scholarly journals Characterization of shifts of koala (Phascolarctos cinereus) intestinal microbial communities associated with antibiotic treatment

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4452 ◽  
Author(s):  
Katherine E. Dahlhausen ◽  
Ladan Doroud ◽  
Alana J. Firl ◽  
Adam Polkinghorne ◽  
Jonathan A. Eisen
Keyword(s):  
Microbial Communities ◽  
Antibiotic Treatment ◽  
Intestinal Flora ◽  
Alpha Diversity ◽  
Intestinal Microbiome ◽  
Rrna Gene ◽  
Phascolarctos Cinereus ◽  
Network Analyses ◽  
Eucalyptus Leaves ◽  
Arboreal Marsupials

Koalas (Phascolarctos cinereus) are arboreal marsupials native to Australia that eat a specialized diet of almost exclusively eucalyptus leaves. Microbes in koala intestines are known to break down otherwise toxic compounds, such as tannins, in eucalyptus leaves. Infections by Chlamydia, obligate intracellular bacterial pathogens, are highly prevalent in koala populations. If animals with Chlamydia infections are received by wildlife hospitals, a range of antibiotics can be used to treat them. However, previous studies suggested that koalas can suffer adverse side effects during antibiotic treatment. This study aimed to use 16S rRNA gene sequences derived from koala feces to characterize the intestinal microbiome of koalas throughout antibiotic treatment and identify specific taxa associated with koala health after treatment. Although differences in the alpha diversity were observed in the intestinal flora between treated and untreated koalas and between koalas treated with different antibiotics, these differences were not statistically significant. The alpha diversity of microbial communities from koalas that lived through antibiotic treatment versus those who did not was significantly greater, however. Beta diversity analysis largely confirmed the latter observation, revealing that the overall communities were different between koalas on antibiotics that died versus those that survived or never received antibiotics. Using both machine learning and OTU (operational taxonomic unit) co-occurrence network analyses, we found that OTUs that are very closely related to Lonepinella koalarum, a known tannin degrader found by culture-based methods to be present in koala intestines, was correlated with a koala’s health status. This is the first study to characterize the time course of effects of antibiotics on koala intestinal microbiomes. Our results suggest it may be useful to pursue alternative treatments for Chlamydia infections without the use of antibiotics or the development of Chlamydia-specific antimicrobial compounds that do not broadly affect microbial communities.

scholarly journals Gut Microbiome Analysis As A Non-Invasive Tool for the Early Diagnosis of Cholangiocarcinoma

2021 ◽  
Author(s):  
Jialiang Li ◽  
Xueyan Li ◽  
Sina Zhang ◽  
Chen Jin ◽  
Zixia Lin ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Gut Microbiome ◽  
Microbial Community Composition ◽  
Intestinal Flora ◽  
Alpha Diversity ◽  
16S Rrna Gene Sequencing ◽  
Intestinal Microbiome ◽  
Rrna Gene ◽  
Non Invasive ◽  
Hepatobiliary Cancer

Abstract BACKGROUNDThe liver-microbiome axis is implicated in the pathogenesis of hepatobiliary cancer, and the role of the gut microbiota in cholangiocarcinoma (CCA) remains unclear.METHODWe conducted a case-control study on the intestinal flora of 33 CCA patients and 47 cholelithiasis individuals. We performed 16S rRNA gene sequencing to identify disease-related gut microbiota and assess the potential of the intestinal microbiome as a non-invasive biomarker for CCA.RESULTWe found that gut microbiome of CCA patients had a significantly higher alpha diversity (Shannon and Observed species indices, p = 0.006 and p = 0.02, respectively) and an overall different microbial community composition (p = 0.032). The genus Muribaculaceae_unclassified was most strongly associated with CCA (p < 0.001). We put forward a disease predictive model including twelve intestinal microbiome genera distinguished CCA patients from CF patients with an area under curve (AUC) of approximately 0.93 (95%CI, 0.85–0.987). The forecasting performance of this model was better than CA19-9. Moreover, genera Ezakiella and Garciella were only observed among intrahepatic cholangiocarcinoma patients. Further, we assessed predicted functional modules alternations CCA patients and uncovered a microbiota pattern specific to CCA.CONCLUSIONOur findings provide evidence of the intestinal microbiome as a non-invasive biomarker for CCA.

scholarly journals Influence of Family Integrated Care on the Intestinal Microbiome of Preterm Infants With Necrotizing Enterocolitis and Enterostomy: A Preliminary Study

