Meta-Analysis of Microbial Communities in Hot Springs: Recurrent Taxa and Complex Shaping Factors beyond pH and Temperature

The study of microbial communities from extreme environments is a fascinating topic. With every study, biologists and ecologists reveal interesting facts and questions that dispel the old belief that these are inhospitable environments. In this work, we assess the microbial diversity of three hot springs from Neuquén, Argentina, using high-throughput amplicon sequencing. We predicted a distinct metabolic profile in the acidic and the circumneutral samples, with the first ones being dominated by chemolithotrophs and the second ones by chemoheterotrophs. Then, we collected data of the microbial communities of hot springs around the world in an effort to comprehend the roles of pH and temperature as shaping factors. Interestingly, there was a covariation between both parameters and the phylogenetic distance between communities; however, neither of them could explain much of the microbial profile in an ordination model. Moreover, there was no correlation between alpha diversity and these parameters. Therefore, the microbial communities’ profile seemed to have complex shaping factors beyond pH and temperature. Lastly, we looked for taxa associated with different environmental conditions. Several such taxa were found. For example, Hydrogenobaculum was frequently present in acidic springs, as was the Sulfolobaceae family; on the other hand, Candidatus Hydrothermae phylum was strongly associated with circumneutral conditions. Interestingly, some singularities related to sites featuring certain taxa were also observed.

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An association between chronic widespread pain and the gut microbiome

Rheumatology ◽

10.1093/rheumatology/keaa847 ◽

2020 ◽

Author(s):

Maxim B Freidin ◽

Maria A Stalteri ◽

Philippa M Wells ◽

Genevieve Lachance ◽

Andrei-Florin Baleanu ◽

...

Keyword(s):

Gut Microbiome ◽

Genome Wide Association Study ◽

Meta Analysis ◽

Alpha Diversity ◽

Amplicon Sequencing ◽

Chronic Widespread Pain ◽

Mendelian Randomisation ◽

Total N ◽

16S Rrna Amplicon Sequencing ◽

A Genome

Abstract Objectives Chronic widespread musculoskeletal pain (CWP) is a characteristic symptom of fibromyalgia, which has been shown to be associated with an altered gut microbiome. Microbiome studies to date have not examined the milder CWP phenotype specifically nor have they explored the role of raised BMI. The aim of this study was to investigate whether the microbiome is abnormal in CWP. Methods CWP was assessed using a standardized screening questionnaire in female volunteers from the TwinsUK cohort including 113 CWP cases and 1623 controls. The stool microbiome was characterised using 16S rRNA amplicon sequencing and amplicon sequence variants (ASVs), and associations with CWP examined using linear mixed-effects models adjusting for BMI, age, diet, family relatedness and technical factors. Results Alpha diversity was significantly lower in CWP cases than controls (Mann–Whitney test, p-values 2.3e-04 and 1.2e-02, respectively). The species Coprococcus comes was significantly depleted in CWP cases (p.adj = 3.04e-03). A genome-wide association study (GWAS) performed for C. comes in TwinsUK followed by meta-analysis with three Dutch cohorts (total n = 3521) resulted in nine suggestive regions, with the most convincing on chromosome 4 near the TRAM1L1 gene (rs76957229, p= 7.4e-8). A Mendelian randomisation study based on the results of the GWAS did not support a causal role for C. comes on the development of CWP. Conclusions We have demonstrated reduced diversity in the microbiome in CWP, indicating an involvement of the gut microbiota in CWP; prospectively the microbiome may offer therapeutic opportunities for this condition.

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Bacterial meta-analysis of chicken cecal microbiota

PeerJ ◽

10.7717/peerj.10571 ◽

2021 ◽

Vol 9 ◽

pp. e10571

Author(s):

Luis Alberto Chica Cardenas ◽

Viviana Clavijo ◽

Martha Vives ◽

Alejandro Reyes

Keyword(s):

