Microbiomes in Suspended Soils of Vascular Epiphytes Differ from Terrestrial Soil Microbiomes and from Each Other

Microbial biodiversity parameters for tropical rainforests remain poorly understood. Whilst the soil microbiome accounts up to 95% of the total diversity of microorganisms in terrestrial ecosystems, the microbiome of suspended soils formed by vascular epiphytes remains completely unexplored. Samples of ground and suspended soils were collected in Cat Tien National Park, southern Vietnam. DNA extraction and sequencing were performed, and libraries of 16s rDNA gene sequences were analyzed. Alpha diversity indices of the microorganisms were the highest in the forest ground soil. In general, the microbiological diversity of all the soil types was found to be similar at the phylum level. Taxonomic composition of the bacterial communities in the suspended soils of plants from the same species are not closer than the taxonomic compositions of the communities in the suspended soils of different plant species. However, the beta diversity analysis revealed significant differences in the movement of mineral elements in terrestrial versus suspended soils. Our data showed that the suspended soils associated with vascular epiphytes were a depository of unique microbiological biodiversity. A contributing factor was the presence of large amounts of organic matter in the suspended soils—deposits collected by the epiphytes—which would have been degraded by termites if it had reached the ground. Further, the nutrient content of the suspended soils was prime for soil respiration activity and taxonomic microbial community biodiversity.

Download Full-text

Effects of Long-term Cotton Continuous Cropping on Soil Microbiome

Scientific Reports ◽

10.1038/s41598-019-54771-1 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 4

Author(s):

Hui Xi ◽

Jili Shen ◽

Zheng Qu ◽

Dingyi Yang ◽

Shiming Liu ◽

...

Keyword(s):

Severe Disease ◽

Soil Microbial Communities ◽

Alpha Diversity ◽

Taxonomic Composition ◽

Soil Microbiome ◽

Continuous Cropping ◽

Bacterial Phyla ◽

Soil Microbial ◽

Microbial Groups

AbstractVerticillium wilt is a severe disease of cotton crops in Xinjiang and affecting yields and quality, due to the continuous cotton cropping in the past decades. The relationship between continuous cropping and the changes induced on soil microbiome remains unclear to date. In this study, the culture types of 15 isolates from Bole (5F), Kuitun (7F), and Shihezi (8F) of north Xinjiang were sclerotium type. Only isolates from field 5F belonged to nondefoliating pathotype, the others belonged to defoliating pathotype. The isolates showed pathogenicity differentiation in cotton. Fungal and bacterial communities in soils had some difference in alpha-diversity, relative abundance, structure and taxonomic composition, but microbial groups showed similarity in the same habitat, despite different sampling sites. The fungal phyla Ascomycota, and the bacterial phyla Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria and Gemmatimonadetes were strongly enriched. Verticillium abundance was significantly and positively correlated with AN, but negatively correlated with soil OM, AK and pH. Moreover, Verticillium was correlated in abundances with 5 fungal and 6 bacterial genera. Overall, we demonstrate that soil microbiome communities have similar responses to long-term continuous cotton cropping, providing new insights into the effects of continuous cotton cropping on soil microbial communities.

Download Full-text

Diversity and community structure of moss- and lichen-dwelling tardigrades (Tardigrada) along an altitudinal gradient in Cuba

Animal Biology ◽

10.1163/15707563-bja10055 ◽

2021 ◽

pp. 1-18

Author(s):

Rogelio Roberto Muñoz-Li ◽

Abdiel Jover Capote

Keyword(s):

Community Structure ◽

Community Organization ◽

Alpha Diversity ◽

Elevational Gradient ◽

Diversity Indices ◽

Taxonomic Composition ◽

Factors Affecting ◽

Lower Elevation ◽

Terrestrial Water ◽

Santiago De Cuba

Abstract Elevation and anthropopression are important factors affecting terrestrial water bear dynamics. In the present study, we characterize the taxonomic composition, diversity, and community structure of tardigrades along an elevational gradient with different anthropopression in Alturas de Boniato, Santiago de Cuba. Samples were collected in four sampling sites and all tardigrades were extracted. Alpha diversity indices were calculated. Hierarchical community organization was determined and variation among sampling sites was calculated using the Jaccard index for beta diversity. Some variables that influenced composition and taxon diversity were also evaluated. A total of 413 tardigrades belonging to seven taxa and five eggs were found. The most abundant taxa were Paramacrobiotus sp., Macrobiotus sp. and Milnesium sp. 1. Differences between sampling sites were largely due to turnover, especially at the higher-elevation sites. Nesting characterized the lower-elevation sites. The variables that had the greatest influence on species composition were anthropopression and a mixture of various macro- and microenvironmental variables.

