Gut and oral bacterial diversity of the lizard Diploderma splendidum investigated using metagenomic analysis

Abstract Background Gut and oral microbial communities are complex and play a key role in their co-evolution with their hosts. However, little is understood about the bacterial community in lizards. In this study, we first investigated the gut and oral bacterial community in Diploderma splendidum from Sichuan Province, China. Metagenomic analysis of feces and oral cavity samples showed distinct differences between Diploderma splendidum and Liolaemus parvus, and L. ruibali and Phymaturus williamsi species. Results Bacteridetes, Firmicutes, Proteobacteria and Fusobacteria were the most abundant phyla in fecal samples. However, the composition of the gut bacterial community of insectivorous lizards (Diploderma splendidum) exhibited unique abundance of phyla Proteobacteria and Chlamydiae when compared with L. parvus, L. ruibali and P. williamsi. Furthermore, Proteobacteria were abundant in oral cavity samples, followed by Actinobacteria, Chlamydiae and Firmicutes. Most striking was that the phylum Chlamydiae was most common in the oral cavity of Diploderma splendidum, when compared with a carnivorous lizard (Varanus komodoensis). In addition, more than 26 bacterial species were detected in the gut and/or oral cavity that were identified as potential human pathogens. Conclusions In this study, metagenomic analysis was carried out to reveal the gut and oral microbiomes, which brought new insight into the complex bacterial community and ecology in Diploderma splendidum.

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Microbial Communities, Metabolites, Fermentation Quality and Aerobic Stability of Whole-Plant Corn Silage Collected from Family Farms in Desert Steppe of North China

Processes ◽

10.3390/pr9050784 ◽

2021 ◽

Vol 9 (5) ◽

pp. 784

Author(s):

Chao Wang ◽

Lin Sun ◽

Haiwen Xu ◽

Na Na ◽

Guomei Yin ◽

...

Keyword(s):

Microbial Communities ◽

Bacterial Diversity ◽

Fungal Diversity ◽

North China ◽

Bacterial Species ◽

Fungal Species ◽

Family Farms ◽

Aerobic Stability ◽

Whole Plant ◽

Lactobacillus Kefiri

Whole-plant corn silages on family farms were sampled in Erdos (S1), Baotou (S2), Ulanqab (S3), and Hohhot (S4) in North China, after 300 d of ensiling. The microbial communities, metabolites, and aerobic stability were assessed. Lactobacillusbuchneri, Acinetobacter johnsonii, and unclassified Novosphingobium were present at greater abundances than others in S2 with greater bacterial diversity and metabolites. Lactobacillus buchneri, Lactobacillus parafarraginis, Lactobacillus kefiri, and unclassified Lactobacillus accounted for 84.5%, and 88.2%, and 98.3% of bacteria in S1, S3, and S4, respectively. The aerobic stability and fungal diversity were greater in S1 and S4 with greater abundances of unclassified Kazachstania, Kazachstania bulderi, Candida xylopsoci, unclassified Cladosporium, Rhizopus microspores, and Candida glabrata than other fungi. The abundances of unclassified Kazachstania in S2 and K. bulderi in S3 were 96.2% and 93.6%, respectively. The main bacterial species in S2 were L. buchneri, A. johnsonii, and unclassified Novosphingobium; Lactobacillus sp. dominated bacterial communities in S1, S3, and S4. The main fungal species in S1 and S4 were unclassified Kazachstania, K. bulderi, C. xylopsoci, unclassified Cladosporium, R. microspores, and C. glabrata; Kazachstania sp. dominated fungal communities in S2 and S3. The high bacterial diversity aided the accumulation of metabolites, and the broad fungal diversity improved the aerobic stability.

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The functional ClpXP protease of Chlamydia trachomatis requires distinct clpP genes from separate genetic loci

Scientific Reports ◽

10.1038/s41598-019-50505-5 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 9

Author(s):

Stefan Pan ◽

Imran T. Malik ◽

Dhana Thomy ◽

Beate Henrichfreise ◽

Peter Sass

Keyword(s):

Chlamydia Trachomatis ◽

Bacterial Species ◽

Human Pathogens ◽

Bacterial Physiology ◽

Sexually Transmitted ◽

Clp Proteases ◽

Obligate Intracellular Pathogen ◽

Antibacterial Target ◽

Insight Into

Abstract Clp proteases play a central role in bacterial physiology and, for some bacterial species, are even essential for survival. Also due to their conservation among bacteria including important human pathogens, Clp proteases have recently attracted considerable attention as antibiotic targets. Here, we functionally reconstituted and characterized the ClpXP protease of Chlamydia trachomatis (ctClpXP), an obligate intracellular pathogen and the causative agent of widespread sexually transmitted diseases in humans. Our in vitro data show that ctClpXP is formed by a hetero-tetradecameric proteolytic core, composed of two distinct homologs of ClpP (ctClpP1 and ctClpP2), that associates with the unfoldase ctClpX via ctClpP2 for regulated protein degradation. Antibiotics of the ADEP class interfere with protease functions by both preventing the interaction of ctClpX with ctClpP1P2 and activating the otherwise dormant proteolytic core for unregulated proteolysis. Thus, our results reveal molecular insight into ctClpXP function, validating this protease as an antibacterial target.

