scholarly journals A Longitudinal Study of the Human Oropharynx Microbiota Over Time Reveals a Common Core and Significant Variations With Self-Reported Disease

2021 ◽  
Vol 11 ◽  
Author(s):  
Lydia Luise Bach ◽  
Asha Ram ◽  
Umer Z. Ijaz ◽  
Thomas J. Evans ◽  
Jan Lindström
Keyword(s):  
Microbial Communities ◽  
Community Composition ◽  
Common Core ◽  
Temporal Stability ◽  
Alpha Diversity ◽  
Molecular Techniques ◽  
Human Pathogens ◽  
Healthy Human ◽  
Culture Independent ◽  
Over Time

Our understanding of human microbial communities, in particular in regard to diseases is advancing, yet the basic understanding of the microbiome in healthy subjects over time remains limited. The oropharynx is a key target for colonization by several important human pathogens. To understand how the oropharyngeal microbiome might limit infections, and how intercurrent infections might be associated with its composition, we characterized the oropharyngeal microbiome of 18 healthy adults, sampled weekly over a 40-weeks using culture-independent molecular techniques. We detected nine phyla, 202 genera and 1438 assignments on OTU level, dominated by Firmicutes, Bacteroidetes, and Proteobacteria on phylum level. Individual microbiomes of participants were characterized by levels of high alpha diversity (mean = 204.55 OTUs, sd = 35.64), evenness (19.83, sd = 9.74) and high temporal stability (mean Pearson’s correlation between samples of 0.52, sd = 0.060), with greater differences in microbiome community composition between than within individuals. Significant changes in community composition were associated with disease states, suggesting that it is possible to detect specific changes in OTU abundance and community composition during illness. We defined the common core microbiota by varying occurrence and abundance thresholds showing that individual core microbiomes share a substantial number of OTUs across participants, chiefly Streptococci and Veillonella. Our results provide insights into the microbial communities that characterize the healthy human oropharynx, community structure and variability, and provide new approaches to define individual and shared cores. The wider implications of this result include the potential for modeling the general dynamics of oropharynx microbiota both in health and in response to antimicrobial treatments or probiotics.

scholarly journals Variability of diatom community composition and structure in mountain streams

Hydrobiologia ◽  
2021 ◽  
Author(s):  
Lorena González-Paz ◽  
María Comesaña ◽  
Isabel Pardo ◽  
José Barquín ◽  
Alejandra Goldenberg-Vilar ◽  
...  
Keyword(s):  
Community Composition ◽  
Temporal Stability ◽  
Ecological Status ◽  
Alpha Diversity ◽  
Small Rivers ◽  
Mountain Range ◽  
Diatom Community ◽  
Northern Spain ◽  
River Types ◽  
Over Time

AbstractSmall rivers support high levels of biodiversity, being especially sensitive to the effects of global change. Temporal records of community composition in minimally impaired streams can be used to explore trends in biodiversity in response to climate change and natural temporal variation. We approached the comparison of two time periods (2003–2008 and 2016–2020) to study whether the composition of diatom assemblages changed over time in twenty-three streams of the mountain range of Picos de Europa (Northern Spain). The stream’s water chemistry indicated significant decreases in N_NO3− and P_PO43− content over time. In these minimally disturbed streams, the specific diatom community was dominated by Achnanthidium pyrenaicum, Achnanthidium minutissimum and Cocconeis euglypta. PERMANOVA analyses did not identify significant changes in diatom assemblage composition between periods or river types. Diatom indices (e.g. IPS, NORTIdiat) indicated high or good ecological status and relatively high alpha diversity values were found in these mountain rivers during the studied years. Although diversity and evenness showed a significant decrease over time, the temporal stability of the river-type diatom reference community between the two periods should be considered as an indicator of biodiversity persistence of high importance when monitoring the ecological status following the reference condition approach.

scholarly journals Global airborne microbial communities controlled by surrounding landscapes and wind conditions

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Romie Tignat-Perrier ◽  
Aurélien Dommergue ◽  
Alban Thollot ◽  
Christoph Keuschnig ◽  
Olivier Magand ◽  
...  
Keyword(s):  
Particulate Matter ◽  
High Altitude ◽  
Microbial Communities ◽  
Atmospheric Chemistry ◽  
Sampling Site ◽  
Temporal Stability ◽  
Fungal Species ◽  
The World ◽  
Bacteria And Fungi ◽  
Over Time

