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29 Sep 2020 at 01:46
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Bibliography on: Microbiome


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RJR: Recommended Bibliography 29 Sep 2020 at 01:46 Created: 


It has long been known that every multicellular organism coexists with large prokaryotic ecosystems — microbiomes — that completely cover its surfaces, external and internal. Recent studies have shown that these associated microbiomes are not mere contamination, but instead have profound effects upon the function and fitness of the multicellular organism. We now know that all MCEs are actually functional composites, holobionts, composed of more prokaryotic cells than eukaryotic cells and expressing more prokaryotic genes than eukaryotic genes. A full understanding of the biology of "individual" eukaryotes will now depend on an understanding of their associated microbiomes.

Created with PubMed® Query: microbiome[tiab] NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)


RevDate: 2020-09-28

Thijssen M, Tacke F, Beller L, et al (2020)

Clinical relevance of plasma virome dynamics in liver transplant recipients.

EBioMedicine, 60:103009 pii:S2352-3964(20)30385-6 [Epub ahead of print].

BACKGROUND: The role of the microbiome in liver transplantation (LT) outcome has received a growing interest in the past decades. In contrast to bacteria, the role of endogenous viral communities, known as the virome, is poorly described. Here, we applied a viral metagenomic approach to study the dynamic evolution of circulating viruses in the plasma of LT recipients and its effect on the clinical course of patients.

METHODS: Patients chronically infected with hepatitis B virus (HBV) that received a LT due to endstage liver disease were included in this study. Longitudinal plasma samples were collected pre- and post-LT. Intact viral particles were isolated and sequenced on an Illumina HiSeq 2500 platform. Short read libraries were analysed with an in-house bioinformatics pipeline. Key endpoints were the dynamics of viral families and post-LT complications.

FINDINGS: The initiation of immunosuppression induced a bloom of the Anelloviridae that dominated the post-LT plasma virome. A variety of post-LT complication were observed. Nephrotoxicity was reported in 38% of the patients and was associated with a high abundance of anelloviruses. Besides nephrotoxicity, 16 (67%) patients experienced flares of viral or bacterial infections in post-transplant follow-up. These flares were recognized by an increased burden of anelloviruses (p < 0.05). Interestingly, no mortality was observed in patients infected with human pegivirus.

INTERPRETATION: These findings suggest a diagnostic potential for the Anelloviridae family in post-LT complications. Furthermore, the impact of human pegivirus infection on post-transplant survival should be further investigated.

FUNDING: This trial was supported by Gilead Sciences grant number BE-2017-000133.

RevDate: 2020-09-26

Malik I, Batra T, Das S, et al (2020)

Light at night affects gut microbial community and negatively impacts host physiology in diurnal animals: Evidence from captive zebra finches.

Microbiological research, 241:126597 pii:S0944-5013(20)30465-1 [Epub ahead of print].

The gastrointestinal tract (GIT) hosts a large number of diverse microorganisms, with mutualistic interactions with the host. Here, in two separate experiments, we investigated whether light at night (LAN) would affect GIT microbiota and, in turn, the host physiology in diurnal zebra finches (Taeniopygia guttata). Experiment I assessed the effects of no-night (LL) and dimly illuminated night (dim light at night, dLAN) on fecal microbiota diversity and host physiology of birds born and raised under 12 h photoperiod (LD; 12 h light: 12 h darkness). Under LL and dLAN, compared to LD, we found a significant increase in the body mass, subcutaneous fat deposition and hepatic accumulation of lipids. Although we found no difference in total 24 h food consumption, LL/ dLAN birds ate also at night, suggesting LAN-induced alteration in daily feeding times. Concurrently, there were marked differences in amplicon sequence and bacterial species richness between LD and LAN, with notable decline in Lactobacillus richness in birds under LL and dLAN. We attributed declined Lactobacillus population as causal (at least partially) to negative effects on the host metabolism. Therefore, in experiment II with similar protocol, birds under LL and dLAN were fed on diet with or without Lactobacillus rhamnosus GG (LGG) supplement. Clearly, LGG supplement ameliorated LL- and dLAN-induced negative effects in zebra finches. These results demonstrate adverse effects of unnatural lighting on GIT bacterial diversity and host physiology, and suggest the role of GIT microbiota in the maintenance of metabolic homeostasis in response to LAN environment in diurnal animals.

RevDate: 2020-09-26

Bakker PAHM, Berendsen RL, Van Pelt JA, et al (2020)

The Soil-Borne Identity: Looking Back to the Future.

Molecular plant pii:S1674-2052(20)30312-9 [Epub ahead of print].

Looking forward includes looking back every now and then. In 2007 David Weller looked back at 30 years of biocontrol of soil-borne pathogens by Pseudomonas and signified that the progress made over decades of research provides a firm foundation to formulate current and future research questions. It has been recognized for more than a century that soil-borne microbes play a significant role in plant growth and health. The recent application of high throughput omics technologies has enabled detailed dissection of the microbial players and molecular mechanisms involved in the complex interactions in plant-associated microbiomes. Here we highlight old and emerging plant microbiome concepts related to plant disease control, and address perspectives that modern-day microbiomics technologies can bring to functionally characterize and exploit plant-associated microbiomes for the benefit of plant health in future microbiome-assisted agriculture.

RevDate: 2020-09-28

Lai WT, Zhao J, Xu SX, et al (2020)

Shotgun metagenomics reveals both taxonomic and tryptophan pathway differences of gut microbiota in bipolar disorder with current major depressive episode patients.

Journal of affective disorders, 278:311-319 pii:S0165-0327(20)32705-1 [Epub ahead of print].

BACKGROUND: The microbiome-gut-brain axis, especially the microbial tryptophan biosynthesis and metabolism pathway (MiTBamp), is closely connected to bipolar disorder with current major depressive episode (BPD).

METHODS: We performed shotgun metagenomics sequencing (SMS) of faecal samples from 25 BPD patients and 28 healthy controls (HCs). Except for the microbiota taxa and MiTBamp analyses, we also built a classification model using the Random Forests (RF) and Boruta algorithm to find the microbial biomarkers for BPD.

RESULTS: Compared to HCs, the phylum Bacteroidetes abundance was significantly reduced, whereas that of the Actinobacteria and Firmicutes were significantly increased in BPD patients. We also identified 38 species increased and 6 species decreased significantly in the BPD group. In the MiTBamp, we identified that two Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologies (KOs) (K00658 and K00837) were significantly lower in the BPD, and five KOs (K01696, K00382, K00626, K01667, and K03781) were significantly higher in the BPD group. We also identified significant genera and species which were closely related to these KOs. Finally, RF classification based on gut microbiota at the genus level can achieve an area under the receiver operating characteristic curve of 0.997.

LIMITATIONS: The features of cross-sectional design, limited sample size, the heterogeneity of bipolar disorders, and a lack of serum/plasma tryptophan concentration measurements.

CONCLUSIONS: The present findings enable a better understanding of changes in gastrointestinal microbiome and MiTBamp in BPD. Alterations of microbes may have potential as biomarkers for distinguishing the BPD patients form HCs.

RevDate: 2020-09-26

Lee JH, Lee KA, WJ Lee (2020)

Drosophila as a model system for deciphering the "host physiology-nutrition-microbiome" axis.

Current opinion in insect science pii:S2214-5745(20)30114-0 [Epub ahead of print].

For metazoans, nutritional stressors, such as undernutrition during growth and development, results in serious outcomes, including growth impairments and organ wasting. When undernutrition is accompanied by other complications, including chronic inflammation, a more complex pathophysiology may emerge, such as environmental enteropathy. Although nutrition is one of the most important environmental factors that influences host physiology, the mechanism by which undernutrition induces host pathophysiology is not fully understood. Recently, gut microbiome was found to alleviate undernutrition-induced pathophysiology in an insect model, revealing the importance of nutrition-microbiome interactions. Here, we discussed how nutrition-microbiome interactions influence host physiology, including growth, tissue homeostasis, immunity, and behavior, by regulating the central metabolic signaling pathways with an emphasis on findings made through Drosophila, an insect model.

RevDate: 2020-09-26

Zhao H, Liu J, Zhu J, et al (2020)

Bacterial composition and community structure of the oropharynx of adults with asthma are associated with environmental factors.

Microbial pathogenesis pii:S0882-4010(20)30871-8 [Epub ahead of print].

The development and exacerbation of asthma are mainly attributed to inflammatory reactions caused by allergens. However, less is known about the development of asthma caused by microbial disorders in the oropharynx and induced by environmental factors. Here, the metagenome of the oropharyngeal microbiome of adults with asthma was analysed to identify their association with air pollutants. Oropharyngeal swabs from patients with asthma were collected in two winters (W1 and W2) with different environmental factor exposures. The bacterial composition and community structure of the oropharynx were analysed through high-throughput sequencing. After analysis, the α-diversity and β-diversity exhibited significant differences between the two groups. LEfSe analysis detected 8 significantly different phyla and 11 significantly different genera between the W1 and W2 groups. Multiple linear regression analyses found that the asthma status might contribute to the alteration of microbial composition. Redundancy analysis showed that NO2 was the only environmental factor that significantly affected the microbial community structure of the oropharynx. The different genera associated with NO2 were Rothia, Actinomyces, Fusobacterium and Leptotrichia. The altered taxa related to PM2.5 were Cupriavidus and Acinetobacter. Actinobacillus and Prevotella showed a highly positive correlation with O3. Moreover, network analysis was carried out to explore the co-occurrence relationships of the main genera, and PICRUSt was conducted to predict bacterial functions. This study showed that environmental factors might cause alteration in the oropharyngeal flora, which might be a potential risk factor of asthma.

RevDate: 2020-09-26

Ruoss JL, Bazacliu C, Russell JT, et al (2020)

Routine Early Antibiotic Use in SymptOmatic Preterm Neonates (REASON): A Pilot Randomized Controlled Trial.

RevDate: 2020-09-26

Khanal P, Maltecca C, Schwab C, et al (2020)

Microbiability of meat quality and carcass composition traits in swine.

Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie [Epub ahead of print].

The impact of gut microbiome composition was investigated at different stages of production (weaning, Mid-test and Off-test) on meat quality and carcass composition traits of 1,123 three-way crossbred pigs. Data were analysed using linear mixed models which included the fixed effects of dam line, contemporary group and gender as well as the random effects of pen, animal and microbiome information at different stages. The contribution of the microbiome to all traits was prominent although it varied over time, increasing from weaning to Off-test for most traits. Microbiability estimates of carcass composition traits were greater than that of meat quality traits. Among all of the traits analysed, belly weight (BEL) had a higher microbiability estimate (0.29 ± 0.04). Adding microbiome information did not affect the estimates of genomic heritability of meat quality traits but affected the estimates of carcass composition traits. Fat depth had a greater decrease (10%) in genomic heritability at Off-test. High microbial correlations were found among different traits, particularly with traits related to fat deposition with a decrease in the genomic correlation up to 20% for loin weight and BEL. This suggested that genomic correlation was partially contributed by genetic similarity of microbiome composition. The results indicated that better understanding of microbial composition could aid the improvement of complex traits, particularly the carcass composition traits in swine by inclusion of microbiome information in the genetic evaluation process.

RevDate: 2020-09-28

Roshan N, Clancy AK, TJ Borody (2020)

Faecal Microbiota Transplantation is Effective for the Initial Treatment of Clostridium difficile Infection: A Retrospective Clinical Review.

Infectious diseases and therapy pii:10.1007/s40121-020-00339-w [Epub ahead of print].

INTRODUCTION: Clostridium difficile (C. difficile) infection (CDI) is commonly recognised as a nosocomial infection but is increasingly identified in patients in the community. Antimicrobial exposure which compromises gut microbiota is the main risk factor for CDI, although antibiotics remain the main treatment for this infection. Faecal microbiota transplantation (FMT) is also an effective treatment for CDI. FMT involves the transfer of microbiota from a healthy donor to an unwell patient. Currently FMT is mostly used after repeated antibiotic treatments fail to cure CDI. This study investigated the effect of FMT as first-line treatment for CDI to avoid repeated antibiotic damage of the microbiome.

METHODS: This retrospective, single-centre study included 59 patients between 2012 and 2017 whose first episode of CDI was treated with FMT. The patients' symptoms and presence of C. difficile in stool samples both at the baseline and post treatment were documented.

RESULTS: Fifty-four patients completed a final stool test 4-8 weeks post treatment in which 98% of patients were negative for C. difficile. There were no adverse effects. There was a significant reduction in abdominal pain, diarrhoea, bloating and blood in the stool at 4-8 weeks post treatment. Data from 24 patients who completed an extended 6 months follow-up showed significant reduction in abdominal pain, diarrhoea and blood in the stool.

CONCLUSION: This study demonstrates the safety and efficacy of FMT as first-line treatment for patients' initial episode of CDI. Future randomised studies are required to confirm FMT as the initial treatment for CDI.

RevDate: 2020-09-28

Vlot AC, Sales JH, Lenk M, et al (2020)

Systemic propagation of immunity in plants.

The New phytologist [Epub ahead of print].

Systemic immunity triggered by local plant-microbe interactions is studied as systemic acquired resistance (SAR) or induced systemic resistance (ISR) depending on the site of induction and the lifestyle of the inducing microorganism. SAR is induced by pathogens interacting with leaves, whereas ISR is induced by beneficial microbes interacting with roots. Although SA is a central component of SAR, additional signals exclusively promote systemic and not local immunity. These signals cooperate in SAR- and possibly also ISR-associated signaling networks that regulate systemic immunity. The non-SA SAR pathway is driven by pipecolic acid or its presumed bioactive derivative N-hydroxy-pipecolic acid. This pathway further regulates inter-plant defense propagation through volatile organic compounds that are emitted by SAR-induced plants and recognized as defense cues by neighboring plants. Both SAR and ISR influence phytohormone cross talk towards enhanced defense against pathogens, which at the same time affects the composition of the plant microbiome. This potentially leads to further changes in plant defense, plant-microbe, and plant-plant interactions. Therefore, we propose that such inter-organismic interactions could be combined in potentially highly effective plant protection strategies.

RevDate: 2020-09-28

Martinson JNV, ST Walk (2020)

Escherichia coli Residency in the Gut of Healthy Human Adults.

EcoSal Plus, 9(1):.

Escherichia coli is one of the most well-studied bacterial species, but several significant knowledge gaps remain regarding its ecology and natural history. Specifically, the most important factors influencing its life as a member of the healthy human gut microbiome are either underevaluated or currently unknown. Distinct E. coli population dynamics have been observed over the past century from a handful of temporal studies conducted in healthy human adults. Early studies using serology up to the most recent studies using genotyping and DNA sequencing approaches have all identified long-lived E. coli residents and short-lived transients. This review summarizes these discoveries and other studies that focused on the underlying mechanisms that lead to establishment and maintenance of E. coli residency in healthy human adults. Many fundamental knowledge gaps remain and are highlighted with the hope of facilitating future studies in this exciting research area.

RevDate: 2020-09-26

Shabat Y, Lichtenstein Y, Y Ilan (2020)

Short-Term Cohousing of Sick with Healthy or Treated Mice Alleviates the Inflammatory Response and Liver Damage.

Inflammation pii:10.1007/s10753-020-01348-0 [Epub ahead of print].

Cohousing of sick with healthy or treated animals is based on the concept of sharing an intestinal ecosystem and coprophagy, the consumption of feces, which includes sharing of the microbiome and of active drug metabolites secreted in the feces or urine. To develop a model for short-term cohousing, enabling the study of the effect of sharing an ecosystem on inflammatory states. To determine the impact of cohousing of sick and healthy mice on the immune-mediated disorders, mice injected with concanavalin A (ConA) were cohoused with healthy or sick mice or with steroid-treated or untreated mice. To determine the effect of cohousing on acetaminophen (APAP)-induced liver damage, APAP-injected mice were cohoused with N-acetyl-cysteine (NAC)-treated or untreated mice. In the ConA-induced immune-mediated hepatitis model, cohousing of sick with healthy mice was associated with the alleviation of liver damage in sick animals. Similarly, a significant decrease in serum ALT was noted in ConA-injected mice kept in the same cage as ConA-injected mice treated with steroids. A trend for reduction in liver enzymes in APAP-injected mice was observed upon cohousing with NAC-treated animals. Cohousing of sick mice with healthy or treated mice ameliorated the immune-mediated inflammatory state induced by ConA and APAP. These models for liver damage can serve as biological systems for determining the effects of alterations in the ecosystem on the immune system.

RevDate: 2020-09-28

Ye C, Xia Z, Tang J, et al (2020)

Unculturable and culturable periodontal-related bacteria are associated with periodontal inflammation during pregnancy and with preterm low birth weight delivery.

Scientific reports, 10(1):15807 pii:10.1038/s41598-020-72807-9.

Recent studies revealed culturable periodontal keystone pathogens are associated with preterm low birth weight (PLBW). However, the oral microbiome is also comprised of hundreds of 'culture-difficult' or 'not-yet-culturable' bacterial species. To explore the potential role of unculturable and culturable periodontitis-related bacteria in preterm low birth weight (PLBW) delivery, we recruited 90 pregnant women in this prospective study. Periodontal parameters, including pocket probing depth, bleeding on probing, and clinical attachment level were recorded during the second trimester and following interviews on oral hygiene and lifestyle habits. Saliva and serum samples were also collected. After delivery, birth results were recorded. Real-time PCR analyses were performed to quantify the levels of periodontitis-related unculturable bacteria (Eubacterium saphenum, Fretibacterium sp. human oral taxon(HOT) 360, TM7 sp. HOT 356, and Rothia dentocariosa), and cultivable bacteria (Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Fusobacterium nucleatum and Prevotella intermedia) in saliva samples. In addition, ELISA analyses were used to determine the IgG titres against periodontal pathogens in serum samples. Subjects were categorized into a Healthy group (H, n = 20) and periodontitis/gingivitis group (PG, n = 70) according to their periodontal status. The brushing duration was significantly lower in the PG group compared to the H group. Twenty-two of 90 subjects delivered PLBW infants. There was no significant difference in periodontal parameters and serum IgG levels for periodontal pathogens between PLBW and healthy delivery (HD) groups. However, ordinal logistic regression analysis revealed that a higher abundance of Treponema denticola, Prevotella intermedia, Fretibacterium sp. HOT360 and lower levels of Rothia dentocariosa were significantly associated with the presence of periodontal disease during pregnancy. Moreover, the amount of Eubacterium saphenum in saliva and serum IgG against Aggregatibacter actinomycetemcomitans were negatively correlated with PLBW. Taken together, unculturable periodontitis-associated bacteria may play an important role both in the presence of periodontal inflammation during pregnancy and subsequent PLBW.

RevDate: 2020-09-28

Xu M, Gao J, Li S, et al (2020)

Metagenomic analysis and identification of emerging pathogens in blood from healthy donors.

Scientific reports, 10(1):15809 pii:10.1038/s41598-020-72808-8.

