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1
Barras, Colin. "Deepest land microbes ever found." New Scientist 249, no. 3323 (February 2021): 14. http://dx.doi.org/10.1016/s0262-4079(21)00308-0.
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Gewin, Virginia. "Live Microbes Found in Ancient Ice." Frontiers in Ecology and the Environment 3, no. 3 (April 2005): 128. http://dx.doi.org/10.2307/3868533.
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Marshall, Michael. "Earth's earliest microbes found in rocks." New Scientist 243, no. 3250 (October 2019): 14. http://dx.doi.org/10.1016/s0262-4079(19)31850-0.
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Li, Wei Tse, Anjali S. Iyangar, Rohan Reddy, Jaideep Chakladar, Valmik Bhargava, Kyoko Sakamoto, Weg M. Ongkeko, and Mahadevan Rajasekaran. "The Bladder Microbiome Is Associated with Epithelial–Mesenchymal Transition in Muscle Invasive Urothelial Bladder Carcinoma." Cancers 13, no. 15 (July 21, 2021): 3649. http://dx.doi.org/10.3390/cancers13153649.
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The intra-tumor microbiome has recently been linked to epithelial–mesenchymal transition (EMT) in a number of cancers. However, the relationship between EMT and microbes in bladder cancer has not been explored. In this study, we profiled the abundance of individual microbe species in the tumor samples of over 400 muscle invasive bladder carcinoma (MIBC) patients. We then correlated microbe abundance to the expression of EMT-associated genes and genes in the extracellular matrix (ECM), which are key players in EMT. We discovered that a variety of microbes, including E. coli, butyrate-producing bacterium SM4/1, and a species of Oscillatoria, were associated with expression of classical EMT-associated genes, including E-cadherin, vimentin, SNAI2, SNAI3, and TWIST1. We also found significant correlations between microbial abundance and the expression of genes in the ECM, specifically collagens and elastin. Lastly, we found that a large number of microbes exhibiting significant correlations to EMT are also associated with clinical prognosis and outcomes. We further determined that the microbes we profiled were likely not environmental contaminants. In conclusion, we discovered that the intra-tumoral microbiome could potentially play a significant role in the regulation of EMT in MIBC.
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Wang, Qianhong, Zheng Hao, Ruirui Ding, Huabing Li, Xiangming Tang, and Feizhou Chen. "Host Dependence of Zooplankton-Associated Microbes and Their Ecological Implications in Freshwater Lakes." Water 13, no. 21 (October 20, 2021): 2949. http://dx.doi.org/10.3390/w13212949.
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Zooplankton is colonized by quite different microbes compared with free-living and particle-associated bacteria, serving as a non-negligible niche of bacteria in aquatic ecosystems. Yet detailed analysis of these bacterial groups is still less known, especially in freshwater lakes. To widen our knowledge of host-microbe interaction and bacterial ecosystem functions, we chose two specific populations of zooplankton, i.e., cladoceran Moina and copepod Calanoids, as hosts from five natural lakes, and illustrated detailed features of their associated bacteria. Through 16S rRNA gene sequencing, we found microbes colonized on Calanoids presented significantly higher α-diversity, stronger bacterial interaction and metabolic function potentials than for Moina. It was also notable that zooplankton-associated bacteria showed a high potential of fatty acid metabolism, which is beneficial for host’s development. Moreover, we found that zooplankton-associated microbes may exert profound effects on biogeochemical cycles in freshwater lakes, since several bacterial members able to participate in carbon and nitrogen cycles were found abundant. Overall, our study expands current understanding of the host-microbe interaction and underlying ecological dynamics in freshwater ecosystem.
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Rediske, Andrea M. "Beautiful Images and Practical Examples Found in Idaho Microbes." Journal of Microbiology & Biology Education 17, no. 2 (May 4, 2016): 308. http://dx.doi.org/10.1128/jmbe.v17i2.1113.
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Kaur, Amandeep, and Sangeeta Sharma. "Biogenic Synthesis of Gold Nanoparticles and their Applications: A Review." Asian Journal of Chemistry 31, no. 12 (November 16, 2019): 2679–97. http://dx.doi.org/10.14233/ajchem.2019.22105.
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The purpose of the present study is to explore the merits and demerits of various biogenic synthesis route of gold nanoparticles using plant materials and microbes. Literature survey indicated that microbe mediated synthesis route is found to be quite effective buttheavailability and feasibility of microbes, enzyme control conditions is of great challenge for the researchers. Among all the available bio-reductants for the synthesis of gold nanoparticles rhizome of Zinger officinale (ginger) has been found more advantageous in accordance with availability, stability, applicability, reaction time, etc. for the fabrication of gold nanoparticles.
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Deng, Lei, Yibiao Huang, Xuejun Liu, and Hui Liu. "Graph2MDA: a multi-modal variational graph embedding model for predicting microbe–drug associations." Bioinformatics 38, no. 4 (November 23, 2021): 1118–25. http://dx.doi.org/10.1093/bioinformatics/btab792.