Abstract The atmosphere is an important route for transporting and disseminating microorganisms over short and long distances. Understanding how microorganisms are distributed in the atmosphere is critical due to their role in public health, meteorology and atmospheric chemistry. In order to determine the dominant processes that structure airborne microbial communities, we investigated the diversity and abundance of both bacteria and fungi from the PM10 particle size (particulate matter of 10 micrometers or less in diameter) as well as particulate matter chemistry and local meteorological characteristics over time at nine different meteorological stations around the world. The bacterial genera Bacillus and Sphingomonas as well as the fungal species Pseudotaeniolina globaosa and Cladophialophora proteae were the most abundant taxa of the dataset, although their relative abundances varied greatly based on sampling site. Bacterial and fungal concentration was the highest at the high-altitude and semi-arid plateau of Namco (China; 3.56 × 106 ± 3.01 × 106 cells/m3) and at the high-altitude and vegetated mountain peak Storm-Peak (Colorado, USA; 8.78 × 104 ± 6.49 × 104 cells/m3), respectively. Surrounding ecosystems, especially within a 50 km perimeter of our sampling stations, were the main contributors to the composition of airborne microbial communities. Temporal stability in the composition of airborne microbial communities was mainly explained by the diversity and evenness of the surrounding landscapes and the wind direction variability over time. Airborne microbial communities appear to be the result of large inputs from nearby sources with possible low and diluted inputs from distant sources.

scholarly journals Time-Dependent Displacement of Commensal Skin Microbes by Pathogens at the Site of Colorectal Surgery

2020 ◽  
Author(s):  
Jennifer Holder-Murray ◽  
Andrew Yeh ◽  
Matthew B Rogers ◽  
Brian Firek ◽  
Brandon Mahler ◽  
...  
Keyword(s):  
Colorectal Surgery ◽  
Alpha Diversity ◽  
Surgical Site Infections ◽  
Clinic Visit ◽  
Clinical Samples ◽  
Rrna Gene ◽  
Skin Microbiome ◽  
Healthy Human ◽  
Culture Independent ◽  
Skin Commensals

Abstract Background Although the healthy human skin microbiome has been the subject of recent studies, it is not known whether alterations among commensal microbes contribute to surgical site infections (SSIs). Our objective in this study was to characterize temporal and spatial variation in the skin microbiota of patients undergoing colorectal surgery and determine if dysbiosis contributes to SSIs. Methods Sixty one adults scheduled to undergo elective colon or rectal resection were identified by convenience sampling. By analyzing bacterial 16S rRNA gene sequences isolated from clinical samples, we used a culture-independent strategy to monitor perioperative changes in microbial diversity of fecal samples and the skin. Results A total of 990 samples from 61 patients were analyzed. Alpha diversity on the skin decreased after surgery but later recovered at the postoperative clinic visit. In most patients, we observed a transient postoperative loss of skin commensals (Corynebacterium and Propionibacterium) at the surgical site, which were replaced by potential pathogens and intestinal anaerobes (eg, Enterobacteriaceae). These changes were not observed on skin that was uninvolved in the surgical incision (chest wall). One patient developed a wound infection. Incisional skin swabs from this patient demonstrated a sharp postoperative increase in the abundance of Enterococcus, which was also cultured from wound drainage. Conclusions We observed reproducible perioperative changes in the skin microbiome following surgery. The low incidence of SSIs in this cohort precluded analysis of associations between dysbiosis and infection. We postulate that real-time monitoring of the skin microbiome could provide actionable findings about the pathogenesis of SSIs.

scholarly journals Bacterial Origin and Community Composition in the Barley Phytosphere as a Function of Habitat and Presowing Conditions

2000 ◽  
Vol 66 (10) ◽  
pp. 4372-4377 ◽  
Author(s):  
Bo Normander ◽  
Jim I. Prosser
Keyword(s):  
Community Composition ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Bacterial Community Composition ◽  
Pcr Amplification ◽  
Molecular Techniques ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacterial Populations ◽  
Culture Independent ◽  
Gradient Gel Electrophoresis