16S Rrna ◽

Sequence Data ◽

Cellulose Degradation ◽

Meta Analysis ◽

Alpha Diversity ◽

Amplicon Sequencing ◽

Short Chain Fatty Acids ◽

Joint Analysis ◽

Poultry Production ◽

Taxonomic Profiling

Poultry production is an industry that generates 90,000 metric tons of chicken meat worldwide. Thus, optimizing chicken growth and sustainable production is of great importance. A central factor determining not only production parameters, but also stability of the immune system and chicken health, is the diversity and variability of the microbiota present throughout the gastrointestinal tract. To date, several studies have investigated the relationship between bacterial communities and the gut microbiome, with limited data to compare. This study aims to create a bacterial meta-analysis based on studies using amplicon sequencing with Illumina sequencing technologies in order to build a baseline for comparison in future analyses of the cecal bacterial composition in chicken. A systematic literature review was performed (SYRF ID: e84f0468-e418-4eec-9da4-b517f1b4809d. Full project URL: https://app.syrf.org.uk/projects/e84f0468-e418-4eec-9da4-b517f1b4809d/detail). From all the available and analyzed manuscripts only nine contained full raw-sequence data available and the corresponding metadata. A total of 324 samples, comprising three different regions within the 16S rRNA gene, were analyzed. Due to the heterogeneity of the data, each region was analyzed independently and an effort for a joint analysis was performed as well. Taxonomic profiling revealed 11 phyla, with Firmicutes as the most prevalent phylum, followed by Bacteroidetes and Proteobacteria. At genus level, 109 genera were found. Shannon metric for alpha diversity showed that factors like type of chickens (Commercial or experimental) and 16S rRNA gene subregion have negligible effect on diversity. Despite the large number of parameters that were taken into account, the identification of common bacteria showed five genera to be common for all sets in at least 50% of the samples. These genera are highly associated to cellulose degradation and short chain fatty acids synthesis. In general, it was possible to identify some commonalities in the bacterial cecal microbial community despite the extensive variability and factors differing from one study to another.

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Circular Economy of Anaerobic Biofilm Microbiomes: A Meta-Analysis Framework for Re-exploration of Amplicon Sequencing Data

10.1101/2020.12.23.424166 ◽

2020 ◽

Author(s):

Ciara Keating ◽

Anna Christine Trego ◽

William Sloan ◽

Vincent O’Flaherty ◽

Umer Zeeshan Ijaz

Keyword(s):

Data Mining ◽

Wastewater Treatment ◽

Anaerobic Digestion ◽

Microbial Communities ◽

High Throughput Sequencing ◽

Meta Analysis ◽

Illumina Miseq ◽

Amplicon Sequencing ◽

Sequencing Data ◽

Analysis Workflow

AbstractUse of high-throughput sequencing is widespread in efforts to understand the microbial communities in natural and engineered systems. Many built ecosystems, in particular those used for engineered wastewater treatment, have harnessed the metabolic capacity of complex microbial communities for the effective removal and recovery of organic pollutants. Recent efforts to better understand and precisely engineer such systems have increasingly used high-throughput sequencing to map the structure and function of wastewater treatment microbiomes. An enormous amount of data is readily available on online repositories such as the National Center for Biotechnology Information Short Read Archive (NCBI SRA). Here, we describe and provide an optimised meta-analysis workflow to utilise this resource to collate heterogenous studies together for anaerobic digestion research. We analysed 16S rRNA gene Illumina Miseq amplicon sequencing data from 31 anaerobic digestion studies (from high-rate digesters), including >1,300 samples. Additionally, we compare several methodological choices: extraction method, v-region, taxonomical database, and the classifier. We demonstrate that collation of data from multiple v-regions can be achieved by using only the taxa for which sequences are available in the reference databases, without losses in diversity trends. This is made possible by focusing on alternative strategies for taxonomic assignments, namely, bayesian lowest common ancestor (BLCA) algorithm which offers increased resolution to the traditional naïve bayesian classifier (NBC). While we demonstrate this using an anaerobic digestion wastewater treatment dataset, this methodology can be translated to perform meta-analysis on amplicon sequences in any field. These findings not only provide a roadmap for meta-analysis in any field, but additionally provide an opportunity to reuse extensive data resources to ultimately advance knowledge of wastewater treatment systems.ImportanceIn this study, we have combined sequencing data from 31 individual studies with the purpose of identifying a meta-analysis workflow which can accurately collate data derived from sequencing different v-regions with minimal data loss and more accurate diversity patterns. While we have used Anaerobic Digestion (AD) communities for our proof-of-concept, our workflow (Fig 1) can be translated to any Illumina MiSeq meta-analysis study, in any field. Thereby, we provide the foundation for intensive data mining of existing amplicon sequencing resources. Such data-mining can provide a global perspective on complex microbial communities.Graphical Abstract

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Coupling Root Diameter With Rooting Depth to Reveal the Heterogeneous Assembly of Root-Associated Bacterial Communities in Soybean

Frontiers in Microbiology ◽

10.3389/fmicb.2021.783563 ◽

2021 ◽

Vol 12 ◽

Author(s):

Wen Luo ◽

Xiaoyu Zai ◽

Jieyu Sun ◽

Da Li ◽

Yuanli Li ◽

...

