endophytic. There were significant differences in bacterial community structure between the root epidermis and endophytic, rhizosheath, rhizosphere soil. Different from bacterial community structure, the community structure of root epidermis fungi was similar to endophytic, but significantly different from rhizosheath and rhizosphere soil.Our method is feasible for separating plant rhizosheath and root epidermis.Conclusions：We suggest that the root epidermiscan act as the interface between the host plant root and the external soil environment.We will have to re-examine the biological and ecological significance of root sheath and microorganisms in rhizosheath, as well as the mechanism of its close relationship with plant root epidermis.This study will provide theoretical and technical guidance for the isolation of plant rhizosheath and the study of microorganisms in it.

scholarly journals Diet is not the primary driver of bacterial community structure in the gut of litter-feeding cockroaches

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Niclas Lampert ◽  
Aram Mikaelyan ◽  
Andreas Brune
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Gut Microbiota ◽  
Bacterial Community Structure ◽  
Amplicon Sequencing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Feeding Groups ◽  
Reducing Conditions ◽  
Primary Driver

Abstract Background Diet is a major determinant of bacterial community structure in termite guts, but evidence of its importance in the closely related cockroaches is conflicting. Here, we investigated the ecological drivers of the bacterial gut microbiota in cockroaches that feed on lignocellulosic leaf litter. Results The physicochemical conditions determined with microsensors in the guts of Ergaula capucina, Pycnoscelus surinamensis, and Byrsotria rothi were similar to those reported for both wood-feeding and omnivorous cockroaches. All gut compartments were anoxic at the center and showed a slightly acidic to neutral pH and variable but slightly reducing conditions. Hydrogen accumulated only in the crop of B. rothi. High-throughput amplicon sequencing of bacterial 16S rRNA genes documented that community structure in individual gut compartments correlated strongly with the respective microenvironmental conditions. A comparison of the hindgut microbiota of cockroaches and termites from different feeding groups revealed that the vast majority of the core taxa in cockroaches with a lignocellulosic diet were present also in omnivorous cockroaches but absent in wood-feeding higher termites. Conclusion Our results indicate that diet is not the primary driver of bacterial community structure in the gut of wood- and litter-feeding cockroaches. The high similarity to the gut microbiota of omnivorous cockroaches suggests that the dietary components that are actually digested do not differ fundamentally between feeding groups.

Impact of an urban effluent on the bacterial community structure in the Arga River (Spain), with special reference to culturable Gram-negative rods

1999 ◽  
Vol 45 (10) ◽  
pp. 826-832 ◽  
Author(s):  
Marisol Goñi-Urriza ◽  
Michèle Capdepuy ◽  
Nathalie Raymond ◽  
Claudine Quentin ◽  
Pierre Caumette
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Heterotrophic Bacteria ◽  
Sampling Station ◽  
Gram Negative ◽  
Structure Changes ◽  
Sampling Zone ◽  
The Impact ◽  
Urban Effluent

The Arga River is an interesting system in which to study the impact of urban effluent pollution because it receives a single effluent in the form of wastewater discharge from the city of Pamplona. To analyze the extent of this discharge, total bacteria, culturable heterotrophic bacteria, and Gram-negative heterotrophic bacteria were enumerated and 409 isolates of the latter were identified. One sampling station was located upstream from the inflow, while five were located up to 30 km downstream. Bacterial counts increased drastically downstream from the wastewater inflow. Total bacterial numbers decreased along the 30 km downstream, the last station attaining similar values to those recorded upstream from the discharge. However, culturable heterotrophic and Gram-negative heterotrophic bacteria levels generally remained significantly higher within the 30 km zone investigated. Among the 409 isolates identified, Aeromonas spp. were the most frequent both upstream and downstream from the discharge. In contrast, although strains belonging to different genera of Enterobacteriaceae were found in all stations, their occurrence was significantly higher just downstream from the polluted discharge. Acinetobacter spp., which were never found upstream, were detected in all stations below the discharge. Our results clearly show that the bacterial community structure changes definitively downstream from the discharge and that Aeromonas were common throughout the sampling zone. Thus they cannot be considered good indicators of pollution in this setting compared to some genera of Enterobacteriaceae or some species ofAcinetobacter, the distribution of which correlated better with the distance from the wastewater discharge.Key words: Aeromonas, Enterobacteriaceae, sewage, freshwater.

