Host species, pathogens and disease associated with divergent nasal microbial communities in tortoises

Diverse bacterial communities are found on every surface of macro-organisms, and they play important roles in maintaining normal physiological functions in their hosts. While the study of microbiomes has expanded with the influx of data enabled by recent technological advances, microbiome research in reptiles lags behind other organisms. We sequenced the nasal microbiomes in a sample of four North American tortoise species, and we found differing community compositions among tortoise species and sampling sites, with higher richness and diversity in Texas and Sonoran desert tortoises. Using these data, we investigated the prevalence and operational taxonomic unit (OTU) diversity of the potential pathogen Pasteurella testudinis and found it to be common, abundant and highly diverse. However, the presence of this bacterium was not associated with differences in bacterial community composition within host species. We also found that the presence of nasal discharge from tortoises at the time of sampling was associated with a decline in diversity and a change in microbiome composition, which we posit is due to the harsh epithelial environment associated with immune responses. Repeated sampling across seasons, and at different points of pathogen colonization, should contribute to our understanding of the causes and consequences of different bacterial communities in these long-lived hosts.

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Dominance of coniferous and broadleaved trees drives bacterial associations with boreal feather mosses

10.1101/2022.01.07.475413 ◽

2022 ◽

Author(s):

Juanita C. Rodríguez-Rodríguez ◽

Yves Bergeron ◽

Steven W. Kembel ◽

Nicole J. Fenton

Keyword(s):

Environmental Conditions ◽

Host Species ◽

Bacterial Communities ◽

Forest Type ◽

Bacterial Community Composition ◽

Tree Canopy ◽

Rrna Gene ◽

Eastern Canada ◽

Spruce Forests ◽

Α Diversity

The composition of ecologically important moss-associated bacterial communities seems to be mainly driven by host species, but may also be shaped by environmental conditions related with tree-canopy dominance. The moss phyllosphere has been studied in coniferous forests while broadleaf forests remain understudied. To determine if host species or environmental conditions defined by tree-canopy dominance drives the bacterial diversity in the moss phyllosphere, we used 16S rRNA gene amplicon sequencing to quantify changes in bacterial communities as a function of host species (Pleurozium schreberi and Ptilium crista-castrensis) and forest type (coniferous black spruce versus deciduous broadleaf trembling aspen) in eastern Canada. Forest type, not host species, was the main factor affecting moss phyllosphere bacterial community composition, though the interaction of both variables was significant. Bacterial α-diversity was highest in spruce forests, while there was greater turnover (β-diversity) and higher γ-diversity in aspen forests. Unexpectedly, Cyanobacteria were much more relatively abundant in aspen than in spruce forests, with the bacterial family Nostocaceae (Cyanobacteria) differing the most between both forest types. Our results suggest that the increasing change in dominance from coniferous to broadleaf trees due to natural and anthropic disturbances is likely to affect the composition of moss-associated bacteria in boreal forests.

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The bacterial communities of Alaskan mosses and their contributions to N2-fixation

Microbiome ◽

10.1186/s40168-021-01001-4 ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Hannah Holland-Moritz ◽

Julia E. M. Stuart ◽

Lily R. Lewis ◽

Samantha N. Miller ◽

Michelle C. Mack ◽

...

Keyword(s):