Download Full-text

Ranking the Biases: The Choice of OTUs vs. ASVs in 16S rRNA Amplicon Data Analysis Has Stronger Effects On Diversity Measures Than Rarefaction and Similarity Threshold

10.21203/rs.3.rs-764430/v1 ◽

2021 ◽

Author(s):

Marlène Chiarello ◽

Mark McCauley ◽

Sébastien Villéger ◽

Colin R Jackson

Keyword(s):

16S Rrna ◽

Beta Diversity ◽

Alpha Diversity ◽

Diversity Indices ◽

Taxonomic Composition ◽

Shannon Index ◽

Minimal Impact ◽

Alpha And Beta Diversity ◽

Methodological Choices ◽

Similarity Threshold

Abstract BackgroundAdvances in the analysis of amplicon sequence datasets have introduced a methodological shift in how research teams investigate microbial biodiversity, away from the classification and downstream analyses of traditional operational taxonomic units (OTUs), and towards the usage of amplicon sequence variants (ASVs). While ASVs have several inherent properties that make them desirable compared to OTUs, questions remain as to the influence that these pipelines have on the ecological patterns being assessed, especially when compared to other methodological choices made when processing data (e.g. rarefaction) and computing diversity indices. ResultsWe compared the respective influences of using ASVs vs. OTU-based pipelines, rarefaction of the community table, and OTU similarity threshold (97% vs. 99%) on the ecological signals detected in freshwater invertebrate and environmental (sediment, seston) 16S rRNA data sets, determining the effects on alpha diversity, beta diversity and taxonomic composition. While the choice of OTU vs. ASV pipeline significantly influenced unweighted alpha and beta diversities and changed the ecological signal detected, weighted indices such as the Shannon index, Bray-Curtis dissimilarity, and weighted Unifrac scores were not impacted by the pipeline followed. By comparison, OTU threshold and rarefaction had a minimal impact effect on all measurements, although rarefaction improved overall signals, especially in OTU-based datasets. The identification of major classes and genera identified revealed significant discrepancies across methodologies. ConclusionWe provide a list of recommendations for the analysis of 16S rRNA amplicon data. We notably recommend the use of ASVs when analyzing alpha-diversity patterns, especially in species-rich or environmental samples. Abundance weighted alpha- and beta-diversity indices should also be preferred compared to ones based on the presence-absence of biological units.

Download Full-text

Multiple bacteria associated with the more dysbiotic genitourinary microbiomes in patients with type 2 diabetes mellitus

Scientific Reports ◽

10.1038/s41598-021-81507-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Hua Zha ◽

Fengping Liu ◽

Zongxin Ling ◽

Kevin Chang ◽

Jiezuan Yang ◽

...

Keyword(s):

Diabetes Mellitus ◽

Type 2 Diabetes ◽

Type 2 Diabetes Mellitus ◽

Alpha Diversity ◽

Amplicon Sequencing ◽

Diversity Indices ◽

Vital Role ◽

Rrna Gene ◽

Beta Glucosidase

AbstractType 2 diabetes mellitus (T2DM) influences the human health and can cause significant illnesses. The genitourinary microbiome profiles in the T2DM patients remain poorly understood. In the current study, a series of bioinformatic and statistical analyses were carried out to determine the multiple bacteria associated with the more dysbiotic genitourinary microbiomes (i.e., those with lower dysbiosis ratio) in T2DM patients, which were sequenced by Illumina-based 16S rRNA gene amplicon sequencing. All the genitourinary microbiomes from 70 patients with T2DM were clustered into three clusters of microbiome profiles, i.e., Cluster_1_T2DM, Cluster_2_T2DM and Cluster_3_T2DM, with Cluster_3_T2DM at the most dysbiotic genitourinary microbial status. The three clustered T2DM microbiomes were determined with different levels of alpha diversity indices, and driven by distinct urinalysis variables. OTU12_Clostridiales and OTU28_Oscillospira were likely to drive the T2DM microbiomes to more dysbiotic status, while OTU34_Finegoldia could play a vital role in maintaining the least dysbiotic T2DM microbiome (i.e., Cluster_1_T2DM). The functional metabolites K08300_ribonuclease E, K01223_6-phospho-beta-glucosidase and K00029_malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) were most associated with Cluster_1_T2DM, Cluster_2_T2DM and Cluster_3_T2DM, respectively. The characteristics and multiple bacteria associated with the more dysbiotic genitourinary microbiomes in T2DM patients may help with the better diagnosis and management of genitourinary dysbiosis in T2DM patients.

