scholarly journals The Lung Microbiome during Health and Disease

2021 ◽  
Vol 22 (19) ◽  
pp. 10872
Author(s):  
Kazuma Yagi ◽  
Gary B. Huffnagle ◽  
Nicholas W. Lukacs ◽  
Nobuhiro Asai
Keyword(s):  
Molecular Techniques ◽  
Microbial Composition ◽  
Healthy Human ◽  
Lung Microbiome ◽  
Large Numbers ◽  
Human Lungs ◽  
Culture Independent ◽  
Microbiome Research ◽  
Microbe Interactions ◽  
Host Microbe Interactions

Healthy human lungs have traditionally been considered to be a sterile organ. However, culture-independent molecular techniques have reported that large numbers of microbes coexist in the lung and airways. The lungs harbor diverse microbial composition that are undetected by previous approaches. Many studies have found significant differences in microbial composition between during health and respiratory disease. The lung microbiome is likely to not only influence susceptibility or causes of diseases but be affected by disease activities or responses to treatment. Although lung microbiome research has some limitations from study design to reporting, it can add further dimensionality to host-microbe interactions. Moreover, there is a possibility that extending understanding to the lung microbiome with new multiple omics approaches would be useful for developing both diagnostic and prognostic biomarkers for respiratory diseases in clinical settings.

scholarly journals Spatial metabolomics of in situ, host-microbe interactions

2019 ◽  
Author(s):  
Benedikt K Geier ◽  
Emilia Sogin ◽  
Dolma Michellod ◽  
Moritz Janda ◽  
Mario Kompauer ◽  
...  
Keyword(s):  
Microbial Interactions ◽  
Host Cells ◽  
Metabolic Phenotype ◽  
Community Members ◽  
Metabolic Phenotypes ◽  
Culture Independent ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
Atmospheric Pressure Mass Spectrometry

Spatial metabolomics describes the location and chemistry of small molecules involved in metabolic phenotypes, defense molecules and chemical interactions in natural communities. Most current techniques are unable to spatially link the genotype and metabolic phenotype of microorganisms in situ at a scale relevant to microbial interactions. Here, we present a spatial metabolomics pipeline (metaFISH) that combines fluorescence in situ hybridization (FISH) microscopy and high-resolution atmospheric pressure mass spectrometry imaging (AP-MALDI-MSI) to image host-microbe symbioses and their metabolic interactions. metaFISH aligns and integrates metabolite and fluorescent images at the micrometer-scale for a spatial assignment of host and symbiont metabolites on the same tissue section. To illustrate the advantages of metaFISH, we mapped the spatial metabolome of a deep-sea mussel and its intracellular symbiotic bacteria at the scale of individual epithelial host cells. Our analytical pipeline revealed metabolic adaptations of the epithelial cells to the intracellular symbionts, a variation in metabolic phenotypes in one symbiont type, and novel symbiosis metabolites. metaFISH provides a culture-independent approach to link metabolic phenotypes to community members in situ - a powerful tool for microbiologists across fields.

scholarly journals Application of a Neutral Community Model To Assess Structuring of the Human Lung Microbiome

mBio ◽  
2015 ◽  
Vol 6 (1) ◽  
Author(s):  
Arvind Venkataraman ◽  
Christine M. Bassis ◽  
James M. Beck ◽  
Vincent B. Young ◽  
Jeffrey L. Curtis ◽  
...  
Keyword(s):  
Oral Cavity ◽  
Bacterial Species ◽  
Neutral Model ◽  
Differential Growth ◽  
Healthy Human ◽  
Bacterial Populations ◽  
Active Selection ◽  
Lung Microbiome ◽  
Human Lungs ◽  
Healthy Lung