Microbial Communities ◽

High Latitude ◽

Host Species ◽

Bacterial Communities ◽

Light Availability ◽

Species Identity ◽

Moss Species ◽

Microbiome Composition ◽

Site Characteristics ◽

Host Identity

Abstract Background Mosses in high-latitude ecosystems harbor diverse bacterial taxa, including N2-fixers which are key contributors to nitrogen dynamics in these systems. Yet the relative importance of moss host species, and environmental factors, in structuring these microbial communities and their N2-fixing potential remains unclear. We studied 26 boreal and tundra moss species across 24 sites in Alaska, USA, from 61 to 69° N. We used cultivation-independent approaches to characterize the variation in moss-associated bacterial communities as a function of host species identity and site characteristics. We also measured N2-fixation rates via 15N2 isotopic enrichment and identified potential N2-fixing bacteria using available literature and genomic information. Results Host species identity and host evolutionary history were both highly predictive of moss microbiome composition, highlighting strong phylogenetic coherence in these microbial communities. Although less important, light availability and temperature also influenced composition of the moss microbiome. Finally, we identified putative N2-fixing bacteria specific to some moss hosts, including potential N2-fixing bacteria outside well-studied cyanobacterial clades. Conclusions The strong effect of host identity on moss-associated bacterial communities demonstrates mosses’ utility for understanding plant-microbe interactions in non-leguminous systems. Our work also highlights the likely importance of novel bacterial taxa to N2-fixation in high-latitude ecosystems.

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Bacterial community composition of the sea grape Caulerpa lentillifera: a comparison between healthy and diseased states

10.1101/2021.06.30.450479 ◽

2021 ◽

Author(s):

German Kopprio ◽

Nguyen Dinh Luyen ◽

Le Huu Cuong ◽

Anna Fricke ◽

Andreas Kunzmann ◽

...

Keyword(s):

Bacterial Communities ◽

Bacterial Community Composition ◽

Operational Taxonomic Unit ◽

Disease Outbreak ◽

Antimicrobial Compounds ◽

Attached Bacteria ◽

Caulerpa Lentillifera ◽

The Family ◽

The Tropics

The bacterial communities of the sea grape Caulerpa lentillifera were studied during a disease outbreak in Vietnam. The Rhodobacteraceae and Rhodovulum dominated the composition of healthy C. lentillifera. Clear differences between healthy and diseased cases were observed at order, genus and Operational Taxonomic Unit (OTU) level. Bacterial diversity was lower in healthy C. lentillifera, probably because of antimicrobial compounds from the macroalgae and/or from Clostridium, Cutibacterium or Micrococcus bacteria. The likely beneficial role of Bradyrhizobium, Paracoccus and Brevundimonas strains on nutrient cycling and phytohormone production was discussed. The white coloration of diseased C. lentillifera may not only be associated with pathogens but also with an oxidative response. Aquibacter, Winogradskyella and other OTUs of the family Flavobacteriaceae were hypothesized as detrimental bacteria, this family comprises some well-known seaweed pathogens. Moreover, Thalassobius OTU 2935 and 1635 may represent detrimental Rhodobacteraceae. Phycisphaera together with other Planctomycetes and Woeseia were probably saprophytes of C. lentillifera. This study offers pioneering insights on the co-occurrence of C. lentillifera-attached bacteria, potential detrimental or beneficial microbes, and a baseline for understanding the C. lentillifera holobiont. Further metagenomic and biotechnological approaches are needed to confirm functions of some microbes on this macroalgae to enhance food security in the tropics.

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Chironomus ramosus Larval Microbiome Composition Provides Evidence for the Presence of Detoxifying Enzymes

Microorganisms ◽

10.3390/microorganisms9081571 ◽

2021 ◽

Vol 9 (8) ◽

pp. 1571

Author(s):

Rotem Sela ◽

Sivan Laviad-Shitrit ◽

Leena Thorat ◽

Bimalendu B. Nath ◽

Malka Halpern

Keyword(s):