Download Full-text

Altered Gut Microbiota in Irritable Bowel Syndrome and Its Association with Food Components

Journal of Personalized Medicine ◽

10.3390/jpm11010035 ◽

2021 ◽

Vol 11 (1) ◽

pp. 35

Author(s):

Zahra A. Barandouzi ◽

Joochul Lee ◽

Kendra Maas ◽

Angela R. Starkweather ◽

Xiaomei S. Cong

Keyword(s):

Irritable Bowel Syndrome ◽

Gut Microbiota ◽

Alpha Diversity ◽

Diversity Indices ◽

Cross Sectional Study ◽

Caffeine Intake ◽

Caffeine Consumption ◽

Cross Sectional ◽

Food Components ◽

Irritable Bowel

The interplay between diet and gut microbiota has gained interest as a potential contributor in pathophysiology of irritable bowel syndrome (IBS). The purpose of this study was to compare food components and gut microbiota patterns between IBS patients and healthy controls (HC) as well as to explore the associations of food components and microbiota profiles. A cross-sectional study was conducted with 80 young adults with IBS and 21 HC recruited. The food frequency questionnaire was used to measure food components. Fecal samples were collected and profiled by 16S rRNA Illumina sequencing. Food components were similar in both IBS and HC groups, except in caffeine consumption. Higher alpha diversity indices and altered gut microbiota were observed in IBS compared to the HC. A negative correlation existed between total observed species and caffeine intake in the HC, and a positive correlation between alpha diversity indices and dietary fiber in the IBS group. Higher alpha diversity and gut microbiota alteration were found in IBS people who consumed caffeine more than 400 mg/d. Moreover, high microbial diversity and alteration of gut microbiota composition in IBS people with high caffeine consumption may be a clue toward the effects of caffeine on the gut microbiome pattern, which warrants further study.

Download Full-text

Strongyloides stercoralis Infestation in a Child: How a Nematode Can Affect Gut Microbiota

International Journal of Molecular Sciences ◽

10.3390/ijms22042131 ◽

2021 ◽

Vol 22 (4) ◽

pp. 2131

Author(s):

Stefania Pane ◽

Anna Sacco ◽

Andrea Iorio ◽

Lorenza Romani ◽

Lorenza Putignani

Keyword(s):

Gut Microbiota ◽

Bacterial Species ◽

Alpha Diversity ◽

Strongyloides Stercoralis ◽

Pulmonary Involvement ◽

Diversity Indices ◽

Parasite Infection ◽

Intestinal Nematode ◽

Immune Mediated ◽

Stool Samples

Background: Strongyloidiasis is a neglected tropical disease caused by the intestinal nematode Strongyloides stercoralis and characterized by gastrointestinal and pulmonary involvement. We report a pediatric case of strongyloidiasis to underline the response of the host microbiota to the perturbation induced by the nematode. Methods: We performed a 16S rRNA-metagenomic analysis of the gut microbiota of a 7-year-old female during and after S. stercolaris infection, investigating three time-point of stool samples’ ecology: T0- during parasite infection, T1- a month after parasite infection, and T2- two months after parasite infection. Targeted-metagenomics were used to investigate ecology and to predict the functional pathways of the gut microbiota. Results: an increase in the alpha-diversity indices in T0-T1 samples was observed compared to T2 and healthy controls (CTRLs). Beta-diversity analysis showed a shift in the relative abundance of specific gut bacterial species from T0 to T2 samples. Moreover, the functional prediction of the targeted-metagenomics profiles suggested an enrichment of microbial glycan and carbohydrate metabolisms in the T0 sample compared with CTRLs. Conclusions: The herein report reinforces the literature suggestion of a putative direct or immune-mediated ability of S. stercolaris to promote the increase in bacterial diversity.