ABSTRACT DNA from phylogenetically diverse microbes is routinely recovered from healthy human lungs and used to define the lung microbiome. The proportion of this DNA originating from microbes adapted to the lungs, as opposed to microbes dispersing to the lungs from other body sites and the atmosphere, is not known. We use a neutral model of community ecology to distinguish members of the lung microbiome whose presence is consistent with dispersal from other body sites and those that deviate from the model, suggesting a competitive advantage to these microbes in the lungs. We find that the composition of the healthy lung microbiome is consistent with predictions of the neutral model, reflecting the overriding role of dispersal of microbes from the oral cavity in shaping the microbial community in healthy lungs. In contrast, the microbiome of diseased lungs was readily distinguished as being under active selection. We also assessed the viability of microbes from lung samples by cultivation with a variety of media and incubation conditions. Bacteria recovered by cultivation from healthy lungs represented species that comprised 61% of the 16S rRNA-encoding gene sequences derived from bronchoalveolar lavage samples.IMPORTANCE  Neutral distribution of microbes is a distinguishing feature of the microbiome in healthy lungs, wherein constant dispersal of bacteria from the oral cavity overrides differential growth of bacteria. No bacterial species consistently deviated from the model predictions in healthy lungs, although representatives of many of the dispersed species were readily cultivated. In contrast, bacterial populations in diseased lungs were identified as being under active selection. Quantification of the relative importance of selection and neutral processes such as dispersal in shaping the healthy lung microbiome is a first step toward understanding its impacts on host health.

scholarly journals Interactions of Bacteriophages and Bacteria at the Airway Mucosa: New Insights Into the Pathophysiology of Asthma

2021 ◽  
Vol 1 ◽  
Author(s):  
Panagiota Tzani-Tzanopoulou ◽  
Dimitrios Skliros ◽  
Spyridon Megremis ◽  
Paraskevi Xepapadaki ◽  
Evangelos Andreakos ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Airway Epithelial Cells ◽  
Molecular Techniques ◽  
Airway Epithelial ◽  
Microbial Composition ◽  
Bacterial Populations ◽  
Tripartite Interactions ◽  
Airway Mucosa ◽  
Culture Independent ◽  
System Disorder

The airway epithelium is the primary site where inhaled and resident microbiota interacts between themselves and the host, potentially playing an important role on allergic asthma development and pathophysiology. With the advent of culture independent molecular techniques and high throughput technologies, the complex composition and diversity of bacterial communities of the airways has been well-documented and the notion of the lungs' sterility definitively rejected. Recent studies indicate that the microbial composition of the asthmatic airways across the spectrum of disease severity, differ significantly compared with healthy individuals. In parallel, a growing body of evidence suggests that bacterial viruses (bacteriophages or simply phages), regulating bacterial populations, are present in almost every niche of the human body and can also interact directly with the eukaryotic cells. The triptych of airway epithelial cells, bacterial symbionts and resident phages should be considered as a functional and interdependent unit with direct implications on the respiratory and overall homeostasis. While the role of epithelial cells in asthma pathophysiology is well-established, the tripartite interactions between epithelial cells, bacteria and phages should be scrutinized, both to better understand asthma as a system disorder and to explore potential interventions.

Enterococcus species diversity in fecal samples of wild marine species as determined by real-time PCR

2017 ◽  
Vol 63 (2) ◽  
pp. 129-136 ◽  
Author(s):  
Aline Weber Medeiros ◽  
Derek Blaese Amorim ◽  
Maurício Tavares ◽  
Tiane Martin de Moura ◽  
Ana Claudia Franco ◽  
...  
Keyword(s):  
Real Time ◽  
Enterococcus Faecalis ◽  
Marine Species ◽  
Molecular Techniques ◽  
Enterococcus Species ◽  
Microbial Composition ◽  
Fecal Samples ◽  
Fur Seals ◽  
Culture Independent ◽  
Red Knot