Emerging infectious pathogens that threaten blood transfusions are known to be present in blood samples from healthy/qualified donors. The objective of this study was to investigate the microbiome of blood from healthy donors from the Luzhou area in southwestern China. Potential pathogens and cytomegalovirus (CMV) infection in the donor blood were identified. Total plasma nucleic acids were extracted from one pool of 5734 samples and were constructed for metagenomics analysis using Illumina sequencing. The microbiome and potential emerging/re-emerging pathogens were identified using bioinformatics analysis. Moreover, CMV antigen was measured via an enzyme-linked immunosorbent assay, and the CMV DNA level was assessed by quantitative RT-PCR. A total of 132 bacterial reads, 65 viral reads and 165 parasitic reads were obtained. The most frequent bacterium was Escherichia coli (95/132, 72%) with 95 reads in 132 bacterial reads, and the most prevalent parasite was Toxoplasma gondii (131/165, 79%). Among the viruses, cytomegalovirus (44/65, 68%) accounted for the highest frequency, followed by Hepatitis E Virus (10/65, 15%). Moreover, the positive rate of CMV-IgG was 46.25% (2652/5734), and the positive rate of CMV-IgM was 5.82% (334/5734). The positive rate of dual positive (IgG+ and IgM+) CMV was 0.07% (4/5734). Twenty-one (0.37%) specimens from 5734 donated blood samples were positive for CMV DNA. The CMV DNA levels ranged from 7.56 × 102 to 3.58 × 103 copies/mL. The current study elucidated the microbiome structure in blood from healthy/qualified donors in the Luzhou area and identified emerging/re-emerging pathogens. This preliminary study contributes to information regarding blood transfusion safety in China.

RevDate: 2020-09-28

Fish KE, Reeves-McLaren N, Husband S, et al (2020)

Unchartered waters: the unintended impacts of residual chlorine on water quality and biofilms.

NPJ biofilms and microbiomes, 6(1):34 pii:10.1038/s41522-020-00144-w.

Disinfection residuals in drinking water protect water quality and public heath by limiting planktonic microbial regrowth during distribution. However, we do not consider the consequences and selective pressures of such residuals on the ubiquitous biofilms that persist on the vast internal surface area of drinking water distribution systems. Using a full scale experimental facility, integrated analyses were applied to determine the physical, chemical and biological impacts of different free chlorine regimes on biofilm characteristics (composition, structure and microbiome) and water quality. Unexpectedly, higher free chlorine concentrations resulted in greater water quality degredation, observable as elevated inorganic loading and greater discolouration (a major cause of water quality complaints and a mask for other failures). High-chlorine concentrations also reduced biofilm cell concentrations but selected for a distinct biofilm bacterial community and inorganic composition, presenting unique risks. The results challenge the assumption that a measurable free chlorine residual necessarily assures drinking water safety.

RevDate: 2020-09-28

Koch C, Huber KJ, Bunk B, et al (2019)

Trophic networks improve the performance of microbial anodes treating wastewater.

NPJ biofilms and microbiomes, 5(1):27 pii:10.1038/s41522-019-0100-y.

Microbial anodes represent a distinct ecological niche that is characterized mainly by the terminal electron acceptor, i.e., the anode potential, and the substrate, i.e., the electron source. Here, we determine the performance and the biofilm community of anode microbiomes while using substrates of increasing complexity (organic acids or organic acids and sugar or real domestic wastewater) to mimic different, practically relevant, trophic levels. α-Diversity values increased with substrate complexity. In addition, the higher abundance value of Deltaproteobacteria in the biofilms corresponds to higher reactor performance (i.e., COD removal, current density, and Coulombic efficiency). In reactors exploiting real wastewater, the diversity of the planktonic microorganisms was only little affected. Microbiome network analysis revealed two important clusters for reactor performance as well as performance-independent pathogen-containing clusters. Interestingly, Geobacter was not found to be integrated in the network underlining its outstanding individual ecological role in line with its importance for the efficiency of the electron harvest for all reactors. The microbiome analysis of different trophic levels and their temporal development from initial colonization to stable treatment demonstrate important principles for the implementation of microbial anodes for wastewater treatment.

RevDate: 2020-09-26

Anonymous (2020)

The Gut Microbiome Dictates Whether Predisposed Mice Develop Leukemia.

Cancer discovery pii:2159-8290.CD-RW2020-139 [Epub ahead of print].

An intact gut microbiome was needed to protect genetically vulnerable mice from developing leukemia.

RevDate: 2020-09-26

Xia W, Zhao J, Zheng Y, et al (2020)

Active soil nitrifying communities revealed by in situ transcriptomics and microcosm-based stable isotope probing.

Applied and environmental microbiology pii:AEM.01807-20 [Epub ahead of print].

Long-term nitrogen (N) field fertilization often results in significant changes in nitrifying communities that catalyze a key step in the global N cycle. However, whether microcosm studies are able to inform the dynamic changes of ammonia-oxidizing bacteria (AOB) and archaea (AOA) communities under field conditions remains poorly understood. This study aimed to evaluate the transcriptional activities of nitrifying communities under in situ conditions, and we found that they were largely similar to 13C-labeled nitrifying communities in the urea-amended microcosms of soils that had received different N fertilization regimes for 22 years. High-throughput sequencing of 16S rRNA genes and transcripts suggested that Nitrosospira cluster 3 -like AOB and Nitrososphaera viennensis-like AOA were significantly stimulated in N fertilized fresh soils. Real-time quantitative PCR demonstrated that the significant increase of AOA and AOB in fresh soils upon nitrogen fertilization could be preserved in the air-dried soils. DNA-based stable isotope probing (SIP) further revealed the greatest labeling of Nitrosospira cluster 3-like AOB and N. viennensis-like AOA, despite the strong advantage of AOB over AOA in the N fertilized soils. Nitrobacter-like nitrite-oxidizing bacteria (NOB) played more important roles than Nitrospira-like NOB in urea-amended SIP microcosms, while the situation was opposite under field conditions. Our results suggest that long-term fertilization selected for physiologically versatile AOB and AOA that could have been adapted to a wide range of substrate ammonium concentrations. It also provides compelling evidences that the dominant communities of transcriptionally active nitrifiers under field conditions were largely similar to those revealed in 13C-labeled microcosms.IMPORTANCEThe role of manipulated microcosm in microbial ecology has been much debated because it cannot entirely represent the in situ situation. We collected soil samples from 20 field plots including 5 different treatments with and without nitrogen fertilizers for 22 years, in order to assess active nitrifying communities by in situ transcriptomics and microcosm-based stable isotope probing. The results showed that chronic N enrichment led to competitive advantages of Nitrosospira cluster 3-like AOB over N. viennensis-like AOA in soils under field conditions. Microcosm labeling revealed similar results of active AOA and AOB, although apparent discrepancy was observed for nitrite-oxidizing bacteria. This study suggests that soil microbiome represents a relatively stable community resulting from complex evolutionary processes over a large time scale, and microcosm can serve as a powerful tool to test the theory of environmental filtering on the key functional microbial guilds.

RevDate: 2020-09-26

Hultman J, Johansson P, J Björkroth (2020)

Longitudinal metatranscriptomic analysis of a meat spoilage microbiome detects abundant continued fermentation and environmental stress responses during shelf life and beyond.

Applied and environmental microbiology pii:AEM.01575-20 [Epub ahead of print].

Microbial food spoilage is a complex phenomenon associated with the succession of the specific spoilage organisms (SSO) over the course of time. We performed a longitudinal metatranscriptomic study on one modified atmosphere packaged (MAP) beef product to increase understanding of the longitudinal behavior of a spoilage microbiome during shelf life and onward. Based on the annotation of the mRNA reads, we recognized three stages related to the active microbiome that were descriptive for the sensory quality of the beef: acceptable product (AP), early spoilage (ES) and late spoilage (LS). Both the 16S RNA taxonomic assignments from the total RNA and functional annotations of the active genes showed that these stages were significantly different from each other. However, the functional gene annotations showed more pronounced difference than the taxonomy assignments. Psychrotrophic lactic acid bacteria (LAB) formed the core of the SSO according to the transcribed reads. Leuconostoc species were the most abundant active LAB throughout the study period, whereas the transcription activity of Streptococcaceae (mainly Lactococcus) increased after the product was spoiled. In the beginning of the experiment, the community managed environmental stress by cold-shock responses which were followed by the expression of the genes involved in managing oxidative stress. Glycolysis, pentose phosphate pathway and pyruvate metabolism were active throughout the study at a relatively stable level. However, the proportional transcription activity of the enzymes in these pathways changed over time.ImportanceIt is generally known which organisms are the typical SSO in foods, whereas the actively transcribed genes and pathways during microbial succession are poorly understood. This knowledge is important since better approaches to food quality evaluation and shelf life determination are needed. Thus, we conducted this study to find longitudinal markers that are connected to quality deterioration in a MAP beef product. These kind of RNA markers could be used to develop novel type of rapid quality analysis tools in the future. New tools are needed since even though SSO can be detected and their concentrations determined using the current microbiological methods, results from these analyses cannot predict how close timewise a spoilage community is from production of clear sensory defects. Main reason for this is that the species composition of a spoilage community does not change dramatically during late shelf life, whereas the ongoing metabolic activities lead to the development of notable sensory deterioration.

RevDate: 2020-09-26

Saxtorph MH, Hallager T, Persson G, et al (2020)

Assessing endometrial receptivity after recurrent implantation failure: a prospective controlled cohort study.

Reproductive biomedicine online pii:S1472-6483(20)30448-X [Epub ahead of print].

RESEARCH QUESTION: What is the prevalence of disrupted markers of endometrial function among women experiencing recurrent implantation failure (RIF), and does the prevalence differ from a control cohort?

DESIGN: Prospective controlled cohort study. In total, 86 women with a history of RIF and 37 women starting their first fertility treatment were recruited for this study. Endometrial and blood profiling were carried out in a hormone-substituted cycle using oestradiol and progesterone. Endometrial biopsies were analysed by histology, immune cell profiling, and the endometrial receptivity array (ERA®) test (Igenomix, Valencia, Spain). The vaginal microbiome was analysed using a NGS-based technology (ArtPRED, Amsterdam, the Netherlands). Blood tests included oestradiol, progesterone, prolactin, thyroid-stimulating hormone, vitamin D and anti-phospholipid antibody levels.

RESULTS: Patients who had experienced RIF produced a range of test abnormalities. Compared with controls, women with RIF had a higher prevalence of chronic endometritis (24% versus 6%), a lower vitamin D level and a borderline lower progesterone level. Women who had experienced RIF had a more favourable vaginal microbiome compared with controls. Although the RIF cohort was older than the controls (mean age 33.8 years versus 30.2 years), no differences between the groups were observed in immune cell profiling and the ERA test.

CONCLUSION: These data demonstrate that a single test or treatment for the endometrial factor in RIF is unlikely to be clinically effective. Diagnosing the endometrium in women with RIF permits targeted rather than blind interventions. Relative vitamin D deficiency, lower mid-luteal progesterone and chronic endometritis are ready targets for treatment. Understanding the role and treatment of an unfavourable vaginal microbiome in RIF needs further investigation.

RevDate: 2020-09-26

Koninckx PR, Ussia A, Adamyan L, et al (2020)

The epidemiology of endometriosis is poorly known as the pathophysiology and diagnosis are unclear.

Best practice & research. Clinical obstetrics & gynaecology pii:S1521-6934(20)30138-3 [Epub ahead of print].

As the diagnosis requires a laparoscopy, we only have data in women with pain and/or infertility. Endometriosis has been considered to be a single disease defined as 'endometrium like glands and stroma outside the uterus'. However, subtle, typical, cystic ovarian and deep endometriosis lesions should be considered to be different pathologies which occur in all combinations and with different severities. All large datasets, especially those based on hospital discharge records, consider endometriosis to be a single disease without taking into account severity. In particular, the variable prevalence and recognition of subtle lesions is problematic. Reliable surgical data are small series not permitting multivariate analysis. Endometriosis is a hereditary disease. The oxidative stress of heavy menstrual bleeding with retrograde menstruation and an altered pelvic microbiome are probably associated with increasingly severe endometriosis. Whether the prevalence is increasing, or whether endometriosis is associated with fat intake or an increased risk of cardiovascular disease is unclear.

RevDate: 2020-09-26

Nairz M, G Weiss (2020)

Iron in health and disease.

Molecular aspects of medicine pii:S0098-2997(20)30108-4 [Epub ahead of print].

RevDate: 2020-09-28

Neubauer V, Petri RM, Humer E, et al (2020)

Starch-Rich Diet Induced Rumen Acidosis and Hindgut Dysbiosis in Dairy Cows of Different Lactations.

Animals : an open access journal from MDPI, 10(10): pii:ani10101727.

Starch-rich diets can cause subacute ruminal acidosis (SARA) in dairy cows with potentially different susceptibility according to lactation number. We wanted to evaluate the bacterial community and the fermentation end products in feces to study susceptibility to hindgut acidosis and dysbiosis. Sixteen dairy cows received a medium-concentrate diet (MC, 40% concentrate, 18.8% starch) for one week and a high-concentrate diet (HC, 60% concentrate, 27.7% starch, DM) for four weeks. Milk yield, dry-matter intake, chewing activity, ruminal pH, milk constituents, and fecal samples for short-chain fatty acids (SCFA), pH, and 16S rRNA-gene sequencing were investigated. The HC feeding caused a reduction in fecal pH, bacterial diversity and richness, an increase in total SCFA, and a separate phylogenetic clustering of MC and HC samples. Ruminal and fecal pH had fair correlation (r = 0.5). Cows in the second lactation (2ndL) had lower dry matter intake (DMI) than cows of third or fourth or more lactations (3rdL; ≥4 L), whereas DMI/kg body weight was lower for ≥4 L than for 2ndL and 3rdL cows. The mean ruminal pH was highest in ≥4 L, whereas the time spent below the SARA threshold was highest for 3rdL cows. The latter also had higher total SCFA in the feces. Our results suggest that hindgut dysbiosis is caused by increased substrate flow to the hindgut, but further investigations are needed to define hindgut acidosis. The 3rdL cows were most susceptible to rumen acidosis and hindgut dysbiosis due to high DMI level, but missing counter regulations, as suggested happening in 2ndL and ≥4 L cows.

RevDate: 2020-09-28

Lee JK, Hern Tan LT, Ramadas A, et al (2020)

Exploring the Role of Gut Bacteria in Health and Disease in Preterm Neonates.

International journal of environmental research and public health, 17(19): pii:ijerph17196963.

The mortality rate of very preterm infants with birth weight <1500 g is as high as 15%. The survivors till discharge have a high incidence of significant morbidity, which includes necrotising enterocolitis (NEC), early-onset neonatal sepsis (EONS) and late-onset neonatal sepsis (LONS). More than 25% of preterm births are associated with microbial invasion of amniotic cavity. The preterm gut microbiome subsequently undergoes an early disruption before achieving bacterial maturation. It is postulated that bacterial gut colonisation at birth and postnatal intestinal dysbacteriosis precede the development of NEC and LONS in very preterm infants. In fact, bacterial colonization patterns in preterm infants greatly differ from term infants due to maternal chorioamnionitis, gestational age, delivery method, feeding type, antibiotic exposure and the environment factor in neonatal intensive care unit (NICU). In this regard, this review provides an overview on the gut bacteria in preterm neonates' meconium and stool. More than 50% of preterm meconium contains bacteria and the proportion increases with lower gestational age. Researchers revealed that the gut bacterial diversity is reduced in preterm infants at risk for LONS and NEC. Nevertheless, the association between gut dysbacteriosis and NEC is inconclusive with regards to relative bacteria abundance and between-sample beta diversity indices. With most studies show a disruption of the Proteobacteria and Firmicutes preceding the NEC. Hence, this review sheds light on whether gut bacteria at birth either alone or in combination with postnatal gut dysbacteriosis are associated with mortality and the morbidity of LONS and NEC in very preterm infants.

RevDate: 2020-09-25

Selway CA, Mills JG, Weinstein P, et al (2020)

Transfer of environmental microbes to the skin and respiratory tract of humans after urban green space exposure.

Environment international, 145:106084 pii:S0160-4120(20)32039-0 [Epub ahead of print].

BACKGROUND: In industrialized countries, non-communicable diseases have been increasing in prevalence since the middle of the 20th century. While the causal mechanisms remain poorly understood, increased population density, pollution, sedentary behavior, smoking, changes in diet, and limited outdoor exposure have all been proposed as significant contributors. Several hypotheses (e.g. Hygiene, Old Friends, and Biodiversity Hypotheses) also suggest that limited environmental microbial exposures may underpin part of this rise in non-communicable diseases. In response, the Microbiome Rewilding Hypothesis proposes that adequate environmental microbial exposures could be achieved by restoring urban green spaces and could potentially decrease the prevalence of non-communicable diseases. However, the microbial interactions between humans and their surrounding environment and the passaging of microbes between both entities remains poorly understood, especially within an urban context.

RESULTS: Here, we survey human skin (n = 90 swabs) and nasal (n = 90 swabs) microbiota of three subjects that were exposed to air (n = 15), soil (n = 15), and leaves (n = 15) from different urban green space environments in three different cities across different continents (Adelaide, Australia; Bournemouth, United Kingdom; New Delhi, India). Using 16S ribosomal RNA metabarcoding, we examined baseline controls (pre-exposure) of both skin (n = 16) and nasal (n = 16) swabs and tracked microbiota transfer from the environment to the human body after exposure events. Microbial richness and phylogenetic diversity increased after urban green space exposure in skin and nasal samples collected in two of the three locations. The microbial composition of skin samples also became more similar to soil microbiota after exposure, while nasal samples became more similar to air samples. Nasal samples were more variable between sites and individuals than skin samples.

CONCLUSIONS: We show that exposure to urban green spaces can increase skin and nasal microbial diversity and alter human microbiota composition. Our study improves our understanding of human-environmental microbial interactions and suggests that increased exposure to diverse outdoor environments may increase the microbial diversity, which could lead to positive health outcomes for non-communicable diseases.

RevDate: 2020-09-25

Rivero-Segura NA, Bello-Chavolla OY, Barrera-Vázquez OS, et al (2020)

Promising biomarkers of human aging: in search of a multi-omics panel to understand the aging process from a multidimensional perspective.

Ageing research reviews pii:S1568-1637(20)30299-3 [Epub ahead of print].

The aging process has been linked to the occurrence of chronic diseases and functional impairments, including cancer, sarcopenia, frailty, metabolic, cardiovascular, and neurodegenerative diseases. Nonetheless, aging is highly variable and heterogeneous and represents a challenge for its characterization. In this sense, intrinsic capacity (IC) stands as a novel perspective by the World Health Organization, which integrates the individual wellbeing, environment, and risk factors to understand aging. However, there is a lack of quantitative and qualitative attributes to define it objectively. Therefore, in this review we attempt to summarize the most relevant and promising biomarkers described in clinical studies at date over different molecular levels, including epigenomics, transcriptomics, proteomics, metabolomics, and the microbiome. To aid gerontologists, geriatricians, and biomedical researchers to understand the aging process through the IC. Aging biomarkers reflect the physiological state of individuals and the underlying mechanisms related to homeostatic changes throughout an individual lifespan; they demonstrated that aging could be measured independently of time (that may explain its heterogeneity) and to be helpful to predict age-related syndromes and mortality. In summary, we highlight the areas of opportunity and gaps of knowledge that must be addressed to fully integrate biomedical findings into clinically useful tools and interventions.

RevDate: 2020-09-25

Łoniewski I, Misera A, Skonieczna-Żydecka K, et al (2020)

Major Depressive Disorder and gut microbiota - Association not causation. A scoping review.

Progress in neuro-psychopharmacology & biological psychiatry pii:S0278-5846(20)30427-9 [Epub ahead of print].