ABSTRACT An understanding of the factors influencing colonization of the rhizosphere is essential for improved establishment of biocontrol agents. The aim of this study was to determine the origin and composition of bacterial communities in the developing barley (Hordeum vulgare) phytosphere, using denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA genes amplified from extracted DNA. Discrete community compositions were identified in the endorhizosphere, rhizoplane, and rhizosphere soil of plants grown in an agricultural soil for up to 36 days. Cluster analysis revealed that DGGE profiles of the rhizoplane more closely resembled those in the soil than the profiles found in the root tissue or on the seed, suggesting that rhizoplane bacteria primarily originated from the surrounding soil. No change in bacterial community composition was observed in relation to plant age. Pregermination of the seeds for up to 6 days improved the survival of seed-associated bacteria on roots grown in soil, but only in the upper, nongrowing part of the rhizoplane. The potential occurrence of skewed PCR amplification was examined, and only minor cases of PCR bias for mixtures of two different DNA samples were observed, even when one of the samples contained plant DNA. The results demonstrate the application of culture-independent, molecular techniques in assessment of rhizosphere bacterial populations and the importance of the indigenous soil population in colonization of the rhizosphere.

scholarly journals Chronic Rhinosinusitis and the Evolving Understanding of Microbial Ecology in Chronic Inflammatory Mucosal Disease

2016 ◽  
Vol 30 (1) ◽  
pp. 321-348 ◽  
Author(s):  
Michael Hoggard ◽  
Brett Wagner Mackenzie ◽  
Ravi Jain ◽  
Michael W. Taylor ◽  
Kristi Biswas ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Chronic Rhinosinusitis ◽  
Inflammatory Diseases ◽  
Modern Technology ◽  
Molecular Techniques ◽  
Modern Culture ◽  
Culture Independent ◽  
New Perspective ◽  
Microbiological Research

SUMMARY Chronic rhinosinusitis (CRS) encompasses a heterogeneous group of debilitating chronic inflammatory sinonasal diseases. Despite considerable research, the etiology of CRS remains poorly understood, and debate on potential roles of microbial communities is unresolved. Modern culture-independent (molecular) techniques have vastly improved our understanding of the microbiology of the human body. Recent studies that better capture the full complexity of the microbial communities associated with CRS reintroduce the possible importance of the microbiota either as a direct driver of disease or as being potentially involved in its exacerbation. This review presents a comprehensive discussion of the current understanding of bacterial, fungal, and viral associations with CRS, with a specific focus on the transition to the new perspective offered in recent years by modern technology in microbiological research. Clinical implications of this new perspective, including the role of antimicrobials, are discussed in depth. While principally framed within the context of CRS, this discussion also provides an analogue for reframing our understanding of many similarly complex and poorly understood chronic inflammatory diseases for which roles of microbes have been suggested but specific mechanisms of disease remain unclear. Finally, further technological advancements on the horizon, and current pressing questions for CRS microbiological research, are considered.

scholarly journals Disturbance and recovery: a synthesis of microbial community reassembly following disturbance across realms

2021 ◽  
Author(s):  
Stephanie Jurburg ◽  
Shane Blowes ◽  
Ashley Shade ◽  
Nico Eisenhauer ◽  
Jonathan Chase
Keyword(s):  
Time Series ◽  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Community Assembly ◽  
Disturbance And Recovery ◽  
Microbial Community Assembly ◽  
Community Reassembly ◽  
Over Time

Disturbances alter the diversity and composition of microbial communities, but whether microbiomes from different environments exhibit similar degrees of resistance or rates of recovery has not been evaluated. Here, we synthesized 86 time series of disturbed mammalian, aquatic, and soil microbiomes to examine how the recovery of microbial richness and community composition differed after disturbance. We found no general patterns in compositional variance (i.e., dispersion) in any microbiomes over time. Only mammalian microbiomes consistently exhibited decreases in richness following disturbance. Importantly, they tended to recover this richness, but not their composition, over time. In contrast, aquatic microbiomes tended to diverge from their pre-disturbance composition following disturbance. By synthesizing microbiome responses across environments, our study aids in the reconciliation of disparate microbial community assembly frameworks, and highlights the role of the environment in microbial community reassembly following disturbance.