Analyses using culture-independent molecular techniques have improved our understanding of microbial composition. The aim of this work was to identify and quantify enterococci in fecal samples of wild marine species using real-time quantitative PCR. Seven Enterococcus species were examined in fecal DNA of South American fur seals (Arctocephalus australis), Subantarctic fur seals (Arctocephalus tropicalis), green turtles (Chelonia mydas), Magellanic penguins (Spheniscus magellanicus), snowy-crowned tern (Sterna trudeaui), white-backed stilt (Himantopus melanurus), white-chinned petrels (Procellaria aequinoctialis), red knot (Calidris canutus), and black-browed albatross (Thalassarche melanophris). All Enterococcus species evaluated were detected in all fecal samples of wild marine species, with a concentration ranging between 106 and 1012 copies/ng of total DNA. Differences in the enterococci distribution were observed. Enterococcus faecalis and Enterococcus mundtii were most abundant in marine mammals. Enterococcus faecalis was frequent in green turtle, Magellanic penguin, snowy-crowned tern, red knot, and black-browed albatross. Enterococcus hirae and Enterococcus gallinarum showed elevated occurrence in white-backed stilt, and Enterococcus faecium in white-chinned petrel. This study showed highest diversity of enterococci in feces of wild marine species than currently available data, and reinforced the use of culture-independent analysis to help us to enhance our understanding of enterococci in gastrointestinal tracts of wild marine species.

scholarly journals Making the invisible visible: exploring host–microbiome interactions across different taxa using data-driven 3D visualization

2021 ◽  
Author(s):  
Susanne H. Landis ◽  
Tom Duscher ◽  
Thomas C.G. Bosch
Keyword(s):  
3D Visualization ◽  
Interactive Media ◽  
Visual Communication Design ◽  
Microbiome Research ◽  
Scientific Poster ◽  
Microbe Interactions ◽  
Health And Disease ◽  
Host Microbe Interactions ◽  
Using Data ◽  
User Friendly

The importance of microbiome research is rapidly gaining momentum for understanding its role in development, evolution, ecology, health and disease. Recent progress in community and single-cell genomic approaches has provided an unprecedented amount of information on the abundance and ecology of microbes in different host organisms and turned them into metaorganisms. A metaorganism is a host and its complete microbial community which is commonly referred to as the microbiome. Over half the cells in a human body are not human but belong to the multitude of species that compose our microbiome. However, linkages between metaorganisms from different taxa and their in situ level of intraspecific dependence (be it growth, division or metabolic activity) are much more scarce. Visualization therefore is crucial for understanding host–microbe interactions as well as overarching concepts in different host organisms. Here we introduce an innovative user-friendly method for interactive visualization of microbiome multi-omics data. The new communication format combines science and visual communication design. Interactive media are used to transform scientific findings on host–microbe interactions in an intuitive way. The method provides access to additional layers of information that cannot be visualized using a traditional platform. We demonstrate the usefulness of this visualization approach using the interactive scientific poster ‘Digital Meta’, which is designed to support not only interdisciplinary co-working but also communication with the general public.

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 The Murine Lung Microbiome Changes During Lung Inflammation and Intranasal Vancomycin Treatment

2015 ◽  
Vol 9 (1) ◽  
pp. 167-179 ◽  
Author(s):  
Kenneth Klingenberg Barfod ◽  
Katleen Vrankx ◽  
Hengameh Chloé Mirsepasi-Lauridsen ◽  
Jitka Stilund Hansen ◽  
Karin Sørig Hougaard ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Lung Inflammation ◽  
Lung Diseases ◽  
Oral Exposure ◽  
Murine Lung ◽  
Microbial Identification ◽  
Adult Mice ◽  
Lung Microbiome ◽  
Culture Independent ◽  
Microbiome Research