One very promising hypothesis of Major Depressive Disorder (MDD) pathogenesis is the gut-brain axis (GBA) dysfunction, which can lead to subclinical inflammation, hypothalamic-pituitary (HPA) axis dysregulation, and altered neural, metabolic and endocrine pathways. One of the most important parts of GBA is gut microbiota, which was shown to regulate different functions in the central nervous system (CNS). The purpose of this scoping review was to present the current state of research on the relationship between MDD and gut microbiota and extract causal relationships. Further, we presented the relationship between the use of probiotics and antidepressants, and the microbiota changes. We evaluated the data from 27 studies aimed to investigate microbial fingerprints associated with depression phenotype. We abstracted data from 16 to 11 observational and clinical studies, respectively; the latter was divided into trials evaluating the effects of psychiatric treatment (n = 3) and probiotic intervention (n = 9) on the microbiome composition and function. In total, the data of 1187 individuals from observational studies were assessed. In clinical studies, there were 490 individuals analysed. In probiotic studies, 220 and 218 patients with MDD received the intervention and non-active study comparator, respectively. It was concluded that in MDD, the microbiota is altered. Although the mechanism of this relationship is unknown, we hypothesise that the taxonomic changes observed in patients with MDD are associated with bacterial proinflammatory activity, reduced Schort Chain Fatty Acids (SCFAs) production, impaired intestinal barrier integrity and neurotransmitter production, impaired carbohydrates, tryptophane and glutamate metabolic pathways. However, only in few publications this effect was confirmed by metagenomic, metabolomic analysis, or by assessment of immunological parameters or intestinal permeability markers. Future research requires standardisation process starting from patient selection, material collection, DNA sequencing, and bioinformatic analysis. We did not observe whether antidepressive medications influence on gut microbiota, but the use of psychobiotics in patients with MDD has great prospects; however, this procedure requires also standardisation and thorough mechanistic research. The microbiota should be treated as an environmental element, which considers the aetiopathogenesis of the disease and provides new possibilities for monitoring and treating patients with MDD.

RevDate: 2020-09-25

Allen-Vercoe E, B Coburn (2020)

A Microbiota-Derived Metabolite Augments Cancer Immunotherapy Responses in Mice.

Cancer cell pii:S1535-6108(20)30479-7 [Epub ahead of print].

Improving the rate of patient response to immune checkpoint blockade therapy is a current clinical goal. An article published in Science suggests that some members of the gut microbiome may provide a key molecule toward this end.

RevDate: 2020-09-25

Gail MH, Wan Y, J Shi (2020)

Power of Microbiome Beta-Diversity Analyses Based on Standard Reference Samples.

American journal of epidemiology pii:5911564 [Epub ahead of print].

A simple method to analyze microbiome beta-diversity computes mean beta-diversity distances from a test sample to standard reference samples. We used reference stool and nasal samples from the Human Microbiome Project and regressed an outcome on mean distances (2df-test) or additionally on squares and cross-product of mean distances (5df-test). We compared the power of 2df- and 5df-tests to the microbiome regression-based kernel association test (MiRKAT). In simulations, MiRKAT had moderately greater power than the 2df-test for discriminating skin versus saliva and skin versus nasal samples, but differences were negligible for skin versus stool and stool versus nasal samples. The 2df-test had slightly greater power than MiRKAT for Dirichlet-Multinomial samples. In associating body mass index with beta-diversity in stool samples from the American Gut Project, the 5df-test yielded smaller p-values than MiRKAT for most taxonomic levels and beta-diversity measures. Unlike procedures like MiRKAT that are based on the beta-diversity matrix, mean distances to reference samples can be analyzed with standard statistical tools and shared or meta-analyzed without sharing primary DNA data. Our data indicate that standard reference tests have comparable power to MiRKAT (and to permutational multivariate analysis of variance), but more simulations and applications are needed to confirm this.

RevDate: 2020-09-25

Saha S, Mara K, Pardi DS, et al (2020)

Durability Of Response To Fecal Microbiota Transplantation After Exposure to Risk Factors for Recurrence In Patients With Clostridioides difficile Infection.

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America pii:5911669 [Epub ahead of print].

BACKGROUND: Fecal microbiota transplantation (FMT) is highly effective for preventing recurrent Clostridioides difficile infection (CDI). Durability (no recurrence despite additional risk factor exposure) of FMT protection is largely unknown. We studied the durability of FMT in patients with recurrent CDI.

METHODS: A retrospective study of adults undergoing FMT for recurrent CDI was conducted. Data collected included demographics, CDI risk factors (comorbidities, healthcare exposure, systemic non-CDI antibiotic use, acid suppressant medications) and future CDI episodes. Durable response to FMT was defined as lack of CDI episodes within 1 year post-FMT despite risk factor exposure. Descriptive statistics, univariate and multivariable Cox proportional hazards regression were used as applicable. Two tailed p<0.05 was considered statistically significant.

RESULTS: Overall 460 patients were included [median age 57 (18-94) years, 65.2% female]. Comorbidities included chronic liver disease, 12.8% (n=59), cancer, 11.7% (n=54), chronic kidney disease, 3.9% (n=18) and inflammatory bowel disease, 21.9% (n=101). Overall, 31.3% (n=144) received antibiotics, 21.7% (n=100) received acid suppressants, 76.8% (n=350) had healthcare exposure after FMT. Of 374 patients with risk factor exposure, 78.1% [95% confidence interval (CI) 72.7%-84.0%] had durable response to FMT at one year. On multivariable analysis, antibiotic use was independently associated with decreased durability of FMT [hazard ratio 0.27 (95% CI, 0.15-0.49), p<0.001].

CONCLUSION: Majority of patients had a durable response to FMT despite exposure to CDI risk factors. Antibiotic exposure after FMT independently predicted loss of durability of FMT. Larger studies are needed to define predictors of durable response in patients with and without exposure to antibiotics.

RevDate: 2020-09-25

Kim GH, Rosiana S, Kirienko NV, et al (2020)

A Simple Nematode Infection Model for Studying Candida albicans Pathogenesis.

Current protocols in microbiology, 59(1):e114.

Candida albicans is an opportunistic fungal pathogen and a model organism to study fungal pathogenesis. It exists as a harmless commensal organism and member of the healthy human microbiome, but can cause life-threatening mucosal and systemic infections. A model host to study C. albicans infection and pathogenesis is the nematode Caenorhabditis elegans. C. elegans is frequently used as a model host to study microbial-host interactions because it can be infected by many human pathogens and there are also close morphological resemblances between the intestinal cells of C. elegans and mammals, where C. albicans infections can occur. This article outlines a detailed methodology for exploiting C. elegans as a host to study C. albicans infection, including a C. elegans egg preparation protocol and an agar-based C. elegans killing protocol to monitor fungal virulence. These protocols can additionally be used to study C. albicans genetic mutants in order to further our understanding of the genes involved in pathogenesis and virulence in C. albicans and the mechanisms of host-microbe interactions. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Preparation of Caenorhabditis elegans eggs Support Protocol 1: Freezing and recovering Caenorhabditis elegans Support Protocol 2: Making superfood agar and OP50 plates Basic Protocol 2: Caenorhabditis elegans/Candida albicans agar killing assay Support Protocol 3: Constructing a worm pick.

RevDate: 2020-09-25

Omori M, Kato-Kogoe N, Sakaguchi S, et al (2020)

Comparative evaluation of microbial profiles of oral samples obtained at different collection time points and using different methods.

Clinical oral investigations pii:10.1007/s00784-020-03592-y [Epub ahead of print].

OBJECTIVES: Recently, the oral microbiome has been found to be associated with oral and general health status. Although various oral sample collection protocols are available, the potential differences between the results yielded by these protocols remain unclear. In this study, we aimed to determine the effects of different time points and methods of oral sample collection on the outcomes of microbiome analysis.

MATERIALS AND METHODS: Oral samples were collected from eight healthy individuals at four different time points: 2 h after eating, immediately after teeth brushing, immediately after waking up, and 2 h after eating on the subsequent day. Four methods of saliva collection were evaluated: spitting, gum chewing, cotton swab, and oral rinse. Oral microbiomes of these samples were compared by analyzing the bacterial 16S rRNA gene sequence data.

RESULTS: The oral microbial composition at the genus level was similar among all sample collection time points and methods. Alpha diversity was not significantly different among the groups, whereas beta diversity was different between the spitting and cotton swab methods. Compared with the between-subject variations, the weighted UniFrac distances between the groups were not minor.

CONCLUSIONS: Although the oral microbiome profiles obtained at different collection time points and using different methods were similar, some differences were detected.

CLINICAL RELEVANCE: The results of the present study suggest that although all the described protocols are useful, comparisons among microbiomes of samples collected by different methods are not appropriate. Researchers must be aware of the issues regarding the impact of saliva collection methods.

RevDate: 2020-09-25

Klinges JG, Maher RL, Vega Thurber RL, et al (2020)

Parasitic "Candidatus Aquarickettsia rohweri" is a marker of disease susceptibility in Acropora cervicornis but is lost during thermal stress.

Environmental microbiology [Epub ahead of print].

Holobiont phenotype results from a combination of host and symbiont genotypes as well as from prevailing environmental conditions that alter the relationships among symbiotic members. Corals exemplify this concept, where shifts in the algal symbiont community can lead to some corals becoming more or less thermally tolerant. Despite linkage between coral bleaching and disease, the roles of symbiotic bacteria in holobiont resistance and susceptibility to disease remains less well understood. This study thus characterizes the microbiome of disease-resistant and -susceptible Acropora cervicornis coral genotypes (hereafter referred to simply as 'genotypes') before and after high temperature-mediated bleaching. We found that the intracellular bacterial parasite "Ca. Aquarickettsia rohweri" was strikingly abundant in disease-susceptible genotypes. Disease-resistant genotypes, however, had notably more diverse and even communities, with correspondingly low abundances of "Ca. Aquarickettsia". Bleaching caused a dramatic reduction of "Ca. Aquarickettsia" within disease-susceptible corals and led to an increase in bacterial community dispersion, as well as the proliferation of opportunists. Our data support the hypothesis that "Ca. Aquarickettsia" species increase coral disease risk through two mechanisms: 1) the creation of host nutritional deficiencies leading to a compromised host-symbiont state, and 2) the opening of niche space for potential pathogens during thermal stress. This article is protected by copyright. All rights reserved.

RevDate: 2020-09-25

Tomizawa Y, Kurokawa S, Ishii D, et al (2020)

Effects of Psychotropics on the Microbiome in Patients with Depression and Anxiety: Considerations in a Naturalistic Clinical Setting.

The international journal of neuropsychopharmacology pii:5911526 [Epub ahead of print].

BACKGROUND: The antibacterial effects of psychotropics may be part of their pharmacological effects when treating depression. However, limited studies have focused on gut microbiota in relation to prescribed medication.

METHOD: We longitudinally investigated the relationship between patients' prescribed medications and intestinal bacterial diversity in a naturalistic treatment course for patients with major depressive disorders and anxiety disorders. Patients were recruited and their stool was collected at three time points during their usual psychiatric treatments. Gut microbiota were analyzed using 16S rRNA gene sequencing. We examined the impact of psychotropics (i.e., antidepressants, anxiolytics, antipsychotics) on their gut microbial diversity and functions.

RESULT: We collected 246 stool samples from 40 patients. Despite no differences in microbial diversity between medication groups at the baseline, over the course of treatment, phylogenic diversity (PD) whole tree diversity decreased in patients on antipsychotics compared to patients without (p=0.027), and beta diversity followed this trend. Based on a fixed-effect model, antipsychotics predicted microbial diversity; the higher doses correlated with less diversity based on the Shannon index and PD whole tree (Estimate = -0.00254, SE = 0.000595, p < 0.0001; Estimate = -0.02644, SE = 0.00833, p = 0.002, respectively).

CONCLUSION: Antipsychotics may play a role in decreasing the alpha diversity of the gut microbiome among patients with depression and anxiety, and our results indicate a relationship with medication dosage. Future studies are warranted and should consider patients' types and doses of antipsychotics in order to further elucidate the mechanisms of gut-brain interactions in psychiatric disorders.

RevDate: 2020-09-25

Saxena A, Mukhopadhyay AK, SP Nandi (2020)

Helicobacter pylori: Perturbation and restoration of gut microbiome.

Journal of biosciences, 45:.

Alternate remedies with natural products provides unlimited opportunities for new drug development. These can be either as pure compounds or as standardized set of compounds. The phytochemicals and secondary metabolites are in great demand for screening bioactive compounds and plays an important role towards drug development. Natural products have many advantages over to synthetic chemical drugs. Helicobacter pylori (H. pylori) a Gram-negative bacteria has been classified as Class I carcinogen by World Health Organization in 1994. Current treatment regimens for H. pylori is 'triple therapy' administrated for two weeks which includes a combination of two antibiotics like Amoxicillin and Clarithromycin and a proton pump inhibitor (PPI) like Lansoprazole, and for 'quadruple therapy' in addition to antibiotics and a PPI, Bismuth is used. Antibiotic resistance can be named as the main factor for failure of treatment of H. pylori infection. The need of the hour is to develop a herbal remedy that could combat the growth of H. pylori. Probiotics can also be used as 'feasible' tool for H. pylori infection management. Present review is an attempt to briefly discuss about the pathogenicity, genetic predisposition, perturbation of gut microbiota due to antibiotic treatment and restoration of healthy gut microbiota with phytochemicals and probiotics.

RevDate: 2020-09-25

Kerdraon L, Barret M, Balesdent MH, et al (2020)

Impact of a resistance gene against a fungal pathogen on the plant host residue microbiome: The case of the Leptosphaeria maculans-Brassica napus pathosystem.

Molecular plant pathology [Epub ahead of print].

Oilseed rape residues are a crucial determinant of stem canker epidemiology as they support the sexual reproduction of the fungal pathogen Leptosphaeria maculans. The aim of this study was to characterize the impact of a resistance gene against L. maculans infection on residue microbial communities and to identify microorganisms interacting with this pathogen during residue degradation. We used near-isogenic lines to obtain healthy and infected host plants. The microbiome associated with the two types of plant residues was characterized by metabarcoding. A combination of linear discriminant analysis and ecological network analysis was used to compare the microbial communities and to identify microorganisms interacting with L. maculans. Fungal community structure differed between the two lines at harvest, but not subsequently, suggesting that the presence/absence of the resistance gene influences the microbiome at the base of the stem whilst the plant is alive, but that this does not necessarily lead to differential colonization of the residues by fungi. Direct interactions with other members of the community involved many fungal and bacterial amplicon sequence variants (ASVs). L. maculans appeared to play a minor role in networks, whereas one ASV affiliated to Plenodomus biglobosus (synonym Leptosphaeria biglobosa) from the Leptosphaeria species complex may be considered a keystone taxon in the networks at harvest. This approach could be used to identify and promote microorganisms with beneficial effects against residue-borne pathogens and, more broadly, to decipher the complex interactions between multispecies pathosystems and other microbial components in crop residues.

RevDate: 2020-09-25

Teufel A, Howard B, Hu P, et al (2020)

Characterization of the Microbiome in the Infant Diapered Area: Insights from Healthy and Damaged Skin.

Experimental dermatology [Epub ahead of print].

It has been recognized for nearly a century that human beings are inhabited by a remarkably dense and diverse microbial ecosystem, yet we are only just beginning to understand and appreciate the many roles that these microbes play in human health and development. Establishment of the microbiome begins at birth but many previous studies on infant skin health have focused on Candida species. Little is known on the full microbial composition across different areas and even less is known on how these communities change during disease/inflammatory states. In this clinical study, infants were recruited during periods of diaper dermatitis (DD) and health to characterize the skin microbiome in these two states. Substantial shifts in the skin microbiome were observed across 4 sites in the diapered area (genitals, intertriginous, buttocks and perianal), as well as, during periods of DD. As DD scores increased, there was a shift in relative abundance that demonstrated higher community percentages of fecal coliforms, such as Enterococcus, and lower percentages of Staphylococcus strains. In high rash samples, the predominant Staphylococcus species is S. aureus, potentially implicating S. aureus as a DD etiological agent. This study provides new information related to the microbiome on infant skin in the diapered area and provides insights into the role of the microbiome in the development of DD.

RevDate: 2020-09-25

Wang M, Li L, Chen Y, et al (2020)

Role of Gut Microbiome and Microbial Metabolites in Alleviating Insulin Resistance After Bariatric Surgery.

Obesity surgery pii:10.1007/s11695-020-04974-7 [Epub ahead of print].

Insulin resistance (IR) is the most common pathophysiological change in patients with type 2 diabetes mellitus (T2DM). Several recent studies have suggested that the gut microbiome and microbial metabolites are involved in the pathogenesis of IR. Bariatric surgery, as an effective treatment for T2DM, can markedly alleviate IR through mechanisms that have not been elucidated. In this review, we summarize the current evidence on the changes in the gut microbiome and microbial metabolites (including lipopolysaccharide, short-chain fatty acids, branched-chain amino acids, aromatic amino acids, bile acids, methylamines, and indole derivatives) after bariatric surgery. Additionally, we discuss the mechanisms that correlate the changes in microbial metabolites with the postoperative alleviation of IR. Furthermore, we discuss the prospect of bariatric surgery as a treatment for T2DM.

RevDate: 2020-09-25

Xu AA, Hoffman K, Gurwara S, et al (2020)

Oral Health and the Altered Colonic Mucosa-Associated Gut Microbiota.

Digestive diseases and sciences pii:10.1007/s10620-020-06612-9 [Epub ahead of print].

BACKGROUND: Systemic diseases have been associated with oral health and gut microbiota. We examined the association between oral health and the community composition and structure of the adherent colonic gut microbiota.

METHODS: We obtained 197 snap-frozen colonic biopsies from 62 colonoscopy-confirmed polyp-free individuals. Microbial DNA was sequenced for the 16S rRNA V4 region using the Illumina MiSeq, and the sequences were assigned to the operational taxonomic unit based on SILVA. We used a questionnaire to ascertain tooth loss, gum disease, and lifestyle factors. We compared biodiversity and relative abundance of bacterial taxa based on the amount of tooth loss and the presence of gum disease. The multivariable negative binomial regression model for panel data was used to estimate the association between the bacterial count and oral health. False discovery rate-adjusted P value (q value) < .05 indicated statistical significance.

RESULTS: More tooth loss and gum disease were associated with lower bacterial alpha diversity. The relative abundance of Faecalibacterium was lower (q values < .05) with more tooth loss. The association was significant after adjusting for age, ethnicity, obesity, smoking, alcohol use, hypertension, diabetes, and the colon segment. The relative abundance of Bacteroides was higher in those with gum disease.

CONCLUSIONS: Oral health was associated with alteration in the community composition and structure of the adherent gut bacteria in the colon. The reduced anti-inflammatory Faecalibacterium in participants with more tooth loss may indicate systemic inflammation. Future studies are warranted to confirm our findings and investigate the systemic role of Faecalibacterium.

RevDate: 2020-09-25

Vale AP, Leggett B, Smyth D, et al (2020)

Challenges in the veterinary microbiology diagnostic laboratory: a novel Acinetobacter species as presumptive cause for feline unilateral conjunctivitis.

Access microbiology, 2(6):acmi000118 pii:000118.

The present study highlights challenges in the veterinary microbiology diagnostic laboratory in the identification of bacteria responsible for infections in veterinary settings, particularly when evidence-based data is lacking. A 1.8-year-old neutered male domestic cat (FIV/FeLV negative) was presented to a veterinary practice in April 2016 with a history of left unilateral mild conjunctivitis that was empirically treated with fusidic acid and chloramphenicol. In January 2017, the same animal was presented with chronic left unilateral conjunctivitis and an eye swab was submitted for microbiological culture and susceptibility testing. Significant growth was not detected in two samples tested. Finally, in February 2017 another eye swab produced a slow growing pure culture identified by VITEK 2 as Neisseria cinerea (94 % confidence). Given the morphology and multidrug resistance profile of the isolate a 16S rRNA PCR was performed for definitive identification. The nucleotide sequence of the PCR amplicon was 99 % homologous to Acinetobacter equi sp. nov. strain 114. Veterinary microbiology diagnostic laboratories play an important role worldwide, not only in preserving animal health and welfare but also in controlling the spread of zoonotic pathogens. The lack of evidence-based information on the ocular microbiome of healthy cats and the complexity of bacterial ecosystems renders the interpretation of results difficult. A further problem for both the laboratory and the clinician is the lack of interpretive criteria for antibiotic susceptibility test results for some types of infections in animals (including those caused by Acinetobacter) and the complete unavailability of criteria for topical antibiotic preparations.