scholarly journals Microbial taxa in dust and excreta associated with the productive performance of commercial meat chicken flocks

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Yugal Raj Bindari ◽  
Robert J. Moore ◽  
Thi Thu Hao Van ◽  
Stephen W. Walkden-Brown ◽  
Priscilla F. Gerber
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Gut Microbiota ◽  
Bacterial Community Structure ◽  
Population Level ◽  
Amplicon Sequencing ◽  
Feed Conversion ◽  
High Performing ◽  
Low Performance ◽  
Feed Conversion Rate

Abstract Background A major focus of research on the gut microbiota of poultry has been to define signatures of a healthy gut and identify microbiota components that correlate with feed conversion. However, there is a high variation in individual gut microbiota profiles and their association with performance. Population level samples such as dust and pooled excreta could be useful to investigate bacterial signatures associated with productivity at the flock-level. This study was designed to investigate the bacterial signatures of high and low-performing commercial meat chicken farms in dust and pooled excreta samples. Poultry house dust and fresh pooled excreta were collected at days 7, 14, 21, 28 and 35 of age from 8 farms of two Australian integrator companies and 389 samples assessed by 16S ribosomal RNA gene amplicon sequencing. The farms were ranked as low (n = 4) or high performers (n = 4) based on feed conversion rate corrected by body weight. Results Permutational analysis of variance based on Bray–Curtis dissimilarities using abundance data for bacterial community structure results showed that company explained the highest variation in the bacterial community structure in excreta (R2 = 0.21, p = 0.001) while age explained the highest variation in the bacterial community structure in dust (R2 = 0.13, p = 0.001). Farm performance explained the least variation in the bacterial community structure in both dust (R2 = 0.03, p = 0.001) and excreta (R2 = 0.01, p = 0.001) samples. However, specific bacterial taxa were found to be associated with high and low performance in both dust and excreta. The bacteria taxa associated with high-performing farms in dust or excreta found in this study were Enterococcus and Candidatus Arthromitus whereas bacterial taxa associated with low-performing farms included Nocardia, Lapillococcus, Brachybacterium, Ruania, Dietzia, Brevibacterium, Jeotgalicoccus, Corynebacterium and Aerococcus. Conclusions Dust and excreta could be useful for investigating bacterial signatures associated with high and low performance in commercial poultry farms. Further studies on a larger number of farms are needed to determine if the bacterial signatures found in this study are reproducible.

scholarly journals Divergence in Gut Bacterial Community Among Life Stages of the Rainbow Stag Beetle Phalacrognathus muelleri (Coleptera: Lucanidae)

Insects ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 719
Author(s):  
Miaomiao Wang ◽  
Xingjia Xiang ◽  
Xia Wan
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Community Structure ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Alpha Diversity ◽  
Illumina Miseq ◽  
Life Stages ◽  
Early Instar

Although stag beetles are popular saprophytic insects, there are few studies about their gut bacterial community. This study focused on the gut bacterial community structure of the rainbow stag beetle (i.e., Phalacrognathus muelleri) in its larvae (three instars) and adult stages, using high throughput sequencing (Illumina Miseq). Our aim was to compare the gut bacterial community structure among different life stages. The results revealed that bacterial alpha diversity increased from the 1st instar to the 3rd instar larvae. Adults showed the lowest gut bacterial alpha diversity. Bacterial community composition was significantly different between larvae and adults (p = 0.001), and 1st instar larvae (early instar) had significant differences with the 2nd (p= 0.007) and 3rd (p = 0.001) instar larvae (final instar). However, there was little difference in the bacterial community composition between the 2nd and 3rd instar larvae (p = 0.059). Our study demonstrated dramatic shifts in gut bacterial community structure between larvae and adults. Larvae fed on decaying wood and adults fed on beetle jelly, suggesting that diet is a crucial factor shaping the gut bacterial community structure. There were significant differences in bacterial community structure between early instar and final instars larvae, suggesting that certain life stages are associated with a defined gut bacterial community.

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