2021 ◽  
Vol 9 ◽  
Author(s):  
Mengyang Yang ◽  
Juan Du ◽  
Qin Yang ◽  
Wenyan Dou ◽  
Min Jiang ◽  
...  
Keyword(s):  
Integrated Care ◽  
Preterm Infants ◽  
Necrotizing Enterocolitis ◽  
Premature Infants ◽  
Intestinal Flora ◽  
Intestinal Microbiome ◽  
Rrna Gene ◽  
Α Diversity ◽  
Family Integrated Care ◽  
Family Integrated

The aim of this study was to investigate the influence of family integrated care (FICare) on the intestinal microbiome of preterm infants with necrotizing enterocolitis and enterostomy. This was a prospective pilot study at Beijing Children's Hospital. Premature infants with an enterostomy who met the enrollment criteria were divided into the 2-week FICare and non-FICare groups (non-randomly). We collected their fecal samples and subjected the intestinal microbiomes to 16S rRNA gene sequencing. Operational taxonomic units (OTU) were analyzed to assess the intestinal microbiome richness, and we then carried out α-diversity, β-diversity, and species clustering analyses and a linear discriminant analysis (LDA) effect size (LEfSe) analysis to identify the differences in the microbial communities between the two groups. There were 12 patients enrolled in the study (FICare, n = 7; non-FICare, n = 5). There were no significant between-group differences in demographic characteristics, or in the relative abundances of phyla and genera. The major bacterial phyla were Proteobacteria, Firmicutes, and Actinobacteria, and Serratia, Enterococcus, Cronobacter, and Bifidobacterium dominated at the genus level. The α-diversity analysis indicated that the intestinal flora was more diverse in the non-FICare group than the FICare group (p &lt; 0.05). However, most of the other indicators did not suggest a difference between the two groups. There was a high proportion of shared OTUs between the two groups, and the PCoA and clustering analyses indicated that the two groups were difficult to distinguish, indicating that the intestinal microbiomes were relatively similar between the groups. In summary, short-term FICare had no significant positive effect on the establishment of intestinal flora diversity in premature infants with necrotizing enterocolitis and enterostomy. The trial was registered in the Chinese Clinical Trial Registry (ChiCTR-OPN-17011801).

scholarly journals Association between the microbiomes of tonsil and saliva samples isolated from pediatric patients subjected to tonsillectomy for the treatment of tonsillar hyperplasia

2020 ◽  
Vol 52 (9) ◽  
pp. 1564-1573
Author(s):  
Da Hyeon Choi ◽  
Jiwon Park ◽  
Ju Kwang Choi ◽  
Kyeong Eun Lee ◽  
Won Hee Lee ◽  
...  
Keyword(s):  
Oral Cavity ◽  
Microbial Communities ◽  
Alpha Diversity ◽  
16S Rrna Gene Sequencing ◽  
Diversity Indices ◽  
Rrna Gene ◽  
Strong Positive Correlation ◽  
Korean Children ◽  
Positive Correlation ◽  
Tonsillar Hyperplasia

Abstract Oral microbes have the capacity to spread throughout the gastrointestinal system and are strongly associated with multiple diseases. Given that tonsils are located between the oral cavity and the laryngopharynx at the gateway of the alimentary and respiratory tracts, tonsillar tissue may also be affected by microbiota from both the oral cavity (saliva) and the alimentary tract. Here, we analyzed the distribution and association of the microbial communities in the saliva and tonsils of Korean children subjected to tonsillectomy because of tonsil hyperplasia (n = 29). The microbiome profiles of saliva and tonsils were established via 16S rRNA gene sequencing. Based on the alpha diversity indices, the microbial communities of the two groups showed high similarities. According to Spearman’s ranking correlation analysis, the distribution of Treponema, the causative bacterium of periodontitis, in saliva and tonsils was found to have a significant positive correlation. Two representative microbes, Prevotella in saliva and Alloprevotella in tonsils, were negatively correlated, while Treponema 2 showed a strong positive correlation between saliva and tonsils. Taken together, strong similarities in the microbial communities of the tonsils and saliva are evident in terms of diversity and composition. The saliva microbiome is expected to significantly affect the tonsil microbiome. Furthermore, we suggest that our study creates an opportunity for tonsillar microbiome research to facilitate the development of novel microbiome-based therapeutic strategies.

scholarly journals Impact of Early Life Antibiotic Exposure and Neonatal Hyperoxia on the Murine Microbiome and Lung Injury