RevDate: 2020-09-25

Mallott EK, Malhi RS, KR Amato (2019)

Assessing the comparability of different DNA extraction and amplification methods in gut microbial community profiling.

Access microbiology, 1(7):e000060 pii:000060.

Automated, high-throughput technologies are becoming increasingly common in microbiome studies to decrease costs and increase efficiency. However, in microbiome studies, small differences in methodology - including storage conditions, wet lab methods, sequencing platforms and data analysis - can influence the reproducibility and comparability of data across studies. There has been limited testing of the effects of high-throughput methods, including microfluidic PCR technologies. In this paper, we compare two extraction methods (the QIAamp DNA Stool Mini Kit and the MoBio PowerSoil DNA Isolation kit), two taq polymerase enzymes (MyTaq HS Red Mix and Accustart II PCR ToughMix), two primer sets (V3-V4 and V4-V5) and two amplification methods (a common two-step PCR protocol and amplicon library preparation on the Fluidigm Access Array system that allows automated multiplexing of primers). Gut microbial community profiles were significantly affected by all variables. While there were no significant differences in alpha diversity measured between the two extraction methods, there was an effect of extraction method on community composition measured by unweighted UniFrac distances. Both amplification method and primers had a significant effect on both alpha diversity and community composition. The relative abundance of Actinobacteria was significantly lower when using the MoBio kit or Fluidigm amplification method, and the relative abundance of Firmicutes was lower when using the Qiagen kit. Microbial community profiles based on Fluidigm-generated amplicon libraries were not comparable to those generated with more commonly used methods. Researchers should carefully consider the limitations and biases that different extraction and amplification methods can introduce into their results. Additionally, more thorough benchmarking of automated and multiplexing methods is necessary to determine the magnitude of the potential trade-off between the quality and the quantity of data.

RevDate: 2020-09-25

Ponni Keerthana K, Radhesh Krishnan S, Ragunath Sengali S, et al (2019)

Microbiome digital signature of MCR genes - an in silico approach to study the diversity of methanogenic population in laboratory-developed and pilot-scale anaerobic digesters.

Access microbiology, 1(5):e000044 pii:000044.

The production of biogas by anaerobic digestion (AD) of organic/biological wastes has a firm place in sustainable energy production. A simple and cost-effective anaerobic jar at a laboratory scale is a prerequisite to study the microbial community involved in biomass conversion and releasing of methane gas. In this study, a simulation was carried out using a laboratory-modified anaerobic-jar-converted digester (AD1) with that of a commercial/pilot-scale anaerobic digester (AD2). Taxonomic profiling of biogas-producing communities by means of high-throughput methyl coenzyme-M reductase α-subunit (mcrA) gene amplicon sequencing provided high-resolution insights into bacterial and archaeal structures of AD assemblages and their linkages to fed substrates and process parameters. Commonly, the bacterial phyla Euryarchaeota , Chordata, Firmicutes and Proteobacteria appeared to dominate biogas communities in varying abundances depending on the apparent process conditions. Key micro-organisms identified from AD were Methanocorpusculum labreanum and Methanobacterium formicicum . Specific biogas production was found to be significantly correlating to Methanosarcinaceae . It can be implied from this study that the metagenomic sequencing data was able to dissect the microbial community structure in the digesters. The data gathered indicates that the anaerobic-jar system could throw light on the population dynamics of the methanogens at laboratory scale and its effectiveness at large-scale production of bio-methane. The genome sequence information of non-cultivable biogas community members, metagenome sequencing including assembly and binning strategies will be highly valuable in determining the efficacy of an anaerobic digester.

RevDate: 2020-09-25

Duperron S, Halary S, Gallet A, et al (2020)

Microbiome-Aware Ecotoxicology of Organisms: Relevance, Pitfalls, and Challenges.

Frontiers in public health, 8:407.

Over the last 15 years, the advent of high-throughput "omics" techniques has revealed the multiple roles and interactions occurring among hosts, their microbial partners and their environment. This microbiome revolution has radically changed our views of biology, evolution, and individuality. Sitting at the interface between a host and its environment, the microbiome is a relevant yet understudied compartment for ecotoxicology research. Various recent works confirm that the microbiome reacts to and interacts with contaminants, with consequences for hosts and ecosystems. In this paper, we thus advocate for the development of a "microbiome-aware ecotoxicology" of organisms. We emphasize its relevance and discuss important conceptual and technical pitfalls associated with study design and interpretation. We identify topics such as functionality, quantification, temporality, resilience, interactions, and prediction as major challenges and promising venues for microbiome research applied to ecotoxicology.

RevDate: 2020-09-25

de Souza-Basqueira M, Ribeiro RM, de Oliveira LC, et al (2020)

Gut Dysbiosis in Chagas Disease. A Possible Link to the Pathogenesis.

Frontiers in cellular and infection microbiology, 10:402.

Chagas disease is caused by the flagellate protozoan Trypanosoma cruzi. Cardiomyopathy and damage to gastrointestinal tissue are the main disease manifestations. There are data suggesting that the immune response to T. cruzi depends on the intestinal microbiota. We hypothesized that Chagas disease is associated with an altered gut microbiome and that these changes are related to the disease phenotype. The stool microbiome from 104 individuals, 73 with Chagas disease (30 with the cardiac, 11 with the digestive, and 32 with the indeterminate form), and 31 healthy controls was characterized using 16S rRNA amplification and sequencing. The QIIME (Quantitative Insights Into Microbial Ecology) platform was used to analyze the data. Alpha and beta diversity indexes did not indicate differences between the groups. However, the relative abundance of Verrucomicrobia, represented primarily by the genus Akkermansia, was significantly lower in the Chagas disease groups, especially the cardiac group, compared to the controls. Furthermore, differences in the relative abundances of Alistipes, Bilophila, and Dialister were observed between the groups. We conclude that T. cruzi infection results in changes in the gut microbiome that may play a role in the myocardial and intestinal inflammation seen in Chagas disease.

RevDate: 2020-09-25

Lee NLY, Huang D, Quek ZBR, et al (2020)

Distinct fungal communities associated with different organs of the mangrove Sonneratia alba in the Malay Peninsula.

IMA fungus, 11:17 pii:42.

Mangrove forests are key tropical marine ecosystems that are rich in fungi, but our understanding of fungal communities associated with mangrove trees and their various organs remains limited because much of the diversity lies within the microbiome. In this study, we investigated the fungal communities associated with the mangrove tree Sonneratia alba throughout Peninsular Malaysia and Singapore. At each sampling location, we collected leaves, fruits, pneumatophores and sediment samples and performed amplicon sequencing of the ribosomal internal transcribed spacer 1 to characterise the associated communities. Results show distinct fungal communities at each sampled location with further differentiation according to the plant part. We find a significant distance decay of similarity, particularly for sediment samples due to the greater variability of sediment environments relative to the more stable fungal habitats provided by living plant organs. We are able to assign taxonomy to the majority of sequences from leaves and fruits, but a much larger portion of the sequences recovered from pneumatophores and sediment samples could not be identified. This pattern underscores the limited mycological research performed in marine environments and demonstrates the need for a concerted research effort on multiple species to fully characterise the coastal microbiome and its role in the functioning of marine ecosystems.

RevDate: 2020-09-25

Khandagale K, Krishna R, Roylawar P, et al (2020)

Omics approaches in Allium research: Progress and way ahead.

PeerJ, 8:e9824 pii:9824.

Background: The genus Allium (Family: Amaryllidaceae) is an economically important group of crops cultivated worldwide for their use as a vegetable and spices. Alliums are also well known for their nutraceutical properties. Among alliums, onion, garlic, leek, and chives cultivated worldwide. Despite their substantial economic and medicinal importance, the genome sequence of any of the Allium is not available, probably due to their large genome sizes. Recently evolved omics technologies are highly efficient and robust in elucidating molecular mechanisms of several complex life processes in plants. Omics technologies, such as genomics, transcriptomics, proteomics, metabolomics, metagenomics, etc. have the potential to open new avenues in research and improvement of allium crops where genome sequence information is limited. A significant amount of data has been generated using these technologies for various Allium species; it will help in understanding the key traits in Allium crops such as flowering, bulb development, flavonoid biosynthesis, male sterility and stress tolerance at molecular and metabolite level. This information will ultimately assist us in speeding up the breeding in Allium crops.

Method: In the present review, major omics approaches, and their progress, as well as potential applications in Allium crops, could be discussed in detail.

Results: Here, we have discussed the recent progress made in Allium research using omics technologies such as genomics, transcriptomics, micro RNAs, proteomics, metabolomics, and metagenomics. These omics interventions have been used in alliums for marker discovery, the study of the biotic and abiotic stress response, male sterility, organ development, flavonoid and bulb color, micro RNA discovery, and microbiome associated with Allium crops. Further, we also emphasized the integrated use of these omics platforms for a better understanding of the complex molecular mechanisms to speed up the breeding programs for better cultivars.

Conclusion: All the information and literature provided in the present review throws light on the progress and potential of omics platforms in the research of Allium crops. We also mentioned a few research areas in Allium crops that need to be explored using omics technologies to get more insight. Overall, alliums are an under-studied group of plants, and thus, there is tremendous scope and need for research in Allium species.

RevDate: 2020-09-25

Houttu V, Boulund U, Grefhorst A, et al (2020)

The role of the gut microbiome and exercise in non-alcoholic fatty liver disease.

Therapeutic advances in gastroenterology, 13:1756284820941745 pii:10.1177_1756284820941745.

In recent years, the human gut microbiome has been found to influence a multitude of non-communicable diseases such as cardiovascular disease and metabolic syndrome, with its components type 2 diabetes mellitus and obesity. It is recognized to be mainly influenced by environmental factors, such as lifestyle, but also genetics may play a role. The interaction of gut microbiota and obesity has been widely studied, but in regard to non-alcoholic fatty liver disease (NAFLD) as a manifestation of obesity and insulin resistance, the causal role of the gut microbiome has not been fully established. The mechanisms by which the gut microbiome influences lipid accumulation, inflammatory responses, and occurrence of fibrosis in the liver are a topic of active research. In addition, the influence of exercise on gut microbiome composition is also being investigated. In clinical trials, exercise reduced hepatic steatosis independently of weight reduction. Other studies indicate that exercise may modulate the gut microbiome. This puts forward the question whether exercise could mediate its beneficial effects on NAFLD via changes in gut microbiome. Yet, the specific mechanisms underlying this potential connection are largely unknown. Thus, associative evidence from clinical trials, as well as mechanistic studies in vivo are called for to elucidate the relationship between exercise and the gut microbiome in NAFLD. Here, we review the current literature on exercise and the gut microbiome in NAFLD.

RevDate: 2020-09-25

Xu R, Tan C, He Y, et al (2020)

Dysbiosis of Gut Microbiota and Short-Chain Fatty Acids in Encephalitis: A Chinese Pilot Study.

Frontiers in immunology, 11:1994.

Background: Encephalitis, the inflammation of the brain, may be caused by an infection or an autoimmune reaction. However, few researches were focused on the gut microbiome characteristics in encephalitis patients.

Methods: A prospective observational study was conducted in an academic hospital in Guangzhou from February 2017 to February 2018. Patients with encephalitis were recruited. Fecal and serum samples were collected at admission. Healthy volunteers were enrolled from a community. Disease severity scores were recorded by specialized physicians, including Glasgow Coma Scale (GCS), Sequential Organ Failure Assessment (SOFA), and Acute Physiology and Chronic Health Evaluation-II (APACHE-II). 16S rRNA sequence was performed to analyze the gut microbiome, then the α-diversities and β-diversities were estimated. Short-chain fatty acids (SCFAs) were extracted from fecal samples and determined by gas chromatography-mass spectrometry. Serum D-lactate (D-LA), intestinal fatty acid-binding protein (iFABP), lipopolysaccharide (LPS), and lipopolysaccharide-binding protein (LBP) were measured by enzyme-linked immunosorbent assay (ELISA). The associations among microbial indexes and clinical parameters were evaluated by Spearman correlation analysis.

Results: In total, twenty-eight patients were recruited for analysis (median age 46 years; 82.1% male; median GCS 6.5; median SOFA 6.5; median APACHE-II 14.5). Twenty-eight age- and sex-matched healthy subjects were selected as controls. The β-diversities between patients and healthy subjects were significantly different. The α-diversities did not show significant differences between these two groups. In the patient group, the abundances of Bacteroidetes, Proteobacteria, and Bacilli were significantly enriched. Accordingly, fecal SCFA levels were decreased in the patient group, whereas serum D-LA, iFABP, LPS, and LBP levels were increased compared with those in healthy subjects. Correlation analyses showed that disease severity had positive correlations with Proteobacteria and Akkermansia but negative correlations with Firmicutes, Clostridia, and Ruminococcaceae abundances. The cerebrospinal fluid albumin-to-serum albumin ratio (CSAR) was positively related to the α-diversity but negatively correlated with the fecal butyrate concentration.

Conclusion: Gut microbiota disruption was observed in encephalitis patients, which manifested as pathogen dominance and health-promoting commensal depletion. Disease severity and brain damage may have associations with the gut microbiota or its metabolites. The causal relationship should be further explored in future studies.

RevDate: 2020-09-25

Molnar J, Mallonee CJ, Stanisic D, et al (2020)

Hidradenitis Suppurativa and 1-Carbon Metabolism: Role of Gut Microbiome, Matrix Metalloproteinases, and Hyperhomocysteinemia.

Frontiers in immunology, 11:1730.

Hidradenitis suppurativa (HS) is a chronic, inflammatory skin condition characterized by painful nodules which suppurate and later develop into scar tissues followed by the development of hypodermal tracts. Although the mechanisms behind HS are not fully understood, it is known that dietary factors play important roles in flare frequency and severity. We hypothesize that the high fat diet (HFD) causes dysbiosis, systemic inflammation, and hyperhomocysteinemia (HHcy) in susceptible individuals, which subsequently elevate inflammatory cytokines such as IL-1β, IL-6, IL-17, and tumor necrosis factor alpha (TNF-α). This increase in dysbiosis-led inflammation coupled with a dysregulation of the 1-carbon metabolism results in an increase in matrix metalloproteinases MMP-2, MMP-8, and MMP-9 along with tissue matrix remodeling in the development and maintenance of the lesions and tracts. This manuscript weaves together the potential roles played by the gut microbiome, HHcy, MMPs, and the 1-carbon metabolism toward HS disease causation in susceptible individuals.

RevDate: 2020-09-25

Szamosi JC, Forbes JD, Copeland JK, et al (2020)

Assessment of Inter-Laboratory Variation in the Characterization and Analysis of the Mucosal Microbiota in Crohn's Disease and Ulcerative Colitis.

Frontiers in microbiology, 11:2028.

Background: In studies evaluating the microbiome, numerous factors can contribute to technical variability. These factors include DNA extraction methodology, sequencing protocols, and data analysis strategies. We sought to evaluate the impact these factors have on the results obtained when the sequence data are independently generated and analyzed by different laboratories.

Methods: To evaluate the effect of technical variability, we used human intestinal biopsy samples resected from individuals diagnosed with an inflammatory bowel disease (IBD), including Crohn's disease (n = 12) and ulcerative colitis (n = 10), and those without IBD (n = 10). Matched samples from each participant were sent to three laboratories and studied using independent protocols for DNA extraction, library preparation, targeted-amplicon sequencing of a 16S rRNA gene hypervariable region, and processing of sequence data. We looked at two measures of interest - Bray-Curtis PERMANOVA R2 values and log2 fold-change estimates of the 25 most-abundant taxa - to assess variation in the results produced by each laboratory, as well the relative contribution to variation from the different extraction, sequencing, and analysis steps used to generate these measures.

Results: The R2 values and estimated differential abundance associated with diagnosis were consistent across datasets that used different DNA extraction and sequencing protocols, and within datasets that pooled samples from multiple protocols; however, variability in bioinformatic processing of sequence data led to changes in R2 values and inconsistencies in taxonomic assignment and abundance estimates.

Conclusion: Although the contribution of DNA extraction and sequencing methods to variability were observable, we find that results can be robust to the various extraction and sequencing approaches used in our study. Differences in data processing methods have a larger impact on results, making comparison among studies less reliable and the combined analysis of bioinformatically processed samples nearly impossible. Our results highlight the importance of making raw sequence data available to facilitate combined and comparative analyses of published studies using common data processing protocols. Study methodologies should provide detailed data processing methods for validation, interpretability, reproducibility, and comparability.

RevDate: 2020-09-25

Zhu Y, Li Y, Liu M, et al (2020)

Guizhi Fuling Wan, Chinese Herbal Medicine, Ameliorates Insulin Sensitivity in PCOS Model Rats With Insulin Resistance via Remodeling Intestinal Homeostasis.

Frontiers in endocrinology, 11:575.

Polycystic ovary syndrome (PCOS) is a common endocrine disease with reproductive dysfunction and metabolic disorder in women of childbearing age. Gastrointestinal microbiome contributes to PCOS through mediating insulin resistance. Guizhi Fuling Wan, Chinese herbal medicine, can treat PCOS with insulin resistance (PCOS-IR), but the underlying mechanism is not clear. The aim of this study was to characterize the exact mechanism of Guizhi Fuling Wan action and whether it is related to the regulation of intestinal flora structure. We induced PCOS-IR rat model by means of letrozole sodium carboxymethyl cellulose (CMC-na) solution combined with high-fat emulsion administration and randomly divided it into blank control group (K), model control group (M), low dose of Guizhi Fuling Wan group (D), middle dose of Guizhi Fuling Wan group (Z), high dose of Guizhi Fuling Wan group (G) and positive drug (Metformin) control group (Y). After 36 days of modeling and treatment, serum and stool samples from all rats were collected for a follow-up analysis. The data display that, compared with K group, elevated testosterone and HOMA-IR, turbulent estrous cycles and polycystic ovaries in M group, indicating the PCOS-IR rat model is successfully established. Increased fasting insulin is associated with higher inflammation(plasma TNF-α, IL-6, and HS-CPR concentration were determined) in M group, and the altered intestinal flora (compared with the K group, in M group the relative abundance of Alloprevotella was decreased significantly, while the relative abundance of Lachnospiraceae UCG-008, Lachnospiraceae NK4A136, Lactobacillus, Ruminiclostridium 9, and Ruminococcaceae UCG-003 was increased significantly) induced the secretion of inflammatory markers. On the other hand, Guizhi Fuling Wan can alleviate inflammation, improve insulin resistence: Lower inflammation decreased fasting insulin can be seen in G group compared with M group, this effect is related to the regulating effect of Guizhi Fuling Wan on intestinal flora (in G group, the relative abundance of Alloprevotella, Ruminococcaceae UCG-003, and Lachnospiraceae UCG-008 was increased significantly, compared with M group). This research demonstrates Guizhi Fuling Wan improve insulin resistance in polycystic ovary syndrome with the underlying mechanism of regulating intestinal flora to control inflammation. It would be useful to promote the therapeutic effect of Guizhi Fuling Wan on PCOS-IR.

RevDate: 2020-09-25

Cai TT, Ye XL, Li RR, et al (2020)

Resveratrol Modulates the Gut Microbiota and Inflammation to Protect Against Diabetic Nephropathy in Mice.

Frontiers in pharmacology, 11:1249.