Aquatic Insects ◽

Bacterial Community Composition ◽

Laboratory Culture ◽

Metagenomic Analysis ◽

Sequence Variants ◽

Microbiota Composition ◽

Detoxifying Enzymes ◽

Toxic Compounds ◽

Microbiome Composition ◽

Bacterial Genes

Chironomids (Diptera; Chironomidae) are aquatic insects that are abundant in freshwater. We aimed to study the endogenous microbiota composition of Chironomus ramosus larvae that were sampled from the Mutha River and a laboratory culture in India. Furthermore, we performed a metagenomic analysis of the larval microbiome, sampled from the Mutha River. Significant differences were found between the bacterial community composition of C. ramosus larvae that were sampled from the Mutha River and the laboratory culture. A total of 54.7% of the amplicon sequence variants (ASVs) that were identified in the larvae from the Mutha River were unique, compared to only 12.9% of unique ASVs that were identified from the laboratory-reared larvae. The four most abundant phyla across all samples were: Proteobacteria, Fusobacteria, Firmicutes, and Bacteroidetes, while the nine most abundant genera were: Aeromonas, Alkanindiges, Breznakia, Cetobacterium, Chryseobacterium, Desulfovibrio, Dysgonomonas, Thiothrix, and Vibrio. Moreover, in the metagenomic analysis, we detected bacterial genes and bacterial pathways that demonstrated the ability to degrade different toxic compounds, detoxify metal, and confer resistance to antibiotics and UV radiation, amongst other functions. The results illuminate the fact that there are detoxifying enzymes in the C. ramosus larval microbiome that possibly play a role in protecting the insect in polluted environments.

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Integration of culture-dependent and independent methods provides a more coherent picture of the pig gut microbiome

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa022 ◽

2020 ◽

Vol 96 (3) ◽

Cited By ~ 2

Author(s):

Gavin J Fenske ◽

Sudeep Ghimire ◽

Linto Antony ◽

Jane Christopher-Hennings ◽

Joy Scaria

Keyword(s):

Bacterial Communities ◽

Bacterial Species ◽

Shotgun Metagenomics ◽

Culture Techniques ◽

Microbiome Composition ◽

Culture Independent ◽

Health And Disease ◽

The Media ◽

And Function ◽

Culture Dependent

ABSTRACT Bacterial communities resident in the hindgut of pigs, have profound impacts on health and disease. Investigations into the pig microbiome have utilized either culture-dependent, or far more commonly, culture-independent techniques using next generation sequencing. We contend that a combination of both approaches generates a more coherent view of microbiome composition. In this study, we surveyed the microbiome of Tamworth breed and feral pigs through the integration high throughput culturing and shotgun metagenomics. A single culture medium was used for culturing. Selective screens were added to the media to increase culture diversity. In total, 46 distinct bacterial species were isolated from the Tamworth and feral samples. Selective screens successfully shifted the diversity of bacteria on agar plates. Tamworth pigs are highly dominated by Bacteroidetes primarily composed of the genus Prevotella whereas feral samples were more diverse with almost equal proportions of Firmicutes and Bacteroidetes. The combination of metagenomics and culture techniques facilitated a greater retrieval of annotated genes than either method alone. The single medium based pig microbiota library we report is a resource to better understand pig gut microbial ecology and function. It allows for assemblage of defined bacterial communities for studies in bioreactors or germfree animal models.

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Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale

Applied and Environmental Microbiology ◽

10.1128/aem.00335-09 ◽

2009 ◽

Vol 75 (15) ◽

pp. 5111-5120 ◽

Cited By ~ 1989

Author(s):

Christian L. Lauber ◽

Micah Hamady ◽

Rob Knight ◽

Noah Fierer

Keyword(s):

Bacterial Community ◽

Soil Ph ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

Spatial Scales ◽

Bacterial Community Composition ◽

Phylogenetic Structure ◽

Soil Bacterial Communities ◽

Soil Bacterial Community Structure ◽

Soil Bacterial

ABSTRACT Soils harbor enormously diverse bacterial populations, and soil bacterial communities can vary greatly in composition across space. However, our understanding of the specific changes in soil bacterial community structure that occur across larger spatial scales is limited because most previous work has focused on either surveying a relatively small number of soils in detail or analyzing a larger number of soils with techniques that provide little detail about the phylogenetic structure of the bacterial communities. Here we used a bar-coded pyrosequencing technique to characterize bacterial communities in 88 soils from across North and South America, obtaining an average of 1,501 sequences per soil. We found that overall bacterial community composition, as measured by pairwise UniFrac distances, was significantly correlated with differences in soil pH (r = 0.79), largely driven by changes in the relative abundances of Acidobacteria, Actinobacteria, and Bacteroidetes across the range of soil pHs. In addition, soil pH explains a significant portion of the variability associated with observed changes in the phylogenetic structure within each dominant lineage. The overall phylogenetic diversity of the bacterial communities was also correlated with soil pH (R2 = 0.50), with peak diversity in soils with near-neutral pHs. Together, these results suggest that the structure of soil bacterial communities is predictable, to some degree, across larger spatial scales, and the effect of soil pH on bacterial community composition is evident at even relatively coarse levels of taxonomic resolution.