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Melissa H. Althouse ◽  
Christopher Stewart ◽  
Weiwu Jiang ◽  
Bhagavatula Moorthy ◽  
Krithika Lingappan
Keyword(s):  
Lung Injury ◽  
Beta Diversity ◽  
Alpha Diversity ◽  
Intestinal Microbiome ◽  
Rrna Gene ◽  
Antibiotic Exposure ◽  
Neonatal Mice ◽  
Intestinal Dysbiosis ◽  
Neonatal Hyperoxia

Abstract Cross talk between the intestinal microbiome and the lung and its role in lung health remains unknown. Perinatal exposure to antibiotics disrupts the neonatal microbiome and may have an impact on the preterm lung. We hypothesized that perinatal antibiotic exposure leads to long-term intestinal dysbiosis and increased alveolar simplification in a murine hyperoxia model. Pregnant C57BL/6 wild type dams and neonatal mice were treated with antibiotics before and/or immediately after delivery. Control mice received phosphate-buffered saline (PBS). Neonatal mice were exposed to 95% oxygen for 4 days or room air. Microbiome analysis was performed using 16S rRNA gene sequencing. Pulmonary alveolarization and vascularization were analyzed at postnatal day (PND) 21. Perinatal antibiotic exposure modified intestinal beta diversity but not alpha diversity in neonatal mice. Neonatal hyperoxia exposure altered intestinal beta diversity and relative abundance of commensal bacteria in antibiotic treated mice. Hyperoxia disrupted pulmonary alveolarization and vascularization at PND 21; however, there were no differences in the degree of lung injury in antibiotic treated mice compared to vehicle treated controls. Our study suggests that exposure to both hyperoxia and antibiotics early in life may cause long-term alterations in the intestinal microbiome, but intestinal dysbiosis may not significantly influence neonatal hyperoxic lung injury.

scholarly journals Impact of Diabetes on the Gut and Salivary IgA Microbiomes

2020 ◽  
Vol 88 (12) ◽  
Author(s):  
Eric L. Brown ◽  
Heather T. Essigmann ◽  
Kristi L. Hoffman ◽  
Noah W. Palm ◽  
Sarah M. Gunter ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Immunoglobulin A ◽  
Alpha Diversity ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Host Immune Responses ◽  
Mucosal Surfaces ◽  
Immune Mediated ◽  
Rrna Gene Sequencing ◽  
Immune Exclusion

ABSTRACT Mucosal surfaces like those present in the lung, gut, and mouth interface with distinct external environments. These mucosal gateways are not only portals of entry for potential pathogens but also homes to microbial communities that impact host health. Secretory immunoglobulin A (SIgA) is the single most abundant acquired immune component secreted onto mucosal surfaces and, via the process of immune exclusion, shapes the architecture of these microbiomes. Not all microorganisms at mucosal surfaces are targeted by SIgA; therefore, a better understanding of the SIgA-coated fraction may identify the microbial constituents that stimulate host immune responses in the context of health and disease. Chronic diseases like type 2 diabetes are associated with altered microbial communities (dysbiosis) that in turn affect immune-mediated homeostasis. 16S rRNA gene sequencing of SIgA-coated/uncoated bacteria (IgA-Biome) was conducted on stool and saliva samples of normoglycemic participants and individuals with prediabetes or diabetes (n = 8/group). These analyses demonstrated shifts in relative abundance in the IgA-Biome profiles between normoglycemic, prediabetic, or diabetic samples distinct from that of the overall microbiome. Differences in IgA-Biome alpha diversity were apparent for both stool and saliva, while overarching bacterial community differences (beta diversity) were also observed in saliva. These data suggest that IgA-Biome analyses can be used to identify novel microbial signatures associated with diabetes and support the need for further studies exploring these communities. Ultimately, an understanding of the IgA-Biome may promote the development of novel strategies to restructure the microbiome as a means of preventing or treating diseases associated with dysbiosis at mucosal surfaces.

scholarly journals Putative functions and co-occurrence patterns of the microbial communities in natural and engineered ecosystems

2021 ◽  
Author(s):  
Yu Xia ◽  
Na Li ◽  
Yiyun Chen ◽  
Weijia Li ◽  
Xuwen He ◽  
...  
Keyword(s):  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Wastewater Treatment Plants ◽  
Rrna Gene ◽  
Natural Environments ◽  
Anaerobic Digesters ◽  
Network Analyses ◽  
Wb Network ◽  
Almost All ◽  
Occurrence Patterns