Oral administration of resveratrol is able to ameliorate the progression of diabetic nephropathy (DN); however, its mechanisms of action remain unclear. Recent evidence suggested that the gut microbiota is involved in the metabolism therapeutics. In the current study, we sought to determine whether the anti-DN effects of resveratrol are mediated through modulation of the gut microbiota using the genetic db/db mouse model of DN. We demonstrate that resveratrol treatment of db/db mice relieves a series of clinical indicators of DN. We then show that resveratrol improves intestinal barrier function and ameliorates intestinal permeability and inflammation. The composition of the gut microbiome was significantly altered in db/db mice compared to control db/m mice. Dysbiosis in db/db mice characterized by low abundance levels of Bacteroides, Alistipes, Rikenella, Odoribacter, Parabacteroides, and Alloprevotella genera were reversed by resveratrol treatment, suggesting a potential role for the microbiome in DN progression. Furthermore, fecal microbiota transplantation, derived from healthy resveratrol-treated db/m mice, was sufficient to antagonize the renal dysfunction, rebalance the gut microbiome and improve intestinal permeability and inflammation in recipient db/db mice. These results indicate that resveratrol-mediated changes in the gut microbiome may play an important role in the mechanism of action of resveratrol, which provides supporting evidence for the gut-kidney axis in DN.

RevDate: 2020-09-25

Balty C, Guillot A, Fradale L, et al (2020)

Biosynthesis of the sactipeptide Ruminococcin C by the human microbiome: Mechanistic insights into thioether bond formation by radical SAM enzymes.

The Journal of biological chemistry pii:RA120.015371 [Epub ahead of print].

Despite its major importance in human health, the metabolic potential of the human gut microbiota is still poorly understood. We have recently shown that biosynthesis of Ruminococcin C (RumC), a novel ribosomally synthesized and post-translationally modified peptide (RiPP) produced by the commensal bacterium Ruminococcus gnavus, requires two radical SAM enzymes (RumMC1 and RumMC2) catalyzing the formation of four Cα-thioether bridges. These bridges, which are essential for RumC's antibiotic properties against human pathogens such as Clostridium perfringens, define two hairpin domains giving this sactipeptide (sulfur-to-α-carbon thioether-containing peptide) an unusual architecture among natural products. We report here the biochemical and spectroscopic characterizations of RumMC2. EPR spectroscopy and mutagenesis data support that RumMC2 is a member of the large family of SPASM-domain radical SAM enzymes characterized by the presence of three [4Fe-4S] clusters. We also demonstrate that this enzyme initiates its reaction by Cα H-atom abstraction and is able to catalyze the formation of non-natural thioether bonds in engineered peptide substrates. Unexpectedly, our data support the formation of a ketoimine rather than an α,β-dehydro-amino acid intermediate during Cα-thioether bridge LC-MS/MS fragmentation. Finally, we explored the roles of the leader peptide and of the RiPP precursor peptide recognition element (RRE), present in myriad RiPP-modifying enzymes. Collectively, our data support a more complex role for the RRE and the core peptide for the installation of post-translational modifications in RiPPs than previously anticipated and suggest a possible reaction intermediate for thioether bond formation.

RevDate: 2020-09-25

Panzer AR, SV Lynch (2020)

Gut Microbial Regulation of Autism Spectrum Disorder Symptoms.

Trends in endocrinology and metabolism: TEM pii:S1043-2760(20)30174-0 [Epub ahead of print].

Relationships between gut microbiome perturbation and autism spectrum disorder (ASD) have been observed in several human studies, but the functional implications and molecular mechanisms by which microbes may influence disease symptomology remain enigmatic. A recently published study by Sharon et al. offers evidence that the gut microbiome has a causative role in ASD and highlights the importance of early-life gut microbial metabolites in shaping mammalian behavior.

RevDate: 2020-09-25

Wu J, Yang D, Gong H, et al (2020)

Multiple omics analysis reveals that high fiber diets promote gluconeogenesis and inhibit glycolysis in muscle.

BMC genomics, 21(1):660 pii:10.1186/s12864-020-07048-1.

BACKGROUND: Meat quality is a complex trait affected by genotypic and environmental factors. In a previous study, it was found that feedstuffs have various effects on the growth rate and meat quality of lambs. However, the underlying mechanisms are still not entirely clear.

RESULTS: In this study, to investigate the mechanisms that impact meat quality in twin sheep fed either with high fiber low protein (HFLP) forage (Ceratoides) or low fiber high protein (LFHP) forage (alfalfa) diets, multi omics techniques were utilized for integration analysis based on the feed nutritional value and the sheep microbiome, transcriptome, metabolome, and fatty acid profile. Results showed that the production performance and the muscle components of lambs were significantly affected by feeds. The essential fatty acid (linoleic acid and arachidonic acid) content of the muscle, based on gas chromatography-mass spectrometry analysis, was increased when lambs were fed with HFLP. The microbes in the lambs' rumen fed a HFLP diet were more diverse than those of the LFHP fed group. Besides, the ratio of Bacteroidetes and Firmicutes in the rumen of the sheep fed a LFHP diet was 2.6 times higher than that of the HFLP fed group. Transcriptome analysis of the muscle revealed that the genes related to glucose metabolic processes and fatty acid biosynthesis were significantly differentially expressed between the two groups. Potential cross talk was found between the sfour omics data layers, which helps to understand the mechanism by which feedstuffs affect meat quality of lambs.

CONCLUSION: Feed systems may affect the epigenetic regulation of genes involved in the glucose metabolic pathway. HFLP feeds could induce gluconeogenesis to maintain glucose levels in blood, resulting in decreased fat content in muscle. The multiple omics analysis showed that the microbiota structure is significantly correlated with the metabolome and gene expression in muscle. This study laid a theoretical foundation for controlling the nutrient intake of sheep; it suggested that its fatty acid spectrum modifications and the removal of meat quality detrimental material could guide sheep feeding for functional mutton.

RevDate: 2020-09-25

Oliveira NF, CLM Silva (2020)

Unveiling the potential of purinergic signaling in schistosomiasis treatment.

Current topics in medicinal chemistry pii:CTMC-EPUB-110198 [Epub ahead of print].

Schistosomiasis is a neglected tropical disease. It is related to long-lasting granulomatous fibrosis and inflammation of target organs, and current sub-optimal pharmacological treatment awakens global public health concerns. Intravascular worms and eggs release antigens and extracellular vesicles that target host endothelial cells, modulate the immune system, and stimulate the release of damage-associated molecular patterns (DAMPs). ATP, one of the most studied DAMP, triggers a cascade of autocrine and paracrine actions through purinergic P2X and P2Y receptors, which are shaped by ectonucleotidases (CD39). Both P2 receptor families, and in particular P2Y1, P2Y2, P2Y12, and P2X7 receptors, have been attracting increasing interest in several inflammatory diseases and drug development. Current data obtained in the murine model unveil a CD39-ADP-P2Y1/P2Y12 receptors signaling pathway linked to liver and mesenteric exacerbations of schistosomal inflammation. Therefore, we propose that members of this purinergic signaling could be putative pharmacological targets to reduce schistosomal morbidity.

RevDate: 2020-09-25

Gayder S, Parcey M, Nesbitt D, et al (2020)

Population Dynamics between Erwinia amylovora, Pantoea agglomerans and Bacteriophages: Exploiting Synergy and Competition to Improve Phage Cocktail Efficacy.

Microorganisms, 8(9): pii:microorganisms8091449.

Bacteriophages are viruses capable of recognizing with high specificity, propagating inside of, and destroying their bacterial hosts. The phage lytic life cycle makes phages attractive as tools to selectively kill pathogenic bacteria with minimal impact on the surrounding microbiome. To effectively harness the potential of phages in therapy, it is critical to understand the phage-host dynamics and how these interactions can change in complex populations. Our model examined the interactions between the plant pathogen Erwinia amylovora, the antagonistic epiphyte Pantoea agglomerans, and the bacteriophages that infect and kill both species. P. agglomerans strains are used as a phage carrier; their role is to deliver and propagate the bacteriophages on the plant surface prior to the arrival of the pathogen. Using liquid cultures, the populations of the pathogen, carrier, and phages were tracked over time with quantitative real-time PCR. The jumbo Myoviridae phage ϕEa35-70 synergized with both the Myoviridae ϕEa21-4 and Podoviridae ϕEa46-1-A1 and was most effective in combination at reducing E. amylovora growth over 24 h. Phage ϕEa35-70, however, also reduced the growth of P. agglomerans. Phage cocktails of ϕEa21-4, ϕEa46-1-A1, and ϕEa35-70 at multiplicities of infections (MOIs) of 10, 1, and 0.01, respectively, no longer inhibited growth of P. agglomerans. When this cocktail was grown with P. agglomerans for 8 h prior to pathogen introduction, pathogen growth was reduced by over four log units over 24 h. These findings present a novel approach to study complex phage-host dynamics that can be exploited to create more effective phage-based therapies.

RevDate: 2020-09-25

Ogawa A, Tanaka R, Hirai N, et al (2020)

Investigation of Biofilms Formed on Steelmaking Slags in Marine Environments for Water Depuration.

International journal of molecular sciences, 21(18): pii:ijms21186945.

Steelmaking slags are a promising resource as artificial seaweed beds for the reconstitution of marine environments. To grow seaweed well, the formation of biofilms is an essential process in biofouling. This study focused on the formation of initial biofilms on steelmaking slag samples and analyzed the resulting bacterial communities using the next-generation sequencing technique. Three types of steelmaking slag were submerged in an area of Ise Bay in Mie Prefecture, Japan, for 3 and 7 days in the summer and winter seasons to allow the formation of biofilms. The bacterial communities of these biofilms were richer in sulfur-oxidizing bacteria compared to the biofilms formed on polyurethane sponges. It was found that Helicobacteraceae dominantly grew on the biofilms formed on the slag samples. This shows that steelmaking slags have potential to be used as artificial seaweed beds and marine water purifiers.

RevDate: 2020-09-25

Drażbo AA, Juśkiewicz J, Józefiak A, et al (2020)

The Fermentation Process Improves the Nutritional Value of Rapeseed Cake for Turkeys-Effects on Performance, Gut Bacterial Population and Its Fermentative Activity.

Animals : an open access journal from MDPI, 10(9): pii:ani10091711.

This experiment investigated the potential inclusion of fermented rapeseed cake (FRC) in turkey diets. The turkeys received diets either not supplemented (C) or supplemented with raw rapeseed cake (RRC) or FRC at 150 g/kg diet. In comparison with RRC, turkeys receiving FRC achieved significantly higher final BW comparable with that noted in the control group. The dietary inclusion of FRC increased the concentrations of propionic and valeric acid in the cecal digesta compared with the control group, and increased the proportion of butyric acid in SCFA profile compared with RRC group. The activities of glycolytic bacterial enzymes in the cecal digesta, were lowest in turkeys fed FRC. Experimental diets did not cause a shift in the relative abundances of the main bacterial phyla or orders in the cecal digesta. FRC increased the abundance of Bacteroidaceae at the family level, but decreased the abundance of Lactobacillus at the genus level compared with birds fed RRC. In conclusion, the dietary inclusion of FRC at 150 g/kg did not compromise bird performance, did not excessively stimulate bacterial activity, and did not cause shifts in the bacterial composition in the cecum. Actually, FCR exerted several beneficial effects that contributed to maintaining gut health in turkeys, which points to its advantage over RRC.

RevDate: 2020-09-25

Gaowa N, Panke-Buisse K, Wang S, et al (2020)

Brisket Disease Is Associated with Lower Volatile Fatty Acid Production and Altered Rumen Microbiome in Holstein Heifers.

Animals : an open access journal from MDPI, 10(9): pii:ani10091712.

Brisket disease is heritable but is also associated with non-genetic risk factors and effects of the disease on the rumen microbiome are unknown. Ten Holstein heifers were exposed to the plateau environment for three months and divided into two groups according to the index of brisket disease, the mean pulmonary arterial pressure (mPAP): brisket disease group (BD, n = 5, mPAP > 63 mmHg) and healthy heifer group (HH, n = 5, mPAP < 41 mmHg). Rumen fluid was collected for analysis of the concentrations of volatile fatty acids (VFAs). Extracted DNA from rumen contents was analyzed using Illumina MiSeq 16S rRNA sequencing technology. The concentration of total VFA and alpha-diversity metrics were significantly lower in BD group (p < 0.05). Ruminococcus and Treponema were significantly decreased in BD heifers (p < 0.05). Correlation analysis indicated that 10 genera were related to the mPAP (p < 0.05). Genera of Anaerofustis, Campylobacter, and Catonella were negatively correlated with total VFA and acetic acid (R < -0.7, p < 0.05), while genera of Blautia, YRC22, Ruminococcus, and Treponema were positively related to total VFA and acetic acid (R > 0.7; p < 0.05). Our findings may be a useful biomarker in future brisket disease work.

RevDate: 2020-09-24

Watts AM, West NP, Zhang P, et al (2020)

The Gut Microbiome of Adults with Allergic Rhinitis Is Characterised by Reduced Diversity and an Altered Abundance of Key Microbial Taxa Compared to Controls.

International archives of allergy and immunology pii:000510536 [Epub ahead of print].

INTRODUCTION: Unique gut microbial colonisation patterns are associated with the onset of allergic disease in infants; however, there is insufficient evidence to determine if aberrant microbial composition patterns persist in adult allergic rhinitis (AR) sufferers.

OBJECTIVE: To compare the gut microbiome composition between adult AR sufferers and controls.

METHODS: Gut microbial composition in stool samples was compared between 57 adult AR sufferers (39.06 ± 13.29 years) and 23 controls (CG; 36.55 ± 10.51 years) via next-generation sequencing of the V3-V4 hypervariable regions of the 16S rRNA gene. Taxonomic classification and identity assignment was performed using a reference-based approach with the NCBI database of 16S rRNA gene sequences.

RESULTS: Species richness determined via the Shannon index was significantly reduced in the AR cohort compared to the CG (4.35 ± 0.59 in AR vs. 4.65 ± 0.55 in CG, p = 0.037); trends for reductions in operational taxonomic unit (OTU) counts, inverse Simpson, and CHAO1 diversity indices were also noted. Bacteroidetes (p = 0.014) was significantly more abundant in the AR group than in the CG. In contrast, the Firmicutes phylum was significantly less abundant in the AR group than in the CG (p = 0.006). An increased abundance of Parabacteroides (p = 0.008) and a reduced abundance of Oxalobacter (p = 0.001) and Clostridiales (p = 0.005) were also observed in the AR cohort compared to the CG.

CONCLUSION: Adult AR sufferers have a distinct gut microbiome profile, marked by a reduced microbial diversity and altered abundance of certain microbes compared to controls. The results of this study provide evidence that unique gut microbial patterns occur in AR sufferers in adulthood and warrant further examination in the form of mechanistic studies.

RevDate: 2020-09-24

Gòdia M, Ramayo-Caldas Y, Zingaretti LM, et al (2020)

A pilot RNA-seq study in 40 pietrain ejaculates to characterize the porcine sperm microbiome.

Theriogenology, 157:525-533 pii:S0093-691X(20)30436-2 [Epub ahead of print].

The microbiome plays a key role in homeostasis and health and it has been also linked to fertility and semen quality in several animal species including swine. Despite the more than likely importance of sperm bacteria on the boar's reproductive ability and the dissemination of pathogens and antimicrobial resistance genes, the high throughput characterization of the swine sperm microbiome remains scarce. We carried RNA-seq on 40 ejaculates each from a different Pietrain boar and found that a proportion of the sequencing reads did not map to the Sus scrofa genome. The current study aimed at using these reads not belonging to pig to carry a pilot study to profile the boar sperm bacterial population and its relation with 7 semen quality traits. We found that the boar sperm contains a broad population of bacteria. The most abundant phyla were Proteobacteria (39.1%), Firmicutes (27.5%), Actinobacteria (14.9%) and Bacteroidetes (5.7%). The predominant species contaminated sperm after ejaculation from soil, faeces and water sources (Bacillus megaterium, Brachybacterium faecium, Bacillus coagulans). Some potential pathogens were also found but at relatively low levels (Escherichia coli, Clostridioides difficile, Clostridium perfringens, Clostridium botulinum and Mycobacterium tuberculosis). We also identified 3 potential antibiotic resistant genes from E. coli against chloramphenicol, Neisseria meningitidis against spectinomycin and Staphylococcus aureus against linezolid. None of these genes were highly abundant. Finally, we classified the ejaculates into categories according to their bacterial features and semen quality parameters and identified two categories that significantly differed for 5 semen quality traits and 13 bacterial features including the genera Acinetobacter, Stenotrophomonas and Rhodobacter. Our results show that boar semen contains a bacterial community, including potential pathogens and putative antibiotic resistance genes, and that these bacteria may affect its reproductive performance.

RevDate: 2020-09-24

AlShahrani I, Hosmani J, AlShahrani A, et al (2020)

High altitude as a possible factor for dysbiosis of salivary microbiome in orthodontic patients.

Archives of oral biology, 119:104917 pii:S0003-9969(20)30295-8 [Epub ahead of print].

BACKGROUND: External stressors such as high altitude and low oxygen are known to affect the human microbiome, and in light of the increased occurrence of dental caries and periodontitis in orthodontic patients, the effect of high altitude and the altered oral environment in orthodontic patients on the oral salivary microbiome was researched.

MATERIALS & METHODS: 31 orthodontic patients from high altitude, Aseer region and 25 orthodontic patients, residing at sea level, as controls were included. DNA isolation was done from the saliva collected from the study participants. V3 area of 16s RNA was targeted by universal primers through PCR to decipher the salivary microbiome in both the groups.

RESULTS: A total of 11 genera belonging to 4 phyla of bacteria were identified in both groups. The most abundant microbiome at the phylum level was: Firmicutes, Bacteroidetes Proteobacteria, and Cyanobacteria. The salivary microbiome was more diverse in sea level controls compared to that of the orthodontic patients at high altitude wherein the presence of only two main phyla: Firmicutes and Proteobacteria were seen. The controls revealed Firmicutes, Proteobacteria, Bacteroidetes and Cyanobacteria.

CONCLUSIONS: The findings of the study suggest that the biodiversity of the salivary microbiome is severely perturbed under the cumulative influences of high altitude and presence of fixed orthodontic appliance. Under these circumstances, a strict and meticulous oral hygiene regimen should be recommended and followed to avoid harmful effects on the periodontal tissues.

RevDate: 2020-09-24

Ni JJ, Yang XL, Zhang H, et al (2020)

Assessing causal relationship from gut microbiota to heel bone mineral density.

Bone pii:S8756-3282(20)30432-4 [Epub ahead of print].

Recent studies have demonstrated the important role played by gut microbiota in regulating bone development, but the evidence of such causal relationship is still sparse in human population. The aim of this study is to assess the causal relationship from gut microbiota to bone development and to identify specific causal bacteria taxa via a Mendelian randomization (MR) approach. A genome-wide association study (GWAS) summary statistic based two-sample MR analysis was performed. Summary statistics of microbiome GWAS (MGWAS) in 1,126 twin pairs of the TwinsUK study was used as discovery sample, and the MGWAS in 984 Dutch participants from the LifeLines-DEEP cohort was used as replication sample. Estimated heel bone mineral density (eBMD) GWAS in 426,824 participants from the UK biobank (UKB) cohort was used as outcome. Bacteria were grouped into taxa features at both order and family levels. In the discovery sample, a total of 25 bacteria features including 9 orders and 16 families were analyzed. Fourteen features (5 orders + 9 families) were nominally significant, including 5 orders (Bacteroidales, Clostridiales, Lactobacillales, Pasteurellales and Verrucomicrobiales) and 9 families (Bacteroidaceae, Clostridiaceae, Lachnospiraceae, Mogibacteriaceae, Pasteurellaceae, Porphyromonadaceae, Streptococcaceae, Verrucomicrobiaceae and Veillonellaceae). One order Clostridiales and its child taxon, family Lachnospiraceae, were successfully replicated in the replication sample (Clostridiales Pdiscovery=3.32×10-3Preplication=7.29×10-3; Lachnospiraceae Pdiscovery=0.03 Preplication=7.29×10-3). Our findings provided evidence of causal relationship from microbiota to bone development, as well as identified specific bacteria taxa that regulated bone mass variation, thus providing new insights into the microbiota mediated bone development mechanism.