Keyword(s):

Bacterial Community ◽

Microbial Communities ◽

Bacterial Communities ◽

Plant Root ◽

Alpha Diversity ◽

Amplicon Sequencing ◽

Root Diameter ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rooting Depth

Root diameter and rooting depth lead to morphological and architectural heterogeneity of plant roots; however, little is known about their effects on root-associated microbial communities. Bacterial community assembly was explored across 156 samples from three rhizocompartments (the rhizosphere, rhizoplane, and endosphere) for different diameters (0.0–0.5 mm, 0.5–1.0 mm, 1.0–2.0 mm, and>2.0 mm) and depths (0–5 cm, 5–10 cm, 10–15 cm, and 15–20 cm) of soybean [Glycine max (L.) Merrill] root systems. The microbial communities of all samples were analyzed using amplicon sequencing of bacterial 16S rRNA genes. The results showed that root diameter significantly affected the rhizosphere and endosphere bacterial communities, while rooting depth significantly influenced the rhizosphere and rhizoplane bacterial communities. The bacterial alpha diversity decreased with increasing root diameter in all three rhizocompartments, and the diversity increased with increasing rooting depth only in the rhizoplane. Clearly, the hierarchical enrichment process of the bacterial community showed a change from the rhizosphere to the rhizoplane to the endosphere, and the bacterial enrichment was higher in thinner or deeper roots (except for the roots at a depth of 15–20 cm). Network analysis indicated that thinner or deeper roots led to higher bacterial network complexity. The core and keystone taxa associated with the specific root diameter class and rooting depth class harbored specific adaptation or selection strategies. Root diameter and rooting depth together affected the root-associated bacterial assembly and network complexity in the root system. Linking root traits to microbiota may enhance our understanding of plant root-microbe interactions and their role in developing environmentally resilient root ecosystems.

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Composition of Rhizosphere Microbial Communities Associated With Healthy and Verticillium Wilt Diseased Cotton Plants

Frontiers in Microbiology ◽

10.3389/fmicb.2021.618169 ◽

2021 ◽

Vol 12 ◽

Author(s):

Feng Wei ◽

Hongjie Feng ◽

Dezheng Zhang ◽

Zili Feng ◽

Lihong Zhao ◽

...

Keyword(s):

Microbial Communities ◽

Mycorrhizal Fungi ◽

Quantitative Polymerase Chain Reaction ◽

Bacterial Biomass ◽

Alpha Diversity ◽

Arbuscular Mycorrhizal ◽

Amplicon Sequencing ◽

Total Biomass ◽

Biomass Ratio ◽

Microbial Groups

Rhizosphere microbial communities are known to be related to plant health; using such an association for crop management requires a better understanding of this relationship. We investigated rhizosphere microbiomes associated with Verticillium wilt symptoms in two cotton cultivars. Microbial communities were profiled by amplicon sequencing, with the total bacterial and fungal DNA quantified by quantitative polymerase chain reaction based on the respective 16S and internal transcribed spacer primers. Although the level of V. dahliae inoculum was higher in the rhizosphere of diseased plants than in the healthy plants, such a difference explained only a small proportion of variation in wilt severities. Compared to healthy plants, the diseased plants had much higher total fungal/bacterial biomass ratio, as represented by quantified total fungal or bacterial DNA. The variability in the fungal/bacterial biomass ratio was much smaller than variability in either fungal or bacterial total biomass among samples within diseased or healthy plants. Diseased plants generally had lower bacterial alpha diversity in their rhizosphere, but such differences in the fungal alpha diversity depended on cultivars. There were large differences in both fungal and bacterial communities between diseased and healthy plants. Many rhizosphere microbial groups differed in their abundance between healthy and diseased plants. There was a decrease in arbuscular mycorrhizal fungi and an increase in several plant pathogen and saprophyte guilds in diseased plants. These findings suggested that V. dahliae infection of roots led to considerable changes in rhizosphere microbial communities, with large increases in saprophytic fungi and reduction in bacterial community.

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The Terrestrial Plastisphere: Diversity and Polymer-Colonizing Potential of Plastic-Associated Microbial Communities in Soil

Microorganisms ◽

10.3390/microorganisms9091876 ◽

2021 ◽

Vol 9 (9) ◽

pp. 1876

Author(s):

Joana MacLean ◽

Sathish Mayanna ◽

Liane G. Benning ◽

Fabian Horn ◽

Alexander Bartholomäus ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Alpha Diversity ◽