Abstract Understanding functions and co-occurrence patterns of microbial communities in various ecosystems enriches the knowledge on ecosystem characteristics and microbial ecology. However, such analyses have rarely been reported. Herein, functions and inter-taxa correlations of microbial communities in a set of natural environments (farmland (SA), forest soil (SB) and Caspian Sea sediments (CSS)) and engineered ecosystems (wastewater treatment plants (FW, WA and WB) and anaerobic digesters (AD)) were studied based on FAPROTAX and network analyses, respectively, by a collection of 115 samples from seven published 16S rRNA gene datasets generated by high-throughput sequencing. The results show that chemoheterotrophy related populations were the most abundant in almost all the communities. Their relative abundances (RAs) in the AD systems were the highest (43.7%±4.2%), followed by those of the soil environments (40.2%±1.9% in SA and 36.4%±2.0% in SB). For each ecosystem, the indicative community and overall community showed differentiations in several function categories. For example, the SA and SB indicative communities showed higher RAs in aerobic chemoheterotrophy, the CSS indicative community showed higher RAs in sulfate respiration, the AD indicative community showed higher RAs in fermentation, and the WB indicative community included higher RAs of predatory/exoparasitic bacteria. Three molecular ecological networks of the communities from the AD, WB and SB datasets were constructed, respectively. The WB network showed the highest proportion of negative correlations (70.4%), possibly attributed to the environmental pressure which aggravated microbial competition. The positively correlated taxa showed lower phylogenetic distances than the negatively correlated taxa on average in each network.

scholarly journals The Microbiota Diversity Following Antibiotic Treatment of Clostridium Difficile Infection

2020 ◽  
Author(s):  
Dana Binyamin ◽  
Orna Nitzan ◽  
Maya Azrad ◽  
Zohar Hamo ◽  
Omry Koren ◽  
...  
Keyword(s):  
Clostridium Difficile ◽  
Gut Microbiota ◽  
Antibiotic Treatment ◽  
Gut Microbiome ◽  
Diarrheal Disease ◽  
Medical Center ◽  
Disease Onset ◽  
Intestinal Microbiome ◽  
Rrna Gene ◽  
Stool Samples

Abstract Background: Clostridium difficile (C. difficile) is a major nosocomial pathogen that infects the human gut and can cause diarrheal disease. A dominant risk factor is antibiotic treatment that disrupts the normal gut microbiota. The aim of the study was to examine the correlation between antibiotic treatment received prior to C. difficile infection (CDI) onset and patient gut microbiota.Methods: Stool samples were collected from patients with CDI, presenting at the Baruch Padeh Medical Center Poriya, Israel. Demographic and clinical information, including previous antibiotic treatments, was collected from patient charts, and CDI severity score was calculated. Bacteria were isolated from stool samples, and gut microbiome was analyzed by sequencing the 16S rRNA gene using the Illumina MiSeq platform and QIIME2.Results: In total, 84 patients with C. difficile infection were enrolled in the study; all had received antibiotics prior to disease onset. Due to comorbidities, 46 patients (55%) had received more than one class of antibiotics. The most common class of antibiotics used was cephalosporins (n=44 cases). The intestinal microbiota of the patients was not uniform. Differences in intestinal microbiome were influenced by the different combinations of antibiotics that the patients had received (p = 0.022)Conclusions: The number of different antibiotics administered has a major impact on the CDI patients gut microbiome, mainly on bacterial richness.

scholarly journals Microbiota diversity following antibiotic treatment of Clostridium difficile infection

2020 ◽  
Author(s):  
Dana Binyamin ◽  
Orna Nitzan ◽  
Maya Azrad ◽  
Zohar Hamo ◽  
Omry Koren ◽  
...  
Keyword(s):  
Clostridium Difficile ◽  
Gut Microbiota ◽  
Antibiotic Treatment ◽  
Gut Microbiome ◽  
Diarrheal Disease ◽  
Medical Center ◽  
Disease Onset ◽  
Intestinal Microbiome ◽  
Rrna Gene ◽  
Stool Samples