RevDate: 2020-09-24

Di Lodovico L, Mondot S, Doré J, et al (2020)

Anorexia nervosa and gut microbiota: A systematic review and quantitative synthesis of pooled microbiological data.

Progress in neuro-psychopharmacology & biological psychiatry pii:S0278-5846(20)30430-9 [Epub ahead of print].

BACKGROUND: Alterations of gut microbiota may play a role in Anorexia Nervosa (AN) through perturbations of the gut-brain axis. Some studies found differences in the gut microbiota of patients with AN compared to healthy controls, but results are heterogeneous. The aim of this work was to systematically review the existing studies comparing gut microbial composition in AN and healthy controls, and to perform a quantitative synthesis of the pooled clinical and microbiological data, when available.

METHODS: A comprehensive literature search was performed to identify human studies investigating relationships between AN and gut microbiota. Microbiome datasets from studies were pooled and analysed focusing on alpha and beta-diversity and the relative abundance of microbial species in patients' gut microbiota compared to healthy controls.

RESULTS: Nine studies were eligible for the systematic review, of which 4 were included in the quantitative synthesis. Preserved alpha-diversity and decreased beta-diversity in AN emerged from the qualitative synthesis, while a slight increase of alpha-diversity (d < 0.4) and comparable beta-diversity were reported by the quantitative synthesis. Out of the 46 common species compared, three had a large combined effect size (d ≥ 0.9) to differentiate patients from controls, namely Alistipes, Parabacterioides and Roseburia. The latter was also correlated with BMI (ρ = 0.29).

CONCLUSIONS: The decrease of butyrate-producing species and the increase of mucine-degrading species may represent hallmarks of the gut microbiota alterations in AN, and therefore potentially interesting therapeutic targets. The heterogeneity of clinical and methodological characteristics hampers the generalizability of the results. Standardized research methods could improve comparability among studies to better identify the alterations of gut microbiota in AN.

RevDate: 2020-09-24

Salavrakos M, Leclercq S, De Timary P, et al (2020)

Microbiome and substances of abuse.

Progress in neuro-psychopharmacology & biological psychiatry pii:S0278-5846(20)30429-2 [Epub ahead of print].

There is a growing amount of evidence showing a reciprocal relation between the gut microbiota and the brain. Substance use disorders (SUD), which are a major cause of preventable morbidity and mortality worldwide, have an influence on the gut microbiota and on the gut-brain axis. The communication between the microbiota and the brain exists through different pathways: (1) the immune response elicited by bacterial products, coupled with alterations of the intestinal barrier allowing these products to enter the bloodstream, (2) the direct and indirect effects of bacterial metabolites such as short chain fatty acids (SCFAs) or tryptophan on the brain, (3) and the hypothalamic-pituitary-adrenal (HPA) axis, whose peripheral afferents can be influenced by the microbiota, and can in turn activate microglia. Among substances of abuse, alcohol has been the subject of the greatest number of studies in this field. In some but not all patients suffering from alcohol-use-disorder (AUD), alcohol alters the composition of the gut microbiota and the permeability of the intestinal barrier, directly and through dysbiosis. It has also been well demonstrated that alcohol induces a peripheral inflammation; it is still unclear whether it induces a central inflammation, as there are contradictory results in human studies. In animal studies, it has been shown that neuroinflammation increases during alcohol withdrawal. Literature on opioids and stimulants is less numerous. Chronic morphine intake induces dysbiosis, increased intestinal permeability and a probable neuroinflammation, which could explain symptoms such as tolerance, hyperalgesia and deficit in reward behavior. Cocaine induces a dysbiosis and conversely the microbiome can modulate the behavioral response to stimulant drugs. Tobacco cessation is associated with an increase in microbiota diversity. Taken together, the findings of our narrative literature review suggest a bidirectional influence in the pathogenesis of substance use disorders.

RevDate: 2020-09-24

Charlys da Costa A, Moron AF, Forney LJ, et al (2020)

Identification of Bacteriophages in the Vagina of Pregnant Women: A Descriptive Study.

BJOG : an international journal of obstetrics and gynaecology [Epub ahead of print].

OBJECTIVE: Determine the presence and identity of extracellular bacteriophage (phage) families, genera and species in the vagina of pregnant women DESIGN: Descriptive, observational cohort study SETTING: São Paulo, Brazil POPULATION: Pregnant women at 21-24 weeks gestation METHODS: Vaginal samples from 107 women whose vaginal microbiome and pregnancy outcomes were previously determined were analyzed for phages by metagenomic sequencing, Main outcome measures Identification of phage families, genera and species RESULTS: Phages were detected in 96 (89.7%) of the samples. Six different phage families were identified: Siphoviridae in 69.2%, Myoviridae in 49.5%, Microviridae in 37.4%, Podoviridae in 20.6%, Herelleviridae in 10.3% and Inviridae in 1.9% of the women. Four different phage families were present in 14 women (13.1%), 3 families in 20 women (18.7%), 2 families in 31 women (29.1%) and 1 family in 31 women (29.1%). The most common phage species detected were Bacillus phages in 48 (43.6%), Escherichia phages in 45 (40.9%), Staphylococcus phages in 40 (36.4%), Gokushovirus in 33 (30.0%) and Lactobacillus phages in 29 (26.4%) women. In a preliminary exploratory analysis, there were no associations between a particular phage family, the number of phage families present in the vagina or any particular phage species and either gestational age at delivery or the bacterial community state type present in the vagina.

CONCLUSIONS: Multiple phages are present in the vagina of most mid-trimester pregnant women.

RevDate: 2020-09-24

Witkin SS, Moron AF, Linhares IM, et al (2020)

The vaginal microbiome in pregnant women: knowledge gaps in relation to clinical relevance.

BJOG : an international journal of obstetrics and gynaecology [Epub ahead of print].

The use of culture-independent assays to determine the composition of the vaginal microbiota in pregnant women has greatly improved our knowledge of the diversity and relative abundance of bacteria present. However, despite advances in bacterial gene amplification technology and computer-assisted determination of microbial composition down to the strain level (even more specific than species), gaps remain in our knowledge of how racial, genetic and clinical factors affect vaginal microbiome composition and its sequelae.

RevDate: 2020-09-24

Ross CN, KR Reveles (2020)

Feasibility of fecal microbiota transplantation via oral gavage to safely alter gut microbiome composition in marmosets.

American journal of primatology [Epub ahead of print].

Disruption of microbial communities within human hosts has been associated with infection, obesity, cognitive decline, cancer risk and frailty, suggesting that microbiome-targeted therapies may be an option for improving healthspan and lifespan. The objectives of this study were to determine the feasibility of delivering fecal microbiota transplants (FMTs) to marmosets via oral gavage and to evaluate if alteration of the gut microbiome post-FMT could be achieved. This was a prospective study of marmosets housed at the Barshop Institute for Longevity and Aging Studies in San Antonio, Texas. Eligible animals included healthy young adult males (age 2-5 years) with no recent medication use. Stool from two donors was combined and administered in 0.5 ml doses to five young recipients once weekly for 3 weeks. Safety outcomes and alterations in the gut microbiome composition via 16S ribosomal RNA sequencing were compared at baseline and monthly up to 6 months post-FMT. Overall, significant differences in the percent relative abundance was seen in FMT recipients at the phylum and family levels from baseline to 1 month and baseline to 6 months post-FMT. In permutational multivariate analysis of variance analyses, treatment status (donor vs. recipient) (p = .056) and time course (p = .019) predicted β diversity (p = .056). The FMT recipients did not experience any negative health outcomes over the course of the treatment. FMT via oral gavage was safe to administer to young adult marmosets. The marmoset microbiome may be altered by FMT; however, progressive changes in the microbiome are strongly driven by the host and its baseline microbiome composition.

RevDate: 2020-09-24

Kinnunen-Grubb M, Sapkota R, Vignola M, et al (2020)

Breeding selection imposed a differential selective pressure on the wheat root-associated microbiome.

FEMS microbiology ecology pii:5911094 [Epub ahead of print].

Plants-microbiome associations are the result of millions of years of co-evolution. Due to breeding-accelerated plant evolution in non-native and highly managed soil, plant-microbe links could have been lost. We hypothesized that post-domestication breeding of wheat changed the root-associated microbiome. To test this, we analyzed root-associated fungal and bacterial communities shortly after emergence of seedlings representing a transect of wheat evolution including modern wheat, landraces, and ancestors. Numbers of observed microbial taxa were highest in landraces bred in low-input agricultural systems, and lowest in ancestors that had evolved in native soils. The microbial communities of modern cultivars were different from those of landraces and ancestors. Old wheat accessions enriched Acidobacteria and Actinobacteria, while modern cultivars enriched OTUs from Candidatus Saccharibacteria, Verrucomicrobia and Firmicutes. The fungal pathogens Fusarium, Neoascochyta and Microdochium enriched in modern cultivars. Both bacterial and fungal communities followed a neutral assembly model when bulk soil was considered as the source community, but accessions of the ancient Triticum turgidum and T. monococcum created a more isolated environment in their roots. In conclusion, wheat root-associated microbiomes have dramatically changed through a transect of breeding history.

RevDate: 2020-09-24

Li TP, Zha SS, Zhou CY, et al (2020)

Newly-introduced Cardinium endosymbiont reduces microbial diversity in the rice brown planthopper Nilaparvata lugens.

FEMS microbiology ecology pii:5911095 [Epub ahead of print].

Symbiotic microorganisms in invertebrates play vital roles in host ecology and evolution. Cardinium, a common intracellular symbiont, is transinfected into the important agricultural pest Nilaparvata lugens (rice brown planthopper) to regulate its reproduction, but how this impacts its microbial community is unknown. Here, we characterized the bacterial microbiota from N. lugens, with or without Cardinium, at different developmental stages and in various adult tissues using 16S rRNA gene sequencing. Upon infection with Cardinium, we found that microbial diversity in the different developmental stages of N. lugens (especially females), and in female midguts and male testes, was lower than in the uninfected control. There was a negative correlation between Cardinium and most related genera and between Bacteroidetes and Proteobacteria. Although the microbial structure varied during Cardinium infection, Acinetobacter spp. was a core microbiome genus. The Cardinium infection enhanced the relative density of midgut-associated Acinetobacter spp., with both bacteria exhibiting tissue-specific tropism. In addition, this infection caused the changes of main microbial functions in N. lugens. These results offer insights into the effects of alien (i.e. newly-introduced from other organism) Cardinium infection on N. lugens-associated microbiotas, aiding in the development of transinfected endosymbionts for pest control.

RevDate: 2020-09-24

Tsang KSW, Cheung MK, Lam RYC, et al (2020)

A preliminary examination of the bacterial, archaeal, and fungal rhizosphere microbiome in healthy and Phellinus noxius-infected trees.

MicrobiologyOpen [Epub ahead of print].

Phellinus noxius is a pathogenic fungus that causes brown root rot disease, resulting in a widespread tree and crop mortality in the tropics and subtropics. Early stages of this disease are largely asymptomatic, hindering early diagnosis and effective treatment. We hypothesized that P. noxius infection would alter the rhizosphere microbiome of infected trees, based on which diagnostic biomarkers could be developed. Here, we examined for the first time the bacterial, archaeal, and fungal rhizosphere microbiome in four species of healthy and P. noxius-infected trees (Ficus microcarpa, Celtis sinensis, Mallotus paniculatus, and Cinnamomum camphora) using high-throughput amplicon sequencing. Results revealed the dominance of Proteobacteria and Actinobacteria in bacteria, Crenarchaeota and Euryarchaeota in archaea, and Ascomycota and Basidiomycota in fungi. Phellinus noxius infection did not affect the alpha diversity of the bacterial rhizosphere microbiome in all four tree species but affected that of archaea and fungi in a tree species-dependent manner. Infection with P. noxius only affected the bacterial rhizosphere composition in M. paniculatus but not the other three tree species. By contrast, P. noxius infection affected the composition of the archaeal and fungal rhizosphere microbiome in all four tree species. Collectively, these results suggest that potential diagnostic biomarkers for brown root rot disease are tree species-specific and should be developed based on different taxonomic groups. Our study has provided insights into the rhizosphere microbiome in healthy and P. noxius-infected trees and laid a solid foundation for future comprehensive studies.

RevDate: 2020-09-24

Ventura M, Milani C, Turroni F, et al (2020)

Envisioning emerging frontiers on human gut microbiota and its applications.

Microbial biotechnology [Epub ahead of print].

The human gut microbiota is involved in multiple health-influencing host interactions during the host's entire life span. Microbes colonize the infant gut instantaneously after birth and subsequently the founding and interactive progress of this early gut microbiota is considered to be driven and modulated by different host- and microbe-associated forces. A rising number of studies propose that the composition of the human gut microbiota in the early stages of life impact on the human health conditions at later stages of life. This notion has powered research aimed at detailed investigations of the infant gut microbiota composition. Nevertheless, the molecular mechanisms supporting the gut microbiome functionality and the interaction of the early gut microbes with the human host remain largely unknown.

RevDate: 2020-09-24

Niemeier-Walsh C, Ryan PH, Meller J, et al (2020)

The Mycobiomes and Bacteriomes of Sputum, Saliva, and Home Dust.

Indoor air [Epub ahead of print].

Respiratory microbiome is an understudied area of research compared to other microbiomes of the human body. The respiratory tract is exposed to an array of environmental pollutants, including microbes. Yet we know very little about the relationship between environmental and respiratory microbiome. The primary aim of our study was to compare the mycobiomes and bacteriomes between three sample types from the same participants, including home dust, saliva, and sputum. Samples were collected from 40 adolescents in a longitudinal cohort. We analyzed the samples using 16s bacterial rDNA and ITS fungal rDNA gene sequencing, as well as quantitative PCR with universal fungal and bacterial primers. Results showed that home dust had the greatest alpha diversity between the three sample types for both bacteria and fungi. Dust had the highest total fungal load and the lowest total bacterial load. Sputum had greater bacterial diversity than saliva, but saliva had greater fungal diversity than sputum. The distribution of major bacterial phyla differed between all sample types. However, the distribution of major fungal classes differed only between sputum and saliva. Future research should examine the biological significance of the taxa found in each sample type based on microbial ecology and associations with health effects.

RevDate: 2020-09-24

Caenepeel C, Sadat Seyed Tabib N, Vieira-Silva S, et al (2020)

Review article: how the intestinal microbiota may reflect disease activity and influence therapeutic outcome in inflammatory bowel disease.

Alimentary pharmacology & therapeutics [Epub ahead of print].

BACKGROUND: Intestinal bacteria produce metabolites and by-products necessary for homeostasis. Imbalance in this equilibrium is linked with multiple pathologies, including inflammatory bowel disease (IBD). The role of the gut microbiota in determining treatment response is becoming apparent, and may act as biomarker for efficacy.

AIM: To describe knowledge about the intestinal microbiota on disease severity and treatment outcomes in IBD METHODS: Descriptive review using PubMed to identify literature on the intestinal microbiota in IBD RESULTS: Severe IBD has a less diverse microbiota with fewer commensal microbiota communities and more opportunistic pathogenic bacteria, originating from the oral cavity or respiratory tract. IBD treatments can alter gut microbiota composition, but in vitro/in vivo studies are needed to prove causation. A diversification of the microbiota is observed during remission. Patients with a more diverse baseline microbiome and higher microbial diversity show better response to anti-tumour necrosis factor-α, vedolizumab and ustekinumab therapy. Higher abundance of short chain fatty acid-producing bacteria, fewer mucus-colonising bacteria and lower abundance of pro-inflammatory bacteria have also been associated with a favourable outcome. Predictive models, based on a combination of microbiota, clinical data and serological markers, have good accuracy for treatment outcome and disease severity.

CONCLUSION: The intestinal microbiota in IBD carries a set of promising biomarkers of disease activity and prediction of therapeutic outcome. Current insights may also help in designing microbiota modulation strategies to improve outcomes in IBD.

RevDate: 2020-09-24

Kline SA, MS Mega (2020)

Stress-Induced Neurodegeneration: The Potential for Coping as Neuroprotective Therapy.

American journal of Alzheimer's disease and other dementias, 35:1533317520960873.

Stress responses are essential for survival, but become detrimental to health and cognition with chronic activation. Chronic hypothalamic-pituitary-adrenal axis release of glucocorticoids induces hypothalamic-pituitary-adrenal axis dysfunction and neuronal loss, decreases learning and memory, and modifies glucocorticoid receptor/mineralocorticoid receptor expression. Elderly who report increased stress are nearly 3 times more likely to develop Alzheimer's disease, have decreased global cognition and faster cognitive decline than those reporting no stress. Patients with mild cognitive impairment are more sensitive to stress compared to healthy elderly and those with Alzheimer's disease. Stress may also transduce neurodegeneration via the gut microbiome. Coping styles determine hippocampal mineralocorticoid receptor expression in mice, indicating that coping modifies cortisol's effect on the brain. Identifying neuroprotective coping strategies that lessen the burden of stress may prevent or slow cognitive decline. Treatments and education designed to reduce stress should be recognized as neuroprotective.

RevDate: 2020-09-24

Kürekci C, Özsoy B, Hassan E, et al (2020)

Effect of essential oil supplementation to diet on meat quality, fatty acid composition, performance parameters and intestinal microbiota of Japanese quails.

Journal of animal physiology and animal nutrition [Epub ahead of print].

The effect of essential oil (EO) supplementation on carcass characteristics of Japanese quails and interactions between ingredients and intestinal morphology were investigated in this study. A total of 250 quails were fed different diet: D1, basal diet (BD); D2, BD plus palmarosa oil (PO; 100 µg/kg diet); D3, BD plus lemon myrtle oil (LMO; 100 µg/kg diet); D4, BD plus α-Tops (mixture of α-terpineol, cineole and terpinene-4-ol; 100 µg/kg diet); and D5, BD plus cyclodextrin. Overall growth performance was determined at multiple time points during 35 days of experiment. Carcass characteristics (fatty acid, pH and colour), intestinal morphology and the expression levels of meat quality-related genes including the insulin-like growth factor (IGF-1), myogenin and avian uncoupling protein (avUCP) were examined at the end of the trial. Additionally, intestinal microbiome of quails was studied by next-generation sequencing-based culture-independent analysis. Although the inclusion of EOs into the diet had no effect on the growth performance of quails and the microbial profile, the significant changes in pH24 and colour (a*) of the quail's breast muscle (p < .05) in the group receiving PO were observed. Additionally, oleic acid content in the breast muscle was significantly higher in the EOs supplemented groups (p < .01). Quails fed the PO supplemented diet had higher villus and relatively rich in oleic acid. The expression levels of IGF-1 and myogenin genes in quail's muscle were not affected, but the expression of avUCP gene was significantly lower in quails fed with LMO and α-Tops (p < .05). The results demonstrated variable effects of these treatments on intestinal morphology. Taken together, dietary inclusion of EOs is found to be beneficial and hence can be recommended for improving the quality of poultry meat.

RevDate: 2020-09-24

Tian Y, Ma Y, Fu Y, et al (2020)

Application of n-of-1 Clinical Trials in Personalized Nutrition Research: A Trial Protocol for Westlake N-of-1 Trials for Macronutrient Intake (WE-MACNUTR).