Amplicon Sequencing ◽

Microbial Colonization ◽

Surface Adhesion ◽

Plastic Debris ◽

16S Rrna Amplicon Sequencing ◽

Study Sites

The concept of a ‘plastisphere microbial community’ arose from research on aquatic plastic debris, while the effect of plastics on microbial communities in soils remains poorly understood. Therefore, we examined the inhabiting microbial communities of two plastic debris ecosystems with regard to their diversity and composition relative to plastic-free soils from the same area using 16S rRNA amplicon sequencing. Furthermore, we studied the plastic-colonizing potential of bacteria originating from both study sites as a measure of surface adhesion to UV-weathered polyethylene (PE) using high-magnification field emission scanning electron microscopy (FESEM). The high plastic content of the soils was associated with a reduced alpha diversity and a significantly different structure of the microbial communities. The presence of plastic debris in soils did not specifically enrich bacteria known to degrade plastic, as suggested by earlier studies, but rather shifted the microbial community towards highly abundant autotrophic bacteria potentially tolerant to hydrophobic environments and known to be important for biocrust formation. The bacterial inoculates from both sites formed dense biofilms on the surface and in micrometer-scale surface cracks of the UV-weathered PE chips after 100 days of in vitro incubation with visible threadlike EPS structures and cross-connections enabling surface adhesion. High-resolution FESEM imaging further indicates that the microbial colonization catalyzed some of the surface degradation of PE. In essence, this study suggests the concept of a ‘terrestrial plastisphere’ as a diverse consortium of microorganisms including autotrophs and other pioneering species paving the way for those members of the consortium that may eventually break down the plastic compounds.

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Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity

Genome Biology ◽

10.1186/s13059-019-1831-z ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 14

Author(s):

Robert C. Kaplan ◽

Zheng Wang ◽

Mykhaylo Usyk ◽

Daniela Sotres-Alvarez ◽

Martha L. Daviglus ◽

...

Keyword(s):

Community Health ◽

Gut Microbiome ◽

Alpha Diversity ◽

Amplicon Sequencing ◽

Shannon Index ◽

Health Study ◽

Rrna Gene ◽

Cross Sectional ◽

Hispanic Community ◽

The Usa

Abstract Background Hispanics living in the USA may have unrecognized potential birthplace and lifestyle influences on the gut microbiome. We report a cross-sectional analysis of 1674 participants from four centers of the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), aged 18 to 74 years old at recruitment. Results Amplicon sequencing of 16S rRNA gene V4 and fungal ITS1 fragments from self-collected stool samples indicate that the host microbiome is determined by sociodemographic and migration-related variables. Those who relocate from Latin America to the USA at an early age have reductions in Prevotella to Bacteroides ratios that persist across the life course. Shannon index of alpha diversity in fungi and bacteria is low in those who relocate to the USA in early life. In contrast, those who relocate to the USA during adulthood, over 45 years old, have high bacterial and fungal diversity and high Prevotella to Bacteroides ratios, compared to USA-born and childhood arrivals. Low bacterial diversity is associated in turn with obesity. Contrasting with prior studies, our study of the Latino population shows increasing Prevotella to Bacteroides ratio with greater obesity. Taxa within Acidaminococcus, Megasphaera, Ruminococcaceae, Coriobacteriaceae, Clostridiales, Christensenellaceae, YS2 (Cyanobacteria), and Victivallaceae are significantly associated with both obesity and earlier exposure to the USA, while Oscillospira and Anaerotruncus show paradoxical associations with both obesity and late-life introduction to the USA. Conclusions Our analysis of the gut microbiome of Latinos demonstrates unique features that might be responsible for health disparities affecting Hispanics living in the USA.

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1H-NMR Profiling Shows as Specific Constituents Strongly Affect the International EVOO Blends Characteristics: The Case of the Italian Oil

Molecules ◽

10.3390/molecules26082233 ◽

2021 ◽

Vol 26 (8) ◽

pp. 2233

Author(s):

Francesca Calò ◽

Chiara Roberta Girelli ◽

Federica Angilè ◽

Laura Del Coco ◽

Lucia Mazzi ◽

...

Keyword(s):

1H Nmr ◽

Metabolic Profile ◽

1H Nmr Spectroscopy ◽

Virgin Olive Oil ◽

Extra Virgin Olive Oil ◽

Minor Components ◽

Multivariate Statistical ◽

Olive Oils ◽

The World ◽

Plateau Level

Considering the growing number of extra virgin olive oil (EVOO) producers in the world, knowing the influence of olive oils with different geographical origins on the characteristics of the final blend becomes an interesting goal. The present work is focused on commercial organic EVOO blends obtained by mixing multiple oils from different geographical origins. These blends have been studied by 1H-NMR spectroscopy supported by multivariate statistical analysis. Specific characteristics of commercial organic EVOO blends originated by mixing oils from Italy, Tunisia, Portugal, Spain, and Greece were found to be associated with the increasing content of the Italian component. A linear progression of the metabolic profile defined characteristics for the analysed samples—up to a plateau level—was found in relation to the content of the main constituent of the Italian oil, the monocultivar Coratina. The Italian constituent percentage appears to be correlated with the fatty acids (oleic) and the polyphenols (tyrosol, hydroxytyrosol, and derivatives) content as major and minor components respectively. These results, which highlight important economic aspects, also show the utility of 1H-NMR associated with chemometric analysis as a powerful tool in this field. Mixing oils of different national origins, to obtain blends with specific characteristics, could be profitably controlled by this methodology.