Download Full-text

Phytoplankton assemblages in Lake Orta: has functional structure recovered in one of the largest acidic lakes in the world?

Journal of Limnology ◽

10.4081/jlimnol.2016.1381 ◽

2016 ◽

Vol 75 (s2) ◽

Cited By ~ 2

Author(s):

Giuseppe Morabito

Keyword(s):

Functional Groups ◽

Diversity Indices ◽

Taxonomic Composition ◽

Ecological Niches ◽

Phytoplankton Species ◽

Phytoplankton Assemblages ◽

Lake Maggiore ◽

Acidic Lakes ◽

Physical Features ◽

She Analysis

Lake Orta (Northern Italy) became one of the world’s largest acidic lakes, following industrial pollution, beginning in the late 1920s. Prior to pollution, Lake Orta supported a rich and diversified phytoplankton community dominated by diatoms, cyanobacteria and dinoflagellates. Their taxonomic composition was comparable to that of the nearby Lake Maggiore, which provides a useful reference comparison. After pollution, Lake Orta was so acidic and contaminated with trace metals that only a few tolerant phytoplankton species persisted, supplemented by sudden and short living outbursts of occasional colonists. The lake was limed in 1989-1990. This has permitted the gradual recovery of its chemistry and biology, and many phytoplankton species that inhabit Lake Maggiore are now re-appearing in Lake Orta. I tested the two hypotheses that Lakes Orta and Maggiore would now have a similar phytoplankton taxonomic assemblages, and similar diversity of functional groups given their similar morphometry, physical features and trophic states. The two hypotheses were tested by comparing the phytoplankton assemblages of lakes Maggiore and Orta for the first 10 years after liming, i.e. 1990 to 2001. Phytoplankton was classified according the Reynolds' Morpho Functional Groups and five diversity indices were calculated (S, number of units; H, Shannon-Wiener; E, evenness; D, dominance; J, equitability). SHE analysis (an analysis of diversity changes based on the relationship among species richness (S), H Index (H) and evenness (E)) was also carried out, in order to compare the long term trend of both functional groups and taxa biodiversity. Both taxonomic and the functional composition differed in the two lakes, likely because chemical quality have played a role in taxaselection. Moreover, it was quite clear that, during the first post-liming decade, Lake Orta’s phytoplankton was characterized by low diversity and evenness and by marked year-to-year fluctuations. However, SHE analysis showed that the colonization rate was higher in Lake Orta than in Lake Maggiore, and that the environmental modifications caused by the liming were opening new ecological niches, allowing some colonists to thrive in the changing, albeit still unusual chemical environment of the lake.

Download Full-text

Comparison of PCR versus PCR-Free DNA Library Preparation for Characterising the Human Faecal Virome

Viruses ◽

10.3390/v13102093 ◽

2021 ◽

Vol 13 (10) ◽

pp. 2093

Author(s):

Shen-Yuan Hsieh ◽

Mohammad A. Tariq ◽

Andrea Telatin ◽

Rebecca Ansorge ◽

Evelien M. Adriaenssens ◽

...

Keyword(s):

Alpha Diversity ◽

Diversity Indices ◽

P Value ◽

Library Preparation ◽

High Genetic Diversity ◽

Sequencing Platform ◽

Viral Genomes ◽

Healthy Donors ◽

Faecal Samples ◽

Sequencing Platforms

The human intestinal microbiota is abundant in viruses, comprising mainly bacteriophages, occasionally outnumbering bacteria 10:1 and is termed the virome. Due to their high genetic diversity and the lack of suitable tools and reference databases, the virome remains poorly characterised and is often referred to as “viral dark matter”. However, the choice of sequencing platforms, read lengths and library preparation make study design challenging with respect to the virome. Here we have compared the use of PCR and PCR-free methods for sequence-library construction on the Illumina sequencing platform for characterising the human faecal virome. Viral DNA was extracted from faecal samples of three healthy donors and sequenced. Our analysis shows that most variation was reflecting the individually specific faecal virome. However, we observed differences between PCR and PCR-free library preparation that affected the recovery of low-abundance viral genomes. Using three faecal samples in this study, the PCR library preparation samples led to a loss of lower-abundance vOTUs evident in their PCR-free pairs (vOTUs 128, 6202 and 8364) and decreased the alpha-diversity indices (Chao1 p-value = 0.045 and Simpson p-value = 0.044). Thus, differences between PCR and PCR-free methods are important to consider when investigating “rare” members of the gut virome, with these biases likely negligible when investigating moderately and highly abundant viruses.