Current developments in nutrition, 4(9):nzaa143 pii:nzaa143.

Personalized dietary recommendations can help with more effective disease prevention. This study aims to investigate the individual postprandial glucose response to diets with diverse macronutrient proportions at both the individual level and population level, and explore the potential of the novel single-patient (n-of-1) trial for personalization of diet. Secondary outcomes include individual phenotypic responses and the effects of dietary ingredients on the composition of gut microbiota. Westlake N-of-1 Trials for Macronutrient Intake is a multiple crossover feeding trial consisting of 3 successive 12-d dietary intervention pairs including a 6-d washout period before each 6-d isocaloric dietary intervention: a 6-d high-fat, low-carbohydrate diet, and a 6-d low-fat, high-carbohydrate diet. The results will help provide personalized dietary recommendations for macronutrients in terms of postprandial blood glucose responses. The proposed n-of-1 trial methods could help in optimizing individual health and advancing health care. This trial was registered with clinicaltrials.gov (NCT04125602).

RevDate: 2020-09-24

Spence JD (2020)

Uses of ultrasound in stroke prevention.

Cardiovascular diagnosis and therapy, 10(4):955-964.

Ultrasound methods are useful in stroke prevention in several ways. Measurement of carotid plaque burden, as either total plaque area (TPA) or total plaque volume (TPV) are strong predictors of cardiovascular risk: much stronger than intima-media thickness, which does not represent true atherosclerosis, but a biologically and genetically distinct phenotype. Measurement of plaque burden is also useful for the study of genetics, and of new risk factors such as toxic products of the intestinal microbiome. Carotid plaque burden is highly correlated with and as predictive of risk as coronary calcium scores, but is less costly and does not require radiation. Furthermore, because carotid plaques change in time over a period of months, they can be used for a new approach to vascular prevention: "Treating arteries instead of treating risk factors". In high-risk patients with asymptomatic carotid stenosis (ACS), this approach, implemented in 2003 in our clinics, was associated with a >80% reduction of stroke and myocardial infarction over 2 years. "Treating arteries without measuring plaque would be like treating hypertension without measuring blood pressure". Ultrasound methods can also be used to assess plaque vulnerability, by detecting echolucency, ulceration and plaque inhomogeneity on assessment of plaque texture. Transcranial Doppler (TCD) embolus detection is useful for risk stratification in patients with ACS; patients with two or more microemboli in an hour of monitoring have a 1-year risk of 15.6%, vs. 1% without microemboli, so this very clearly distinguishes which patients with ACS could benefit from intervention. TCD saline studies are more sensitive than trans-esophageal echocardiography for detection of patent foramen ovale, and more predictive of recurrent stroke. These methods should be more widely used, to reduce the increasing burden of stroke in our aging populations.

RevDate: 2020-09-24

Xu J, Y Yang (2020)

Implications of gut microbiome on coronary artery disease.

Cardiovascular diagnosis and therapy, 10(4):869-880.

Despite the enormous progress achieved in diagnosis and medical therapy of coronary artery disease (CAD) in the last decades, CAD continues to represent the leading cause of morbidity and mortality worldwide, leading to a massive health-care cost and social burden. Due to the dynamic and complex nature of CAD, the mechanisms underlying the progression of atherosclerotic plaque were largely unknown. With the development of metagenomics and bioinformatics, humans are gradually understanding the important role of the gut microbiome on their hosts. Trillions of microbes colonize in the human gut, they digest and absorb nutrients, as well as participate in a series of human functions and regulate the pathogenesis of diseases, including the cardiovascular disease (CVD) that has received much attention. Meanwhile, metabolomics studies have revealed associations between gut microbiota-derived metabolic bioactive signaling modules, including trimethylamine-N-oxide (TMAO), short-chain fatty acids (SCFAs), and bile acids (BAs), with the progression of CAD. Disturbance of the gut microbiome and microbial metabolites are important factors leading to CAD, which has become a novel target for CAD prevention and treatment. This review provides a brief overview of gut microbiome composition in CAD patients according to the recently reported studies, summarizes the underlying mechanisms, and highlights the prognostic value of the gut microbiome in CAD.

RevDate: 2020-09-24

Vuong HE, Pronovost GN, Williams DW, et al (2020)

The maternal microbiome modulates fetal neurodevelopment in mice.

Nature pii:10.1038/s41586-020-2745-3 [Epub ahead of print].

'Dysbiosis' of the maternal gut microbiome, in response to challenges such as infection1, altered diet2 and stress3 during pregnancy, has been increasingly associated with abnormalities in brain function and behaviour of the offspring4. However, it is unclear whether the maternal gut microbiome influences neurodevelopment during critical prenatal periods and in the absence of environmental challenges. Here we investigate how depletion and selective reconstitution of the maternal gut microbiome influences fetal neurodevelopment in mice. Embryos from antibiotic-treated and germ-free dams exhibited reduced brain expression of genes related to axonogenesis, deficient thalamocortical axons and impaired outgrowth of thalamic axons in response to cell-extrinsic factors. Gnotobiotic colonization of microbiome-depleted dams with a limited consortium of bacteria prevented abnormalities in fetal brain gene expression and thalamocortical axonogenesis. Metabolomic profiling revealed that the maternal microbiome regulates numerous small molecules in the maternal serum and the brains of fetal offspring. Select microbiota-dependent metabolites promoted axon outgrowth from fetal thalamic explants. Moreover, maternal supplementation with these metabolites abrogated deficiencies in fetal thalamocortical axons. Manipulation of the maternal microbiome and microbial metabolites during pregnancy yielded adult offspring with altered tactile sensitivity in two aversive somatosensory behavioural tasks, but no overt differences in many other sensorimotor behaviours. Together, our findings show that the maternal gut microbiome promotes fetal thalamocortical axonogenesis, probably through signalling by microbially modulated metabolites to neurons in the developing brain.

RevDate: 2020-09-24

Nelson C, Giraldo-Silva A, F Garcia-Pichel (2020)

A symbiotic nutrient exchange within the cyanosphere microbiome of the biocrust cyanobacterium, Microcoleus vaginatus.

The ISME journal pii:10.1038/s41396-020-00781-1 [Epub ahead of print].

Microcoleus vaginatus plays a prominent role as both primary producer and pioneer in biocrust communities from dryland soils. And yet, it cannot fix dinitrogen, essential in often nitrogen-limited drylands. But a diazotroph-rich "cyanosphere" has been described in M. vaginatus, hinting that there exists a C for N exchange between the photoautotroph and heterotrophic diazotrophs. We provide evidence for this by establishing such a symbiosis in culture and by showing that it is selective and dependent on nitrogen availability. In natural populations, provision of nitrogen resulted in loss of diazotrophs from the cyanosphere of M. vaginatus compared to controls, but provision of phosphorus did not. Co-culturing of pedigreed cyanosphere diazotroph isolates with axenic M. vaginatus resulted in copious growth in C and N-free medium, but co-culture with non-cyanosphere diazotrophs or other heterotrophs did not. Unexpectedly, bundle formation in M. vaginatus, diacritical to the genus but not seen in axenic culture, was restored in vitro by imposed nitrogen limitation or, even more strongly, by co-culture with diazotrophic partners, implicating this trait in the symbiosis. Our findings provide direct evidence for a symbiotic relationship between M. vaginatus and its cyanosphere and help explain how it can be a global pioneer in spite of its genetic shortcomings.

RevDate: 2020-09-24

Simin J, Fornes R, Liu Q, et al (2020)

Antibiotic use and risk of colorectal cancer: a systematic review and dose-response meta-analysis.

British journal of cancer pii:10.1038/s41416-020-01082-2 [Epub ahead of print].

BACKGROUND: It is understudied whether the posed association of oral antibiotics with colorectal cancer (CRC) varies between antibiotic spectrums, colorectal continuum, and if a non-linear dose-dependent relationship is present.

DESIGN: Three electronic databases and a trial platform were searched for all relevant studies, from inception until February 2020, without restrictions. Random-effects meta-analyses provided pooled effect-sizes (ES) with 95% confidence intervals (CI). Dose-response analyses modelling the relationship between number of days exposed to antibiotics and CRC risk were extended to non-linear multivariable random-effects models.

RESULTS: Of 6483 identified publications ten were eligible, including 4.1 million individuals and over 73,550 CRC cases. The pooled CRC risk was increased among individuals who ever-used antibiotics (ES = 1.17, 95%CI 1.05-1.30), particularly for broad-spectrum antibiotics (ES = 1.70, 95%CI 1.26-2.30), but not for narrow-spectrum antibiotic (ES = 1.11, 95% 0.93-1.32). The dose-response analysis did not provide strong evidence of any particular dose-response association, and the risk patterns were rather similar for colon and rectal cancer.

DISCUSSION: The antibiotic use associated CRC risk seemingly differs between broad- and narrow-spectrum antibiotics, and possibly within the colorectal continuum. It remains unclear whether this association is causal, requiring more mechanistic studies and further clarification of drug-microbiome interactions.

RevDate: 2020-09-24

Laue HE, Korrick SA, Baker ER, et al (2020)

Prospective associations of the infant gut microbiome and microbial function with social behaviors related to autism at age 3 years.

Scientific reports, 10(1):15515 pii:10.1038/s41598-020-72386-9.

The hypothesized link between gut bacteria and autism spectrum disorder (ASD) has been explored through animal models and human studies with microbiome assessment after ASD presentation. We aimed to prospectively characterize the association between the infant/toddler gut microbiome and ASD-related social behaviors at age 3 years. As part of an ongoing birth cohort gut bacterial diversity, structure, taxa, and function at 6 weeks (n = 166), 1 year (n = 158), 2 years (n = 129), and 3 years (n = 140) were quantified with 16S rRNA gene and shotgun metagenomic sequencing (n = 101 six weeks, n = 103 one year). ASD-related social behavior was assessed at age 3 years using Social Responsiveness Scale (SRS-2) T-scores. Covariate-adjusted linear and permutation-based models were implemented. Microbiome structure at 1 year was associated with SRS-2 total T-scores (p = 0.01). Several taxa at 1, 2, and 3 years were associated with SRS-2 performance, including many in the Lachnospiraceae family. Higher relative abundance of Adlercreutzia equolifaciens and Ruminococcus torques at 1 year related to poorer SRS-2 performance. Two functional pathways, L-ornithine and vitamin B6 biosynthesis, were associated with better social skills at 3 years. Our results support potential associations between early-childhood gut microbiome and social behaviors. Future mechanistic studies are warranted to pinpoint sensitive targets for intervention.

RevDate: 2020-09-24

Huey SL, Jiang L, Fedarko MW, et al (2020)

Nutrition and the Gut Microbiota in 10- to 18-Month-Old Children Living in Urban Slums of Mumbai, India.

mSphere, 5(5): pii:5/5/e00731-20.

In this cross-sectional study, we describe the composition and diversity of the gut microbiota among undernourished children living in urban slums of Mumbai, India, and determine how nutritional status, including anthropometric measurements, dietary intakes from complementary foods, feeding practices, and micronutrient concentrations, is associated with their gut microbiota. We collected rectal swabs from children aged 10 to 18 months living in urban slums of Mumbai participating in a randomized controlled feeding trial and conducted 16S rRNA sequencing to determine the composition of the gut microbiota. Across the study cohort, Proteobacteria dominated the gut microbiota at over 80% relative abundance, with Actinobacteria representation at <4%, suggesting immaturity of the gut. Increased microbial α-diversity was associated with current breastfeeding, greater head circumference, higher fat intake, and lower hemoglobin concentration and weight-for-length Z-score. In redundancy analyses, 47% of the variation in Faith's phylogenetic diversity (Faith's PD) could be accounted for by age and by iron and polyunsaturated fatty acid intakes. Differences in community structure (β-diversity) of the microbiota were observed among those consuming fats and oils the previous day compared to those not consuming fats and oils the previous day. Our findings suggest that growth, diet, and feeding practices are associated with gut microbiota metrics in undernourished children, whose gut microbiota were comprised mainly of Proteobacteria, a phylum containing many potentially pathogenic taxa.IMPORTANCE The impact of comprehensive nutritional status, defined as growth, nutritional blood biomarkers, dietary intakes, and feeding practices, on the gut microbiome in children living in low-resource settings has remained underreported in microbiome research. Among undernourished children living in urban slums of Mumbai, India, we observed a high relative abundance of Proteobacteria, a phylum including many potentially pathogenic species similar to the composition in preterm infants, suggesting immaturity of the gut, or potentially a high inflammatory burden. We found head circumference, fat and iron intake, and current breastfeeding were positively associated with microbial diversity, while hemoglobin and weight for length were associated with lower diversity. Findings suggest that examining comprehensive nutrition is critical to gain more understanding of how nutrition and the gut microbiota are linked, particularly in vulnerable populations such as children in urban slum settings.

RevDate: 2020-09-24

Musich T, Thovarai V, Venzon DJ, et al (2020)

A prime/boost vaccine regimen alters the rectal microbiome and impacts immune responses and viremia control post-SIV infection in male and female rhesus macaques.

Journal of virology pii:JVI.01225-20 [Epub ahead of print].

An efficacious HIV vaccine will likely require induction of both mucosal and systemic immune responses. We compared the immunogenicity and protective efficacy of two mucosal/systemic vaccine regimens and investigated their effect on the rectal microbiome. Rhesus macaques were primed twice mucosally with replication-competent Adenovirus type 5 host range mutant (Ad5hr)-SIV recombinants and boosted twice intramuscularly with ALVAC-SIV recombinant plus SIV gp120 protein, or with DNA encoding SIV genes and rhesus IL-12, plus SIV gp120 protein. Controls received empty Ad5hr vector and alum adjuvant only. Both regimens elicited strong, comparable mucosal and systemic cellular and humoral immunity. Pre-vaccination rectal microbiomes of males and females differed and significantly changed over the course of immunization, most strongly in females post-Ad5hr immunizations. Following repeated low dose intrarectal SIV challenges, both vaccine groups exhibited modest, significantly reduced acute viremia. Male and female controls exhibited similar acute viral loads; however, vaccinated females, but not males, exhibited lower acute viremia compared to same-sex controls. Few differences in adaptive immune responses were observed between the sexes. Striking differences in correlations of the rectal microbiome of males and females with acute viremia and immune responses associated with protection were seen and point to effects of the microbiome on vaccine-induced immunity and viremia control. Our study clearly demonstrates direct effects of a mucosal SIV vaccine regimen on the rectal microbiome and validates our previously reported SIV vaccine-induced sex bias. Sex and the microbiome are critical factors that should not be overlooked in vaccine design and evaluation.IMPORTANCE Differences in HIV pathogenesis between males and females, including immunity post-infection, have been well documented as have steroid hormone effects on the microbiome, known to influence mucosal immune responses. Few studies have applied this knowledge to vaccine trials. We investigated two SIV vaccine regimens combining mucosal priming immunizations and systemic protein boosting. We again report a vaccine-induced sex bias, with female rhesus macaques but not males displaying significantly reduced acute viremia. The vaccine regimens, especially the mucosal primes, significantly altered the rectal microbiome. The greatest effects were in females. Striking differences in correlations of prevalent rectal bacteria with viral loads and potentially protective immune responses were observed between female and male macaques. Effects of the microbiome on vaccine-induced immunity and viremia control require further study by microbiome transfer. However, the findings presented highlight the critical importance of considering effects of sex and the microbiome in vaccine design and evaluation.

RevDate: 2020-09-24

Koti M, Ingersoll MA, Gupta S, et al (2020)

Sex Differences in Bladder Cancer Immunobiology and Outcomes: A Collaborative Review with Implications for Treatment.

European urology oncology pii:S2588-9311(20)30140-1 [Epub ahead of print].

CONTEXT: Urothelial carcinoma of the bladder (UCB) exhibits significant sexual dimorphism in the incidence, etiology, and response to intravesical immunotherapy. Environmental factors such as tobacco use and clinical management issues such as delayed presentation have widely been associated with sex differences in UCB outcomes. Emerging findings from immune checkpoint blockade trials are suggestive of differential outcomes in females compared with males. Sex-specific differences in the way immune system functions and responds to pathogenic insults are well established. As such, an in-depth understanding of the genetic and epigenetic factors contributing to sex-associated differences in response to immunomodulatory therapies is needed urgently for improved management of UCB.

OBJECTIVE: To review the associations between patient sex and clinical outcomes, with a focus on the incidence, host intrinsic features, and response to therapies in UCB.

EVIDENCE ACQUISITION: Using the PubMed database, this narrative review evaluates published findings from mouse model-based and clinical cohort studies to identify factors associated with sex and clinical outcomes in bladder cancer. A scoping review of the key findings on epidemiology, genetic, hormonal, immune physiology, and clinical outcomes was performed to explore potential factors that could have implications in immunomodulatory therapy design.

EVIDENCE SYNTHESIS: Sex-associated differences in UCB incidence and clinical outcomes are influenced by sex hormones, local bladder resident immune populations, tumor genetics, and bladder microbiome. In the context of therapeutic outcomes, sex differences are prominent in response to bacillus Calmette-Guérin immunotherapy used in the treatment of non-muscle-invasive bladder cancer. Similarly, with respect to tumor molecular profiles in muscle-invasive bladder cancer, tumors from females show enrichment of the basal subtype.

CONCLUSIONS: Among proposed tumor/host intrinsic factors that may influence response to immune-based therapies, patient sex remains a challenging consideration that deserves further attention. Evidence to date supports a multifactorial origin of sexual dimorphism in the incidence and outcomes of UCB.

PATIENT SUMMARY: In this review, we highlight the sex-associated host and tumor intrinsic features that may potentially drive differential disease progression and therapeutic response in urothelial carcinoma of the bladder.

RevDate: 2020-09-24

Tasnim S, Miller AL, Jupiter DC, et al (2020)

Effects of proton pump inhibitor use on the esophageal microbial community.

BMC gastroenterology, 20(1):312 pii:10.1186/s12876-020-01460-3.

BACKGROUND: Changes in the esophageal microbiome correlate with esophageal disease, but the effects of proton pump inhibitor (PPI) drugs are incompletely characterized. Our objective was to identify the effects of PPI use on the microbial community of the esophagus.

METHODS: Mucosal biopsies of the distal esophagus were analyzed using a customized esophageal microbiome qPCR panel array (EMB). Patient demographics, use of PPIs, duration of use and dose were recorded.

RESULTS: Fifty-eight patients were included. Mean age was 60.5 years. Ninety percent (52/58) of patients were on PPIs. Mean dose was 42.7 mg. Mean duration of use was 2.5 years. The use of PPIs led to a significant difference in absolute levels of only one organism, Actinomyces, in the entire array (p < 0.01). Among patients who used proton pump inhibitors, there was no significant association between dose and absolute levels of any organism. Similarly, there was no association between duration of use and absolute levels of any organism.

CONCLUSIONS: PPI use does not seem to cause significant changes in the distal esophageal microbial community. Future studies with larger sample sizes and esophageal pH testing should be performed to determine the level of acidity and its relationship to the microbial community.

RevDate: 2020-09-24

Kim B, Cho EJ, Yoon JH, et al (2020)

Pathway-Based Integrative Analysis of Metabolome and Microbiome Data from Hepatocellular Carcinoma and Liver Cirrhosis Patients.

Cancers, 12(9): pii:cancers12092705.