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Transition of Bacterial Diversity and Composition in Tongue Microbiota during the First Two Years of Life

mSphere ◽

10.1128/msphere.00187-19 ◽

2019 ◽

Vol 4 (3) ◽

Cited By ~ 1

Author(s):

Shinya Kageyama ◽

Mikari Asakawa ◽

Toru Takeshita ◽

Yukari Ihara ◽

Shunsuke Kanno ◽

...

Keyword(s):

Oral Cavity ◽

Bacterial Diversity ◽

Bacterial Species ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Oral Microbiota ◽

Bacterial Composition ◽

Content Type ◽

Operational Taxonomic Units ◽

Rrna Gene Sequencing

ABSTRACTNewborns are constantly exposed to various microbes from birth; hence, diverse commensal bacteria colonize the oral cavity. However, how or when these bacteria construct a complex and stable ecosystem remains unclear. This prospective cohort study examined the temporal changes in bacterial diversity and composition in tongue microbiota during infancy. We longitudinally collected a total of 464 tongue swab samples from 8 infants (age of <6 months at baseline) for approximately 2 years. We also collected samples from 32 children (aged 0 to 2 years) and 73 adults (aged 20 to 29 years) cross-sectionally as control groups. Bacterial diversities and compositions were determined by 16S rRNA gene sequencing. The tongue bacterial diversity in infancy, measured as the number of observed operational taxonomic units (OTUs), rapidly increased and nearly reached the same level as that in adults by around 80 weeks. The overall tongue bacterial composition in the transitional phase, 80 to 120 weeks, was more similar to that of adults than to that of the early exponential phase (EEP), 10 to 29 weeks, according to analysis of similarities. Dominant OTUs in the EEP corresponding toStreptococcus perorisandStreptococcus lactariusexponentially decreased immediately after EEP, around 30 to 49 weeks, whereas several OTUs corresponding toGranulicatella adiacens,Actinomyces odontolyticus, andFusobacterium periodonticumreciprocally increased during the same period. These results suggest that a drastic compositional shift of tongue microbiota occurs before the age of 1 year, and then bacterial diversity and overall bacterial composition reach levels comparable to those in adults by the age of 2 years.IMPORTANCEEvaluating the development of oral microbiota during infancy is important for understanding the subsequent colonization of bacterial species and the process of formation of mature microbiota in the oral cavity. We examined tongue microbiota longitudinally collected from 8 infants and found that drastic compositional shifts in tongue microbiota occur before the age of 1 year, and then bacterial diversity and overall bacterial composition reach levels comparable to those in adults by the age of 2 years. These results may be helpful for preventing the development of various diseases associated with oral microbiota throughout life.

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The Microbial Signature Provides Insight into the Mechanistic Basis of Coral Success across Reef Habitats

mBio ◽

10.1128/mbio.00560-16 ◽

2016 ◽

Vol 7 (4) ◽

Cited By ~ 78

Author(s):

Alejandra Hernandez-Agreda ◽

William Leggat ◽

Pim Bongaerts ◽

Tracy D. Ainsworth

Keyword(s):

Bacterial Community ◽

Microbial Communities ◽

Microbial Interactions ◽

Environmental Distribution ◽

Core Microbiome ◽

Spatial And Temporal Scales ◽

Select Group ◽

Mechanistic Basis ◽

Number Of Bacteria ◽

Insight Into

ABSTRACT For ecosystems vulnerable to environmental change, understanding the spatiotemporal stability of functionally crucial symbioses is fundamental to determining the mechanisms by which these ecosystems may persist. The coral Pachyseris speciosa is a successful environmental generalist that succeeds in diverse reef habitats. The generalist nature of this coral suggests it may have the capacity to form functionally significant microbial partnerships to facilitate access to a range of nutritional sources within different habitats. Here, we propose that coral is a metaorganism hosting three functionally distinct microbial interactions: a ubiquitous core microbiome of very few symbiotic host-selected bacteria, a microbiome of spatially and/or regionally explicit core microbes filling functional niches (<100 phylotypes), and a highly variable bacterial community that is responsive to biotic and abiotic processes across spatial and temporal scales (>100,000 phylotypes). We find that this coral hosts upwards of 170,000 distinct phylotypes and provide evidence for the persistence of a select group of bacteria in corals across environmental habitats of the Great Barrier Reef and Coral Sea. We further show that a higher number of bacteria are consistently associated with corals on mesophotic reefs than on shallow reefs. An increase in microbial diversity with depth suggests reliance by this coral on bacteria for nutrient acquisition on reefs exposed to nutrient upwelling. Understanding the complex microbial communities of host organisms across broad biotic and abiotic environments as functionally distinct microbiomes can provide insight into those interactions that are ubiquitous niche symbioses and those that provide competitive advantage within the hosts’ environment. IMPORTANCE Corals have been proposed as the most diverse microbial biosphere. The high variability of microbial communities has hampered the identification of bacteria playing key functional roles that contribute to coral survival. Exploring the bacterial community in a coral with a broad environmental distribution, we found a group of bacteria present across all environments and a higher number of bacteria consistently associated with mesophotic corals (60 to 80 m). These results provide evidence of consistent and ubiquitous coral-bacterial partnerships and support the consideration of corals as metaorganisms hosting three functionally distinct microbiomes: a ubiquitous core microbiome, a microbiome filling functional niches, and a highly variable bacterial community.