Download Full-text

Diversity Indices of Plant Communities and Their Rhizosphere Microbiomes: An Attempt to Find the Connection

Microorganisms ◽

10.3390/microorganisms9112339 ◽

2021 ◽

Vol 9 (11) ◽

pp. 2339

Author(s):

Aleksei O. Zverev ◽

Arina A. Kichko ◽

Aleksandr G. Pinaev ◽

Nikolay A. Provorov ◽

Evgeny E. Andronov

Keyword(s):

Microbial Communities ◽

Plant Communities ◽

Plant Diversity ◽

Beta Diversity ◽

Mutual Influence ◽

Plant Root ◽

Alpha Diversity ◽

Diversity Indices ◽

Alpha And Beta Diversity ◽

Highly Correlated

The rhizosphere community represents an “ecological interface” between plant and soil, providing the plant with a number of advantages. Despite close connection and mutual influence in this system, the knowledge about the connection of plant and rhizosphere diversity is still controversial. One of the most valuable factors of this uncertainty is a rough estimation of plant diversity. NGS sequencing can make the estimations of the plant community more precise than classical geobotanical methods. We investigate fallow and crop sites, which are similar in terms of environmental conditions and soil legacy, yet at the same time are significantly different in terms of plant diversity. We explored amplicons of both the plant root mass (ITS1 DNA) and the microbial communities (16S rDNA); determined alpha- and beta-diversity indices and their correlation, and performed differential abundance analysis. In the analysis, there is no correlation between the alpha-diversity indices of plants and the rhizosphere microbial communities. The beta-diversity between rhizosphere microbial communities and plant communities is highly correlated (R = 0.866, p = 0.01). ITS1 sequencing is effective for the description of plant root communities. There is a connection between rhizosphere communities and the composition of plants, but on the alpha-diversity level we found no correlation. In the future, the connection of alpha-diversities should be explored using ITS1 sequencing, even in more similar plant communities—for example, in different synusia.

Download Full-text

Sputum Microbiome Composition in Patients With Squamous Cell Lung Carcinoma

10.21203/rs.3.rs-902707/v1 ◽

2021 ◽

Author(s):

E. D. Baranova ◽

V. G. Druzhinin ◽

L. V. Matskova ◽

P. S. Demenkov ◽

V. P . Volobaev ◽

...

Keyword(s):

Squamous Cell ◽

Inflammatory Responses ◽

Alpha Diversity ◽

Taxonomic Composition ◽

16S Rrna Genes ◽

Rrna Genes ◽

Cell Lung Carcinoma ◽

Microbiome Composition ◽

Β Diversity ◽

Genome Damage

Abstract Recent findings indicate that the microbiome can have a significant impact on the development of lung cancer by inducing inflammatory responses, causing dysbiosis and generating genome damage. The aim of this study was to search for bacterial markers of squamous cell carcinoma (LUSC). In the study, the taxonomic composition of the sputum microbiome of 40 men with untreated LUSC was compared with 40 healthy controls. Next Generation sequencing of bacterial 16S rRNA genes was used to determine the taxonomic composition of the respiratory microbiome. There was no differences in alpha diversity between the LUSC and control groups. Meanwhile, differences in the structure of bacterial communities (β diversity) among patients and controls differed significantly in sputum samples (pseudo-F = 1.65; p = 0.026). Only Streptococcus, Bacillus, Gemella and Haemophilus were found to be significantly increased in patients with LUSC compared to the control subjects, while 19 bacterial genera were significantly reduced, indicating a decrease in beta diversity in the microbiome of patients with LUSC. From our study, Streptococcus (Streptococcus agalactiae) emerges as the most likely LUSC biomarker, but more research is needed to confirm this assumption.

Download Full-text