Aberrations of the human microbiome are associated with diverse liver diseases, including hepatocellular carcinoma (HCC). Even if we can associate specific microbes with particular diseases, it is difficult to know mechanistically how the microbe contributes to the pathophysiology. Here, we sought to reveal the functional potential of the HCC-associated microbiome with the human metabolome which is known to play a role in connecting host phenotype to microbiome function. To utilize both microbiome and metabolomic data sets, we propose an innovative, pathway-based analysis, Hierarchical structural Component Model for pathway analysis of Microbiome and Metabolome (HisCoM-MnM), for integrating microbiome and metabolomic data. In particular, we used pathway information to integrate these two omics data sets, thus providing insight into biological interactions between different biological layers, with regard to the host's phenotype. The application of HisCoM-MnM to data sets from 103 and 97 patients with HCC and liver cirrhosis (LC), respectively, showed that this approach could identify HCC-related pathways related to cancer metabolic reprogramming, in addition to the significant metabolome and metagenome that make up those pathways.

RevDate: 2020-09-24

Buchovec I, Gricajeva A, Kalėdienė L, et al (2020)

Antimicrobial Photoinactivation Approach Based on Natural Agents for Control of Bacteria Biofilms in Spacecraft.

International journal of molecular sciences, 21(18): pii:ijms21186932.

A spacecraft is a confined system that is inhabited by a changing microbial consortium, mostly originating from life-supporting devices, equipment collected in pre-flight conditions, and crewmembers. Continuous monitoring of the spacecraft's bioburden employing culture-based and molecular methods has shown the prevalence of various taxa, with human skin-associated microorganisms making a substantial contribution to the spacecraft microbiome. Microorganisms in spacecraft can prosper not only in planktonic growth mode but can also form more resilient biofilms that pose a higher risk to crewmembers' health and the material integrity of the spacecraft's equipment. Moreover, bacterial biofilms in space conditions are characterized by faster formation and acquisition of resistance to chemical and physical effects than under the same conditions on Earth, making most decontamination methods unsafe. There is currently no reported method available to combat biofilm formation in space effectively and safely. However, antibacterial photodynamic inactivation based on natural photosensitizers, which is reviewed in this work, seems to be a promising method.

RevDate: 2020-09-23

Hoque MN, Istiaq A, Rahman MS, et al (2020)

Microbiome dynamics and genomic determinants of bovine mastitis.

Genomics pii:S0888-7543(20)31029-6 [Epub ahead of print].

The milk of lactating cows presents a complex ecosystem of interconnected microbial communities which can influence the pathophysiology of mastitis. We hypothesized possible dynamic shifts of microbiome composition and genomic features with different pathological conditions of mastitis (Clinical Mastitis; CM, Recurrent CM; RCM, Subclinical Mastitis; SCM). To evaluate this hypothesis, we employed whole metagenome sequencing (WMS) in 20 milk samples (CM, 5; RCM, 6; SCM, 4; H, 5) to unravel the microbiome dynamics, interrelation, and relevant metabolic functions. The WMS data mapped to 442 bacterial, 58 archaeal and 48 viral genomes with distinct variation in microbiome composition (CM > H > RCM > SCM). Furthermore, we identified a number of microbial genomic features, including 333, 304, 183 and 50 virulence factors-associated genes (VFGs) and 48, 31, 11 and 6 antibiotic resistance genes (ARGs) in CM, RCM, SCM, and H-microbiomes, respectively. We also detected different metabolic pathway and functional genes associated with mastitis pathogenesis. Therefore, profiling microbiome dynamics in different conditions of mastitis and associated microbial genomic features contributes to developing microbiome-based diagnostics and therapeutics for bovine mastitis.

RevDate: 2020-09-23

Khanna S, Pardi DS, Jones C, et al (2020)

RBX7455, a Room Temperature-Stable, Orally-Administered Investigational Live Biotherapeutic, is Safe, Effective, and Shifts Patients' Microbiomes in a Phase 1 Study for Recurrent Clostridioides difficile Infections.

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America pii:5910606 [Epub ahead of print].

BACKGROUND: Recurrent Clostridioides difficile infections (rCDI) are a global public health threat. To reduce rCDI, microbiota-restoring therapies are needed, particularly standardized, easy-to-administer formulations.

METHODS: This Phase I open-label trial assessed the safety, efficacy in preventing rCDI recurrence, and intestinal microbiome effects of RBX7455, a room temperature-stable, orally administered investigational live biotherapeutic. Adult participants with one or more prior episodes of rCDI received: four RBX7455 capsules twice daily for four days (Group 1); four RBX7455 capsules twice daily for two days (Group 2); or two RBX7455 capsules twice daily for two days (Group 3). For all groups, the first dose was administered in clinic, with remaining doses self-administered at home. Adverse events were monitored during and for 6 months after treatment. Treatment success was defined as rCDI prevention through 8 weeks after treatment. Participants' microbiome composition was assessed prior to and for 6 months after treatment.

RESULTS: Nine of 10 Group 1 patients (90%), 8 of 10 Group 2 patients (80%), and 10 of 10 Group 3 patients (100%) were recurrence-free at the 8-week endpoint with durability to 6 months. Seventy-five treatment-emergent adverse events were observed in 27 participants with no serious investigational product-related events. Prior to treatment, participants' microbiomes were dissimilar from the RBX7455 composition with decreased Bacteroidia- and Clostridia-class bacteria, whereas after treatment, responders' microbiomes showed increased Bacteroidia and Clostridia.

CONCLUSIONS: Three dosing regimens of RBX7455 were safe and effective at preventing rCDI. Responders' microbiomes converged toward the composition of RBX7455. These results support its continued clinical evaluation.


RevDate: 2020-09-23

Walters KE, JBH Martiny (2020)

Alpha-, beta-, and gamma-diversity of bacteria varies across habitats.

PloS one, 15(9):e0233872 pii:PONE-D-20-14241.

Bacteria are essential parts of ecosystems and are the most diverse organisms on the planet. Yet, we still do not know which habitats support the highest diversity of bacteria across multiple scales. We analyzed alpha-, beta-, and gamma-diversity of bacterial assemblages using 11,680 samples compiled by the Earth Microbiome Project. We found that soils contained the highest bacterial richness within a single sample (alpha-diversity), but sediment assemblages displayed the highest gamma-diversity. Sediment, biofilms/mats, and inland water exhibited the most variation in community composition among geographic locations (beta-diversity). Within soils, agricultural lands, hot deserts, grasslands, and shrublands contained the highest richness, while forests, cold deserts, and tundra biomes consistently harbored fewer bacterial species. Surprisingly, agricultural soils encompassed similar levels of beta-diversity as other soil biomes. These patterns were robust to the alpha- and beta- diversity metrics used and the taxonomic binning approach. Overall, the results support the idea that spatial environmental heterogeneity is an important driver of bacterial diversity.

RevDate: 2020-09-23

Avagimyan A, Manukyan I, Navasardyan G, et al (2020)


Georgian medical news.

This review article introduces a topical multidisciplinary issue such as the atherogenic impact of oral cavity dysbiosis. Pathophysiological mechanisms and pathoimmunobiochemical aspects of the atherosclerosis initiation and atheroma destabilization are observed in this manuscript. Dysbiosis of the oral microbiome is a revolutionary and contemporary risk factor for CVD development and burdening, consequently, understanding the fundamental foundations of the pathogenesis of rearrangement of the morphofunctional constant of the myocardium will allow to exact the preferred mode of cardio- and vasoprotection, which will properly affect the functional parameters of CVD and in the long term will improve both the quality of life and the prognosis. patients of the cardiological profile.

RevDate: 2020-09-23

Barnes CJ, Rasmussen L, Asplund M, et al (2020)

Comparing DADA2 and OTU clustering approaches in studying the bacterial communities of atopic dermatitis.

Journal of medical microbiology [Epub ahead of print].

Introduction. The pathogenesis of atopic dermatitis (AD) is not yet fully understood, but the bacterial composition of AD patients' skin has been shown to have an increased abundance of Staphylococcus aureus. More recently, coagulase-negative Staphylococcus (CoNS) species were shown to be able to inhibit S. aureus, but further studies are required to determine the effects of Staphylococcus community variation in AD.Aim. Here we investigated whether analysing metabarcoding data with the more recently developed DADA2 approach improves metabarcoding analyses compared to the previously used operational taxonomic unit (OTU) clustering, and can be used to study Staphylococcus community dynamics.Methods. The bacterial 16S rRNA region from tape strip samples of the stratum corneum of AD patients (non-lesional skin) and non-AD controls was metabarcoded. We processed metabarcoding data with two different bioinformatic pipelines (an OTU clustering method and DADA2), which were analysed with and without technical replication (sampling strategy).Results. We found that OTU clustering and DADA2 performed well for community-level studies, as demonstrated by the identification of significant differences in the skin bacterial communities associated with AD. However, the OTU clustering approach inflated bacterial richness, which was worsened by not having technical replication. Data processed with DADA2 likely handled sequencing errors more effectively and thereby did not inflate molecular richness.Conclusion. We believe that DADA2 represents an improvement over an OTU clustering approach, and that biological replication rather than technical replication is a more effective use of resources. However, neither OTU clustering nor DADA2 gave insights into Staphylococcus community dynamics, and caution should remain in not overinterpreting the taxonomic assignments at lower taxonomic ranks.

RevDate: 2020-09-23

Morar N, JA Skorburg (2020)

Why We Never Eat Alone: The Overlooked Role of Microbes and Partners in Obesity Debates in Bioethics.

Journal of bioethical inquiry pii:10.1007/s11673-020-10047-2 [Epub ahead of print].

Debates about obesity in bioethics tend to unfold in predictable epicycles between individual choices and behaviours (e.g., restraint, diet, exercise) and the oppressive socio-economic structures constraining them (e.g., food deserts, advertising). Here, we argue that recent work from two cutting-edge research programmes in microbiology and social psychology can advance this conceptual stalemate in the literature. We begin in section 1 by discussing two promising lines of obesity research involving the human microbiome and relationship partners. Then, in section 2, we show how this research has made viable novel strategies for fighting obesity, including microbial therapies and dyad-level interventions. Finally, in section 3, we consider objections to our account and conclude by arguing that attention to the most immediate features of our biological and social environment offers a middle ground solution, while also raising important new issues for bioethicists.

RevDate: 2020-09-23

Rademacher J, Poddubnyy D, U Pleyer (2020)

Uveitis in spondyloarthritis.

Therapeutic advances in musculoskeletal disease, 12:1759720X20951733 pii:10.1177_1759720X20951733.

Uveitis is the most frequent extra-articular manifestation of axial spondyloarthritis (SpA), occurring in up to one-third of the patients. In the majority of patients, uveitis is acute, anterior and unilateral and presents with photosensitivity, sudden onset of pain and blurred vision. Topical steroids are an effective treatment; however, recurrent or refractory cases may need conventional disease-modifying antirheumatic drugs or biological treatment with monoclonal tumor necrosis factor (TNF) inhibitors, thus also influencing treatment strategy of the underlying SpA. Though the exact pathogenesis of SpA and uveitis remains unknown, both seem to result from the interaction of a specific, mostly shared genetical background (among other HLA-B27 positivity), external influences such as microbiome, bacterial infection or mechanical stress and activation of the immune system resulting in inflammation. Up to 40% of patients presenting with acute anterior uveitis (AAU) have an undiagnosed SpA. Therefore, an effective referral strategy for AAU patients is needed to shorten the diagnostic delay of SpA and enable an early effective treatment. Further, the risk for ophthalmological manifestations increases with the disease duration in SpA; and patients presenting with ocular symptoms should be referred to an ophthalmologist. Thus, a close collaboration between patient, rheumatologist and ophthalmologist is needed to optimally manage ocular inflammation in SpA.

RevDate: 2020-09-23

Neil K, Allard N, Grenier F, et al (2020)

Highly efficient gene transfer in the mouse gut microbiota is enabled by the Incl2 conjugative plasmid TP114.

Communications biology, 3(1):523 pii:10.1038/s42003-020-01253-0.

The gut microbiota is a suspected hotspot for bacterial conjugation due to its high density and diversity of microorganisms. However, the contribution of different conjugative plasmid families to horizontal gene transfer in this environment remains poorly characterized. Here, we systematically quantified the transfer rates in the mouse intestinal tract for 13 conjugative plasmids encompassing 10 major incompatibility groups. The vast majority of these plasmids were unable to perform conjugation in situ or only reached relatively low transfer rates. Surprisingly, IncI2 conjugative plasmid TP114 was identified as a proficient DNA delivery system in this environment, with the ability to transfer to virtually 100% of the probed recipient bacteria. We also show that a type IV pilus present in I-complex conjugative plasmids plays a crucial role for the transfer of TP114 in the mouse intestinal microbiota, most likely by contributing to mating pair stabilization. These results provide new insights on the mobility of genes in the gut microbiota and highlights TP114 as a very efficient DNA delivery system of interest for microbiome editing tools.

RevDate: 2020-09-23

Tao C, Li R, Xiong W, et al (2020)

Bio-organic fertilizers stimulate indigenous soil Pseudomonas populations to enhance plant disease suppression.

Microbiome, 8(1):137 pii:10.1186/s40168-020-00892-z.

BACKGROUND: Plant diseases caused by fungal pathogen result in a substantial economic impact on the global food and fruit industry. Application of organic fertilizers supplemented with biocontrol microorganisms (i.e. bioorganic fertilizers) has been shown to improve resistance against plant pathogens at least in part due to impacts on the structure and function of the resident soil microbiome. However, it remains unclear whether such improvements are driven by the specific action of microbial inoculants, microbial populations naturally resident to the organic fertilizer or the physical-chemical properties of the compost substrate. The aim of this study was to seek the ecological mechanisms involved in the disease suppressive activity of bio-organic fertilizers.

RESULTS: To disentangle the mechanism of bio-organic fertilizer action, we conducted an experiment tracking Fusarium wilt disease of banana and changes in soil microbial communities over three growth seasons in response to the following four treatments: bio-organic fertilizer (containing Bacillus amyloliquefaciens W19), organic fertilizer, sterilized organic fertilizer and sterilized organic fertilizer supplemented with B. amyloliquefaciens W19. We found that sterilized bioorganic fertilizer to which Bacillus was re-inoculated provided a similar degree of disease suppression as the non-sterilized bioorganic fertilizer across cropping seasons. We further observed that disease suppression in these treatments is linked to impacts on the resident soil microbial communities, specifically by leading to increases in specific Pseudomonas spp.. Observed correlations between Bacillus amendment and indigenous Pseudomonas spp. that might underlie pathogen suppression were further studied in laboratory and pot experiments. These studies revealed that specific bacterial taxa synergistically increase biofilm formation and likely acted as a plant-beneficial consortium against the pathogen.

CONCLUSION: Together we demonstrate that the action of bioorganic fertilizer is a product of the biocontrol inoculum within the organic amendment and its impact on the resident soil microbiome. This knowledge should help in the design of more efficient biofertilizers designed to promote soil function. Video Abstract.

RevDate: 2020-09-23

Jiménez RR, Alvarado G, Sandoval J, et al (2020)

Habitat disturbance influences the skin microbiome of a rediscovered neotropical-montane frog.

BMC microbiology, 20(1):292 pii:10.1186/s12866-020-01979-1.

BACKGROUND: The skin microbiome serves as a first line defense against pathogens in vertebrates. In amphibians, it has the potential to protect against the chytrid fungus Batrachochytrium dendrobatis (Bd), a likely agent of amphibian declines. Alteration of the microbiome associated with unfavorable environmental changes produced by anthropogenic activities may make the host more susceptible to pathogens. Some amphibian species that were thought to be "extinct" have been rediscovered years after population declines in the late 1980s probably due to evolved Bd-resistance and are now threatened by anthropogenic land-use changes. Understanding the effects of habitat disturbance on the host skin microbiome is relevant for understanding the health of these species, along with its susceptibility to pathogens such as Bd. Here, we investigate the influence of habitat alteration on the skin bacterial communities as well as specifically the putative Bd-inhibitory bacterial communities of the montane frog Lithobates vibicarius. This species, after years of not being observed, was rediscovered in small populations inhabiting undisturbed and disturbed landscapes, and with continuous presence of Bd.

RESULTS: We found that cutaneous bacterial communities of tadpoles and adults differed between undisturbed and disturbed habitats. The adults from disturbed habitats exhibited greater community dispersion than those from undisturbed habitats. We observed a higher richness of putative Bd-inhibitory bacterial strains in adults from disturbed habitats than in those from undisturbed habitats, as well as a greater number of these potential protective bacteria with a high relative abundance.

CONCLUSIONS: Our findings support the microbial "Anna Karenina principle", in which disturbance is hypothesized to cause greater microbial dispersion in communities, a so-called dysbiosis, which is a response of animal microbiomes to stress factors that decrease the ability of the host or its microbiome to regulate community composition. On the positive side, the high richness and relative abundance of putative Bd-inhibitory bacteria may indicate the development of a defense mechanism that enhances Bd-protection, attributed to a co-occurrence of more than 30-years of host and pathogen in these disturbed habitats. Our results provide important insight into the influence of human-modified landscapes on the skin microbiome and health implications of Bd-survivor species.


RJR Experience and Expertise


Robbins holds BS, MS, and PhD degrees in the life sciences. He served as a tenured faculty member in the Zoology and Biological Science departments at Michigan State University. He is currently exploring the intersection between genomics, microbial ecology, and biodiversity — an area that promises to transform our understanding of the biosphere.


Robbins has extensive experience in college-level education: At MSU he taught introductory biology, genetics, and population genetics. At JHU, he was an instructor for a special course on biological database design. At FHCRC, he team-taught a graduate-level course on the history of genetics. At Bellevue College he taught medical informatics.


Robbins has been involved in science administration at both the federal and the institutional levels. At NSF he was a program officer for database activities in the life sciences, at DOE he was a program officer for information infrastructure in the human genome project. At the Fred Hutchinson Cancer Research Center, he served as a vice president for fifteen years.


Robbins has been involved with information technology since writing his first Fortran program as a college student. At NSF he was the first program officer for database activities in the life sciences. At JHU he held an appointment in the CS department and served as director of the informatics core for the Genome Data Base. At the FHCRC he was VP for Information Technology.


While still at Michigan State, Robbins started his first publishing venture, founding a small company that addressed the short-run publishing needs of instructors in very large undergraduate classes. For more than 20 years, Robbins has been operating The Electronic Scholarly Publishing Project, a web site dedicated to the digital publishing of critical works in science, especially classical genetics.


Robbins is well-known for his speaking abilities and is often called upon to provide keynote or plenary addresses at international meetings. For example, in July, 2012, he gave a well-received keynote address at the Global Biodiversity Informatics Congress, sponsored by GBIF and held in Copenhagen. The slides from that talk can be seen HERE.


Robbins is a skilled meeting facilitator. He prefers a participatory approach, with part of the meeting involving dynamic breakout groups, created by the participants in real time: (1) individuals propose breakout groups; (2) everyone signs up for one (or more) groups; (3) the groups with the most interested parties then meet, with reports from each group presented and discussed in a subsequent plenary session.


Robbins has been engaged with photography and design since the 1960s, when he worked for a professional photography laboratory. He now prefers digital photography and tools for their precision and reproducibility. He designed his first web site more than 20 years ago and he personally designed and implemented this web site. He engages in graphic design as a hobby.

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E-mail: RJR8222@gmail.com

Collection of publications by R J Robbins

Reprints and preprints of publications, slide presentations, instructional materials, and data compilations written or prepared by Robert Robbins. Most papers deal with computational biology, genome informatics, using information technology to support biomedical research, and related matters.

Research Gate page for R J Robbins

ResearchGate is a social networking site for scientists and researchers to share papers, ask and answer questions, and find collaborators. According to a study by Nature and an article in Times Higher Education , it is the largest academic social network in terms of active users.

Curriculum Vitae for R J Robbins

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Curriculum Vitae for R J Robbins

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