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Low Pore Connectivity Increases Bacterial Diversity in Soil

Applied and Environmental Microbiology ◽

10.1128/aem.03085-09 ◽

2010 ◽

Vol 76 (12) ◽

pp. 3936-3942 ◽

Cited By ~ 139

Author(s):

Jennifer K. Carson ◽

Vanesa Gonzalez-Quiñones ◽

Daniel V. Murphy ◽

Christoph Hinz ◽

Jeremy A. Shaw ◽

...

Keyword(s):

Bacterial Community ◽

Water Potential ◽

Bacterial Diversity ◽

Pore Space ◽

Bacterial Species ◽

Chemical Properties ◽

Fundamental Principle ◽

Pore Connectivity ◽

Competition Theory ◽

Water Potentials

ABSTRACTOne of soil microbiology's most intriguing puzzles is how so many different bacterial species can coexist in small volumes of soil when competition theory predicts that less competitive species should decline and eventually disappear. We provide evidence supporting the theory that low pore connectivity caused by low water potential (and therefore low water content) increases the diversity of a complex bacterial community in soil. We altered the pore connectivity of a soil by decreasing water potential and increasing the content of silt- and clay-sized particles. Two textures were created, without altering the chemical properties or mineral composition of the soil, by adding silt- and clay-sized particles of quartz to a quartz-based sandy soil at rates of 0% (sand) or 10% (silt+clay). Both textures were incubated at several water potentials, and the effect on the active bacterial communities was measured using terminal restriction fragment length polymorphism (TRFLP) of bacterial 16S rRNA. Bacterial richness and diversity increased as water potential decreased and soil became drier (P< 0.012), but they were not affected by texture (P> 0.553). Bacterial diversity increased at water potentials of ≤2.5 kPa in sand and ≤4.0 kPa in silt+clay, equivalent to ≤56% water-filled pore space (WFPS) in both textures. The bacterial community structure in soil was affected by both water potential and texture (P< 0.001) and was correlated with WFPS (sum of squared correlations [δ2] = 0.88,P< 0.001). These findings suggest that low pore connectivity is commonly experienced by soil bacteria under field conditions and that the theory of pore connectivity may provide a fundamental principle to explain the high diversity of bacteria in soil.

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Paraburkholderia edwinii protects Aspergillus sp. from phenazines by acting as a toxin sponge

10.1101/2021.03.28.437412 ◽

2021 ◽

Author(s):

Kurt M. Dahlstrom ◽

Dianne K. Newman

Keyword(s):

Microbial Communities ◽

Bacterial Species ◽

Acid Stress ◽

Human Infection ◽

Common Mechanism ◽

The Novel ◽

Human Pathogens ◽

Fungal Partner ◽

Redox Active ◽

Aspergillus Sp

SummaryMany environmentally and clinically important fungi are sensitive to toxic, bacterially-produced, redox-active molecules called phenazines. Despite being vulnerable to phenazine-assault, fungi inhabit microbial communities that contain phenazine producers. Because many fungi cannot withstand phenazine challenge, but some bacterial species can, we hypothesized that bacterial partners may protect fungi in phenazine-replete environments. In the first soil sample we collected, we co-isolated several such physically associated pairings. We discovered the novel species Paraburkholderia edwinii and demonstrated it can protect a co-isolated Aspergillus species from phenazine-1-carboxylic acid (PCA) by sequestering it, acting as a toxin sponge; in turn, it also gains protection. When challenged with PCA, P. edwinii changes its morphology, forming aggregates within the growing fungal colony. Further, the fungal partner triggers P. edwinii to sequester PCA and maintains conditions that limit PCA toxicity by promoting an anoxic and highly reducing environment. A mutagenic screen revealed this program depends on the stress-inducible transcriptional repressor HrcA. We show that one relevant stressor in response to PCA challenge is fungal acidification and that acid stress causes P. edwinii to behave as though the fungus were present. Finally, we reveal this phenomenon as widespread among Paraburkholderia with moderate specificity among bacterial and fungal partners, including plant and human pathogens. Our discovery suggests a common mechanism by which fungi can gain access to phenazine-replete environments, and provides a tractable model system for its study. These results have implications for how rhizosphere microbial communities as well as plant and human infection sites are policed for fungal membership.

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