scholarly journals Co-cultivation of microbial sub-communities in microfluidic droplets facilitates high-resolution genomic dissection of microbial ‘dark matter’

2020 ◽  
Vol 12 (11) ◽  
pp. 263-274
Author(s):  
James Y Tan ◽  
Sida Wang ◽  
Gregory J Dick ◽  
Vincent B Young ◽  
David H Sherman ◽  
...  
Keyword(s):  
Dark Matter ◽  
Microbial Communities ◽  
Ecological Interactions ◽  
Healthy Human ◽  
Encapsulated Cells ◽  
Microfluidic Droplets ◽  
The Family ◽  
Culture Independent ◽  
Genomic Characterization

Abstract While the ‘unculturable’ majority of the bacterial world is accessible with culture-independent tools, the inability to study these bacteria using culture-dependent approaches has severely limited our understanding of their ecological roles and interactions. To circumvent cultivation barriers, we utilize microfluidic droplets as localized, nanoliter-size bioreactors to co-cultivate subsets of microbial communities. This co-localization can support ecological interactions between a reduced number of encapsulated cells. We demonstrated the utility of this approach in the encapsulation and co-cultivation of droplet sub-communities from a fecal sample collected from a healthy human subject. With the whole genome amplification and metagenomic shotgun sequencing of co-cultivated sub-communities from 22 droplets, we observed that this approach provides accessibility to uncharacterized gut commensals for study. The recovery of metagenome-assembled genomes from one droplet sub-community demonstrated the capability to dissect the sub-communities with high-genomic resolution. In particular, genomic characterization of one novel member of the family Neisseriaceae revealed implications regarding its participation in fatty acid degradation and production of atherogenic intermediates in the human gut. The demonstrated genomic resolution and accessibility to the microbial ‘dark matter’ with this methodology can be applied to study the interactions of rare or previously uncultivated members of microbial communities.

scholarly journals Culture-Dependent and -Independent Characterization of Microbial Communities Associated with a Shallow Submarine Hydrothermal System Occurring within a Coral Reef off Taketomi Island, Japan

2007 ◽  
Vol 73 (23) ◽  
pp. 7642-7656 ◽  
Author(s):  
Hisako Hirayama ◽  
Michinari Sunamura ◽  
Ken Takai ◽  
Takuro Nunoura ◽  
Takuro Noguchi ◽  
...  
Keyword(s):  
Coral Reef ◽  
Microbial Communities ◽  
Hydrothermal System ◽  
Hydrothermal Activity ◽  
Molecular Techniques ◽  
Maximum Temperature ◽  
Rrna Gene ◽  
Type I ◽  
Optimum Growth ◽  
Culture Independent

ABSTRACT Microbial communities in a shallow submarine hydrothermal system near Taketomi Island, Japan, were investigated using cultivation-based and molecular techniques. The main hydrothermal activity occurred in a craterlike basin (depth, ∼23 m) on the coral reef seafloor. The vent fluid (maximum temperature, >52°C) contained 175 μM H2S and gas bubbles mainly composed of CH4 (69%) and N2 (29%). A liquid serial dilution cultivation technique targeting a variety of metabolism types quantified each population in the vent fluid and in a white microbial mat located near the vent. The most abundant microorganisms cultivated from both the fluid and the mat were autotrophic sulfur oxidizers, including mesophilic Thiomicrospira spp. and thermophilic Sulfurivirga caldicuralii. Methane oxidizers were the second most abundant organisms in the fluid; one novel type I methanotroph exhibited optimum growth at 37°C, and another novel type I methanotroph exhibited optimum growth at 45°C. The number of hydrogen oxidizers cultivated only from the mat was less than the number of sulfur and methane oxidizers, although a novel mesophilic hydrogen-oxidizing member of the Epsilonproteobacteria was isolated. Various mesophilic to hyperthermophilic heterotrophs, including sulfate-reducing Desulfovibrio spp., iron-reducing Deferribacter sp., and sulfur-reducing Thermococcus spp., were also cultivated. Culture-independent 16S rRNA gene clone analysis of the vent fluid and mat revealed highly diverse archaeal communities. In the bacterial community, S. caldicuralii was identified as the predominant phylotype in the fluid (clonal frequency, 25%). Both bacterial clone libraries indicated that there were bacterial communities involved in sulfur, hydrogen, and methane oxidation and sulfate reduction. Our results indicate that there are unique microbial communities that are sustained by active chemosynthetic primary production rather than by photosynthetic production in a shallow hydrothermal system where sunlight is abundant.