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Rhizobacterial communities of five co-occurring desert halophytes

PeerJ ◽

10.7717/peerj.5508 ◽

2018 ◽

Vol 6 ◽

pp. e5508 ◽

Cited By ~ 3

Author(s):

Yan Li ◽

Yan Kong ◽

Dexiong Teng ◽

Xueni Zhang ◽

Xuemin He ◽

...

Keyword(s):

Bacterial Community ◽

Community Composition ◽

Plant Species ◽

Bacterial Communities ◽

Bacterial Community Composition ◽

Community Diversity ◽

Species Identity ◽

Halostachys Caspica ◽

Lycium Ruthenicum ◽

Limonium Gmelinii

BackgroundRecently, researches have begun to investigate the microbial communities associated with halophytes. Both rhizobacterial community composition and the environmental drivers of community assembly have been addressed. However, few studies have explored the structure of rhizobacterial communities associated with halophytic plants that are co-occurring in arid, salinized areas.MethodsFive halophytes were selected for study: these co-occurred in saline soils in the Ebinur Lake Nature Reserve, located at the western margin of the Gurbantunggut Desert of Northwestern China. Halophyte-associated bacterial communities were sampled, and the bacterial 16S rDNA V3–V4 region amplified and sequenced using the Illumina Miseq platform. The bacterial community diversity and structure were compared between the rhizosphere and bulk soils, as well as among the rhizosphere samples. The effects of plant species identity and soil properties on the bacterial communities were also analyzed.ResultsSignificant differences were observed between the rhizosphere and bulk soil bacterial communities. Diversity was higher in the rhizosphere than in the bulk soils. Abundant taxonomic groups (from phylum to genus) in the rhizosphere were much more diverse than in bulk soils. Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Planctomycetes were the most abundant phyla in the rhizosphere, while Proteobacteria and Firmicutes were common in bulk soils. Overall, the bacterial community composition were not significantly differentiated between the bulk soils of the five plants, but community diversity and structure differed significantly in the rhizosphere. The diversity ofHalostachys caspica,Halocnemum strobilaceumandKalidium foliatumassociated bacterial communities was lower than that ofLimonium gmeliniiandLycium ruthenicumcommunities. Furthermore, the composition of the bacterial communities ofHalostachys caspicaandHalocnemum strobilaceumwas very different from those ofLimonium gmeliniiandLycium ruthenicum. The diversity and community structure were influenced by soil EC, pH and nutrient content (TOC, SOM, TON and AP); of these, the effects of EC on bacterial community composition were less important than those of soil nutrients.DiscussionHalophytic plant species played an important role in shaping associated rhizosphere bacterial communities. When salinity levels were constant, soil nutrients emerged as key factors structuring bacterial communities, while EC played only a minor role. Pairwise differences among the rhizobacterial communities associated with different plant species were not significant, despite some evidence of differentiation. Further studies involving more halophyte species, and individuals per species, are necessary to elucidate plant species identity effects on the rhizosphere for co-occurring halophytes.

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The Prenatal Microbiome: A New Player for Human Health

High-Throughput ◽

10.3390/ht7040038 ◽

2018 ◽

Vol 7 (4) ◽

pp. 38 ◽

Cited By ~ 11

Author(s):

Valeria D’Argenio

Keyword(s):

Health Status ◽

Microbial Communities ◽

Fetal Development ◽

Reproductive Medicine ◽

Current Knowledge ◽

Human Microbiome ◽

Future Perspectives ◽

Microbiome Composition ◽

Umbilical Blood ◽

Technological Advances

The last few years have featured an increasing interest in the study of the human microbiome and its correlations with health status. Indeed, technological advances have allowed the study of microbial communities to reach a previously unthinkable sensitivity, showing the presence of microbes also in environments usually considered as sterile. In this scenario, microbial communities have been described in the amniotic fluid, the umbilical blood cord, and the placenta, denying a dogma of reproductive medicine that considers the uterus like a sterile womb. This prenatal microbiome may play a role not only in fetal development but also in the predisposition to diseases that may develop later in life, and also in adulthood. Thus, the aim of this review is to report the current knowledge regarding the prenatal microbiome composition, its association with pathological processes, and the future perspectives regarding its manipulation for healthy status promotion and maintenance.