Most microbiome research related to airway diseases has focused on the gut microbiome. This is despite advances in culture independent microbial identification techniques revealing that even healthy lungs possess a unique dynamic microbiome. This conceptual change raises the question; if lung diseases could be causally linked to local dysbiosis of the local lung microbiota. Here, we manipulate the murine lung and gut microbiome, in order to show that the lung microbiota can be changed experimentally. We have used four different approaches: lung inflammation by exposure to carbon nano-tube particles, oral probiotics and oral or intranasal exposure to the antibiotic vancomycin. Bacterial DNA was extracted from broncho-alveolar and nasal lavage fluids, caecum samples and compared by DGGE. Our results show that: the lung microbiota is sex dependent and not just a reflection of the gut microbiota, and that induced inflammation can change lung microbiota. This change is not transferred to offspring. Oral probiotics in adult mice do not change lung microbiome detectible by DGGE. Nasal vancomycin can change the lung microbiome preferentially, while oral exposure does not. These observations should be considered in future studies of the causal relationship between lung microbiota and lung diseases.

scholarly journals Meta-analysis of diets used in Drosophila microbiome research and introduction of the Drosophila Dietary Composition Calculator (DDCC)

2020 ◽  
Author(s):  
Danielle N.A. Lesperance ◽  
Nichole A. Broderick
Keyword(s):  
Meta Analysis ◽  
Standard Diet ◽  
Dietary Composition ◽  
Community Resources ◽  
Nutritional Content ◽  
Web Based ◽  
Microbiome Composition ◽  
Microbiome Research ◽  
Microbe Interactions ◽  
Host Microbe Interactions

AbstractWhile the term standard diet is commonly used in studies using Drosophila melanogaster, more often than not these diets are anything but standard, making it difficult to contextualize results in the broader scope of the field. This is especially evident in microbiome studies, despite diet having a pivotal role in microbiome composition and resulting host-microbe interactions. Here, we performed a meta-analysis of diets used in fly microbiome research and provide a web-based tool for researchers to determine the nutritional content of diets of interest. Our goal is for these community resources to aid in contextualizing both past and future microbiome studies (with utility to other fields as well) to better understand how individual lab diets can contribute to observed phenotypes.

scholarly journals Recent advances in understanding the ecology of the lung microbiota and deciphering the gut-lung axis

2020 ◽  
Vol 319 (4) ◽  
pp. L710-L716 ◽  
Author(s):  
Kent A. Willis ◽  
Justin D. Stewart ◽  
Namasivayam Ambalavanan
Keyword(s):  
Next Generation Sequencing ◽  
Ecological Perspective ◽  
Next Generation ◽  
Sequencing Technologies ◽  
Lung Microbiome ◽  
Recent Advances ◽  
Organ Systems ◽  
Culture Independent ◽  
Microbiome Research ◽  
Generation Sequencing

A rapidly expanding new field of lung research has been produced by the emergence of culture-independent next-generation sequencing technologies. While pulmonary microbiome research lags behind the exploration of the microbiome in other organ systems, the field is maturing and has recently produced multiple exciting discoveries. In this mini-review, we will explore recent advances in our understanding of the lung microbiome and the gut-lung axis from an ecological perspective.

scholarly journals Missing Links: the Role of Primates in Understanding the Human Microbiome

mSystems ◽  
2019 ◽  
Vol 4 (3) ◽  
Author(s):  
Katherine R. Amato
Keyword(s):  
Life History ◽  
Life History Theory ◽  
Human Microbiome ◽  
Cultural Influences ◽  
Microbiome Research ◽  
Allocation Patterns ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
Host Life ◽  
Energy Balances

ABSTRACT The gut microbiome can influence host energy balances and metabolic programming. While this information is valuable in a disease context, it also has important implications for understanding host energetics from an ecological and evolutionary perspective. Here I argue that gut microbial influences on host life history—the timing of events that make up an organism's life—are an overlooked but robust area of study given that variation in life history is linked directly to host energetic budgets and allocation patterns. Additionally, while cultural influences on life history complicate the exploration of these links in humans, nonhuman primates represent an alternative system in which more robust associations can be made. By integrating human and nonhuman primate microbiome research within the context of life history theory, we will be able to more effectively pinpoint microbial contributions to host phenotypes. This information will improve our understanding of host-microbe interactions in health and disease and will transform the fields of ecology and evolution more generally.

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