scholarly journals Changes in Soil Microbial Communities across an Urbanization Gradient: A Local-Scale Temporal Study in the Arid Southwestern USA

2021 ◽  
Vol 9 (7) ◽  
pp. 1470
Author(s):  
Yongjian Chen ◽  
Adalee Martinez ◽  
Sydney Cleavenger ◽  
Julia Rudolph ◽  
Albert Barberán
Keyword(s):  
Microbial Communities ◽  
Community Composition ◽  
Mycorrhizal Fungi ◽  
Marker Gene ◽  
Soil Microbial Communities ◽  
Ecosystem Functions ◽  
Ammonia Oxidizing Bacteria ◽  
Human Pathogens ◽  
Urbanization Gradient ◽  
Southwestern Usa

Urban development is one of the leading causes of biodiversity change. Understanding how soil microorganisms respond to urbanization is particularly important because they are crucial for the provisioning of ecosystem functions and services. Here, we collected monthly soil samples over one year across three locations representing an urbanization gradient (low-moderate-high) in the arid Southwestern USA, and we characterized their microbial communities using marker gene sequencing. Our results showed that microbial richness and community composition exhibited nonsignificant changes over time regardless of the location. Soil fungal richness was lower in moderately and highly urbanized locations, but soil bacterial/archaeal richness was not significantly different among locations. Both bacteria/archaea and fungi exhibited significant differences in community composition across locations. After inferring potential functional groups, soils in the highly urbanized location had lower proportions of arbuscular mycorrhizal fungi and soil saprotrophic fungi but had higher proportions of bacterial taxa involved in aromatic compound degradation, human pathogens, and intracellular parasites. Furthermore, ammonia-oxidizing bacteria were more abundant in the highly urbanized location, but ammonia-oxidizing archaea were more abundant in lowly and moderately urbanized locations. Together, these results highlight the significant changes in belowground microbial communities across an urbanization gradient, and these changes might have important implications for aboveground–belowground interactions, nutrient cycling, and human health.

scholarly journals Reproducibility and repeatability of six high-throughput 16S rDNA sequencing protocols for microbiota profiling

2017 ◽  
Author(s):  
Sajan C. Raju ◽  
Sonja Lagström ◽  
Pekka Ellonen ◽  
Willem M. de Vos ◽  
Johan G. Eriksson ◽  
...  
Keyword(s):  
Large Scale ◽  
Alpha Diversity ◽  
Epidemiological Studies ◽  
Molecular Techniques ◽  
16S Rdna Sequencing ◽  
High Reproducibility ◽  
Rdna Sequencing ◽  
Culture Independent ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

AbstractCulture-independent molecular techniques and advances in next generation sequencing (NGS) technologies make large-scale epidemiological studies on microbiota feasible. A challenge using NGS is to obtain high reproducibility and repeatability, which is mostly attained through robust amplification. We aimed to assess the reproducibility of saliva microbiota by comparing triplicate samples. The microbiota was produced with simplified in-house 16S amplicon assays taking advantage of large number of barcodes. The assays included primers with Truseq (TS-tailed) or Nextera (NX-tailed) adapters and either with dual index or dual index plus a 6-nt internal index. All amplification protocols produced consistent microbial profiles for the same samples. Although, in our study, reproducibility was highest for the TS-tailed method. Five replicates of a single sample, prepared with the TS-tailed 1-step protocol without internal index sequenced on the HiSeq platform provided high alpha-diversity and low standard deviation (mean Shannon and Inverse Simpson diversity was 3.19 ± 0.097 and 13.56 ± 1.634 respectively). Large-scale profiling of microbiota can consistently be produced by all 16S amplicon assays. The TS-tailed-1S dual index protocol is preferred since it provides repeatable profiles on the HiSeq platform and are less labour intensive.

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