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Bacterial Diversity of Breast Milk in Healthy Spanish Women: Evolution from Birth to Five Years Postpartum

Nutrients ◽

10.3390/nu13072414 ◽

2021 ◽

Vol 13 (7) ◽

pp. 2414

Author(s):

Laura Sanjulián ◽

Alexandre Lamas ◽

Rocío Barreiro ◽

Alberto Cepeda ◽

Cristina A. Fente ◽

...

Keyword(s):

Breast Milk ◽

16S Rrna ◽

Human Milk ◽

Alpha Diversity ◽

Amplicon Sequencing ◽

Maternal Body Mass Index ◽

16S Rrna Amplicon Sequencing ◽

Spanish Women ◽

Calcium Magnesium ◽

Abundant Genus

The objective of this work was to characterize the microbiota of breast milk in healthy Spanish mothers and to investigate the effects of lactation time on its diversity. A total of ninety-nine human milk samples were collected from healthy Spanish women and were assessed by means of next-generation sequencing of 16S rRNA amplicons and by qPCR. Firmicutes was the most abundant phylum, followed by Bacteroidetes, Actinobacteria, and Proteobacteria. Accordingly, Streptococcus was the most abundant genus. Lactation time showed a strong influence in milk microbiota, positively correlating with Actinobacteria and Bacteroidetes, while Firmicutes was relatively constant over lactation. 16S rRNA amplicon sequencing showed that the highest alpha-diversity was found in samples of prolonged lactation, along with wider differences between individuals. As for milk nutrients, calcium, magnesium, and selenium levels were potentially associated with Streptococcus and Staphylococcus abundance. Additionally, Proteobacteria was positively correlated with docosahexaenoic acid (DHA) levels in breast milk, and Staphylococcus with conjugated linoleic acid. Conversely, Streptococcus and trans-palmitoleic acid showed a negative association. Other factors such as maternal body mass index or diet also showed an influence on the structure of these microbial communities. Overall, human milk in Spanish mothers appeared to be a complex niche shaped by host factors and by its own nutrients, increasing in diversity over time.

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Development of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan

Scientific Reports ◽

10.1038/s41598-021-91615-3 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Kazutoshi Yoshitake ◽

Gaku Kimura ◽

Tomoko Sakami ◽

Tsuyoshi Watanabe ◽

Yukiko Taniuchi ◽

...

Keyword(s):

Time Series ◽

Microbial Communities ◽

Pacific Coast ◽

Three Dimensional ◽

Amplicon Sequencing ◽

Metagenomic Data ◽

Shotgun Metagenomics ◽

Functional Features ◽

Pacific Coast Of Japan ◽

Marine Microbial Communities

AbstractAlthough numerous metagenome, amplicon sequencing-based studies have been conducted to date to characterize marine microbial communities, relatively few have employed full metagenome shotgun sequencing to obtain a broader picture of the functional features of these marine microbial communities. Moreover, most of these studies only performed sporadic sampling, which is insufficient to understand an ecosystem comprehensively. In this study, we regularly conducted seawater sampling along the northeastern Pacific coast of Japan between March 2012 and May 2016. We collected 213 seawater samples and prepared size-based fractions to generate 454 subsets of samples for shotgun metagenome sequencing and analysis. We also determined the sequences of 16S rRNA (n = 111) and 18S rRNA (n = 47) gene amplicons from smaller sample subsets. We thereafter developed the Ocean Monitoring Database for time-series metagenomic data (http://marine-meta.healthscience.sci.waseda.ac.jp/omd/), which provides a three-dimensional bird’s-eye view of the data. This database includes results of digital DNA chip analysis, a novel method for estimating ocean characteristics such as water temperature from metagenomic data. Furthermore, we developed a novel classification method that includes more information about viruses than that acquired using BLAST. We further report the discovery of a large number of previously overlooked (TAG)n repeat sequences in the genomes of marine microbes. We predict that the availability of this time-series database will lead to major discoveries in marine microbiome research.

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