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The dilution effect limits plasmid horizontal transmission in multispecies bacterial communities

Microbiology ◽

10.1099/mic.0.001086 ◽

2021 ◽

Vol 167 (9) ◽

Author(s):

Anastasia Kottara ◽

Laura Carrilero ◽

Ellie Harrison ◽

James P. J. Hall ◽

Michael A. Brockhurst

Keyword(s):

Host Species ◽

Bacterial Communities ◽

Horizontal Transmission ◽

Dilution Effect ◽

Infection Risk ◽

Host Cells ◽

Evolutionary Innovation ◽

Genomic Divergence ◽

Plasmid Diversity ◽

Plasmid Conjugation

By transferring ecologically important traits between species, plasmids drive genomic divergence and evolutionary innovation in their bacterial hosts. Bacterial communities are often diverse and contain multiple coexisting plasmids, but the dynamics of plasmids in multi-species communities are poorly understood. Here, we show, using experimental multi-species communities containing two plasmids, that bacterial diversity limits the horizontal transmission of plasmids due to the ‘dilution effect’; this is an epidemiological phenomenon whereby living alongside less proficient host species reduces the expected infection risk for a focal host species. In addition, plasmid horizontal transmission was also affected by plasmid diversity, such that the rate of plasmid conjugation was reduced from co-infected host cells carrying both plasmids. In diverse microbial communities, plasmid spread may be limited by the dilution effect and plasmid–plasmid interactions, reducing the rate of horizontal transmission.

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Quorum Sensing Regulates the Hydrolytic Enzyme Production and Community Composition of Heterotrophic Bacteria in Coastal Waters

Frontiers in Microbiology ◽

10.3389/fmicb.2021.780759 ◽

2021 ◽

Vol 12 ◽

Author(s):

Marion Urvoy ◽

Raphaël Lami ◽

Catherine Dreanno ◽

Daniel Delmas ◽

Stéphane L’Helguen ◽

...

Keyword(s):

Quorum Sensing ◽

Community Composition ◽

Coastal Waters ◽

Bacterial Communities ◽

Heterotrophic Bacteria ◽

Bacterial Community Composition ◽

Marine Ecosystem ◽

Hydrolytic Enzyme ◽

Enzymatic Activities ◽

Hydrolytic Activities

Heterotrophic microbial communities play a central role in biogeochemical cycles in the ocean by degrading organic matter through the synthesis of extracellular hydrolytic enzymes. Their hydrolysis rates result from the community’s genomic potential and the differential expression of this genomic potential. Cell-cell communication pathways such as quorum sensing (QS) could impact both aspects and, consequently, structure marine ecosystem functioning. However, the role of QS communications in complex natural assemblages remains largely unknown. In this study, we investigated whether N-acylhomoserine lactones (AHLs), a type of QS signal, could regulate both hydrolytic activities and the bacterial community composition (BCC) of marine planktonic assemblages. To this extent, we carried out two microcosm experiments, adding five different AHLs to bacterial communities sampled in coastal waters (during early and peak bloom) and monitoring their impact on enzymatic activities and diversity over 48 h. Several specific enzymatic activities were impacted during both experiments, as early as 6 h after the AHL amendments. The BCC was also significantly impacted by the treatments after 48 h, and correlated with the expression of the hydrolytic activities, suggesting that changes in hydrolytic intensities may drive changes in BCC. Overall, our results suggest that QS communication could participate in structuring both the function and diversity of marine bacterial communities.

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