Abstract Background: Clostridium difficile (C. difficile) is a major nosocomial pathogen that infects the human gut and can cause C. difficile infection (CDI), a diarrheal disease. A dominant risk factor is antibiotic treatment, which disrupts the normal gut microbiota. The aim of the study was to examine the correlation between antibiotic treatment received prior to CDI onset and patient gut microbiota during the infection.Methods: Stool samples were collected from patients with CDI, presenting at the Baruch Padeh Medical Center Poriya, Israel. Demographic and clinical information, including previous antibiotic treatments, was collected from patient charts, and CDI severity score was calculated. Bacteria were isolated from stool samples, and gut microbiome was analyzed by sequencing the 16S rRNA gene, using the Illumina MiSeq platform and QIIME2.Results: In total, 84 patients with CDI were enrolled in the study; all had received antibiotics prior to disease onset. Due to comorbidities, 46 patients (55%) received more than one class of antibiotics. The most common class of antibiotics used was cephalosporins (n=44 cases). The intestinal microbiota of the patients was not uniform. Differences in intestinal microbiome were influenced by the different numbers of antibiotics families that the patients received (p = 0.022)Conclusions: The number of different antibiotics amount has a major impact on the gut microbiome of CDI patients, particularly on its bacterial richness.

scholarly journals Locally Adapted Mimulus Ecotypes Differentially Impact Rhizosphere Bacterial and Archaeal Communities in an Environment-Dependent Manner

2020 ◽  
Vol 4 (1) ◽  
pp. 53-63 ◽  
Author(s):  
Alan W. Bowsher ◽  
Patrick J. Kearns ◽  
Damian Popovic ◽  
David B. Lowry ◽  
Ashley Shade
Keyword(s):  
Microbial Communities ◽  
Plant Root ◽  
Alpha Diversity ◽  
Local Environment ◽  
Rrna Gene ◽  
Transplant Experiment ◽  
Dependent Manner ◽  
Reciprocal Transplant Experiment ◽  
Soil Microbial Community Structure ◽  
Host Identity

Plant root−microbe interactions influence plant productivity, health, and resistance to stress. Although there is evidence that plant species and even genotypes can alter soil microbial community structure, environmental conditions can potentially outweigh plant genetic effects. Here, we used a reciprocal transplant experiment to understand the contributions of the environment and the host plant to rhizosphere microbiome composition in locally adapted ecotypes of Mimulus guttatus (syn. Erythranthe guttata). Two genotypes of a coastal ecotype and two genotypes of an inland ecotype were planted at coastal and inland sites. After 3 months, we collected rhizosphere and bulk soil and assessed microbial communities by 16S rRNA gene sequencing. We found that local environment (coastal versus inland site) strongly influenced rhizosphere communities, at least in part due to distinct local microbial species pools. Host identity played a smaller role: at each site, the ecotypes exhibited remarkably similar composition of microbial communities at the class level, indicating that divergent M. guttatus ecotypes recruit phylogenetically similar rhizosphere communities, even in environments to which they are maladapted. Nevertheless, the two ecotypes significantly differed in community composition at both sites due, in part, to an exclusive set of taxa associated with each ecotype. They also differed in alpha diversity at the inland site. Although this indicates that locally adapted M. guttatus ecotypes are genetically diverged in factors shaping rhizosphere communities, our findings highlight the context-specific interactions between host identity and local environment that shape those communities. [Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

scholarly journals Exposure to airborne bacteria depends upon vertical stratification and vegetation complexity

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jake M. Robinson ◽  
Christian Cando-Dumancela ◽  
Rachael E. Antwis ◽  
Ross Cameron ◽  
Craig Liddicoat ◽  
...  
Keyword(s):  
Green Space ◽  
Habitat Type ◽  
Alpha Diversity ◽  
Vertical Stratification ◽  
Rrna Gene ◽  
Urban Landscapes ◽  
Near Surface ◽  
Urban Green ◽  
Urban Green Spaces ◽  
Network Analyses

AbstractExposure to biodiverse aerobiomes supports human health, but it is unclear which ecological factors influence exposure. Few studies have investigated near-surface green space aerobiome dynamics, and no studies have reported aerobiome vertical stratification in different urban green spaces. We used columnar sampling and next generation sequencing of the bacterial 16S rRNA gene, combined with geospatial and network analyses to investigate urban green space aerobiome spatio-compositional dynamics. We show a strong effect of habitat on bacterial diversity and network complexity. We observed aerobiome vertical stratification and network complexity that was contingent on habitat type. Tree density, closer proximity, and canopy coverage associated with greater aerobiome alpha diversity. Grassland aerobiomes exhibited greater proportions of putative pathogens compared to scrub, and also stratified vertically. We provide novel insights into the urban ecosystem with potential importance for public health, whereby the possibility of differential aerobiome exposures appears to depend on habitat type and height in the airspace. This has important implications for managing urban landscapes for the regulation of aerobiome exposure.

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