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Abstract Motivation Accumulated clinical studies show that microbes living in humans interact closely with human hosts, and get involved in modulating drug efficacy and drug toxicity. Microbes have become novel targets for the development of antibacterial agents. Therefore, screening of microbe–drug associations can benefit greatly drug research and development. With the increase of microbial genomic and pharmacological datasets, we are greatly motivated to develop an effective computational method to identify new microbe–drug associations. Results In this article, we proposed a novel method, Graph2MDA, to predict microbe–drug associations by using variational graph autoencoder (VGAE). We constructed multi-modal attributed graphs based on multiple features of microbes and drugs, such as molecular structures, microbe genetic sequences and function annotations. Taking as input the multi-modal attribute graphs, VGAE was trained to learn the informative and interpretable latent representations of each node and the whole graph, and then a deep neural network classifier was used to predict microbe–drug associations. The hyperparameter analysis and model ablation studies showed the sensitivity and robustness of our model. We evaluated our method on three independent datasets and the experimental results showed that our proposed method outperformed six existing state-of-the-art methods. We also explored the meaning of the learned latent representations of drugs and found that the drugs show obvious clustering patterns that are significantly consistent with drug ATC classification. Moreover, we conducted case studies on two microbes and two drugs and found 75–95% predicted associations have been reported in PubMed literature. Our extensive performance evaluations validated the effectiveness of our proposed method. Availability and implementation Source codes and preprocessed data are available at https://github.com/moen-hyb/Graph2MDA. Supplementary information Supplementary data are available at Bioinformatics online.
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Замшин, А. И. "Correspondence About the article of the Privat-docent V. F. Maslovkago: "To the doctrine of self-infection of maternity hospitals"." Journal of obstetrics and women's diseases 6, no. 5 (September 24, 2020): 530–31. http://dx.doi.org/10.17816/jowd65530-531.
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Privat-docent V. F. Maslovsky in his work "On the doctrine of self-infection of maternity hospitals", which appeared in the April book "Journal of obstetrics and women's diseases" for the current year, reproaches me for limiting myself to studying only the biological properties of microbes found, and says (p.332): "it is currently impossible to determine the property of microbes according to the state of culture, due to insufficient information about their biological properties."In this regard, I should note that it is the biological properties of known microbes that are currently being studied; in particular, this can be said about the desired microbe in my workstaph. R. aureus.
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Mwafulirwa, Samuel. "Isolation Characterization and Diversity of Indigenous Pesticide Degrading Microbes from Selected Agro Ecological Zones of Malawi." Asian Plant Research Journal 11, no. 3 (May 22, 2023): 29–40. http://dx.doi.org/10.9734/aprj/2023/v11i3213.
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Pesticide xenobiotics have a great impact on bio argumentation, bio-magnification, and environment degradation regardless of being adopted by green revolution technologies. Bioremediation is widely accepted because it’s cheap, practical at the same time environmentally friendly. Bioremediation advocates indigenous microbes use to degrade pesticides, therefore a study has been performed to show prospects of degrading microorganisms. The study isolated microbes from different agro ecological zones to assess their capacity to utilize some pesticide as sole carbon source complimented by the presence of laccase gene. Biochemical test and genetic characterization using 16S rDNA genes were used in identification. Diversified species and strains of genus Enterobacter, Klebsiella, Pseudomonas, Pantoea and Leclercia, were found to degrade cypermethrin and acetochlor but no microbe was found to degrade dimethoate. The study adds new strain of microbes involved in degradation of cypermethrin and acetochlor and also strains that that can degrade both. The study puts proposition that pest infestation in fields is a result of abundance of xenobiotic degrading microbes due to natural selection pressure not pesticide resistance of the pest.
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Council, Sarah E., Amy M. Savage, Julie M. Urban, Megan E. Ehlers, J. H. Pate Skene, Michael L. Platt, Robert R. Dunn, and Julie E. Horvath. "Diversity and evolution of the primate skin microbiome." Proceedings of the Royal Society B: Biological Sciences 283, no. 1822 (January 13, 2016): 20152586. http://dx.doi.org/10.1098/rspb.2015.2586.
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Skin microbes play a role in human body odour, health and disease. Compared with gut microbes, we know little about the changes in the composition of skin microbes in response to evolutionary changes in hosts, or more recent behavioural and cultural changes in humans. No studies have used sequence-based approaches to consider the skin microbe communities of gorillas and chimpanzees, for example. Comparison of the microbial associates of non-human primates with those of humans offers unique insights into both the ancient and modern features of our skin-associated microbes. Here we describe the microbes found on the skin of humans, chimpanzees, gorillas, rhesus macaques and baboons. We focus on the bacterial and archaeal residents in the axilla using high-throughput sequencing of the 16S rRNA gene. We find that human skin microbial communities are unique relative to those of other primates, in terms of both their diversity and their composition. These differences appear to reflect both ancient shifts during millions of years of primate evolution and more recent changes due to modern hygiene.
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Lewin, Gina R., Apollo Stacy, Kelly L. Michie, Richard J. Lamont, and Marvin Whiteley. "Large-scale identification of pathogen essential genes during coinfection with sympatric and allopatric microbes." Proceedings of the National Academy of Sciences 116, no. 39 (August 19, 2019): 19685–94. http://dx.doi.org/10.1073/pnas.1907619116.
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Recent evidence suggests that the genes an organism needs to survive in an environment drastically differ when alone or in a community. However, it is not known if there are universal functions that enable microbes to persist in a community and if there are functions specific to interactions between microbes native to the same (sympatric) or different (allopatric) environments. Here, we ask how the essential functions of the oral pathogen Aggregatibacter actinomycetemcomitans change during pairwise coinfection in a murine abscess with each of 15 microbes commonly found in the oral cavity and 10 microbes that are not. A. actinomycetemcomitans was more abundant when coinfected with allopatric than with sympatric microbes, and this increased fitness correlated with expanded metabolic capacity of the coinfecting microbes. Using transposon sequencing, we discovered that 33% of the A. actinomycetemcomitans genome is required for coinfection fitness. Fifty-nine “core” genes were required across all coinfections and included genes necessary for aerobic respiration. The core genes were also all required in monoinfection, indicating the essentiality of these genes cannot be alleviated by a coinfecting microbe. Furthermore, coinfection with some microbes, predominately sympatric species, induced the requirement for over 100 new community-dependent essential genes. In contrast, in other coinfections, predominately with nonoral species, A. actinomycetemcomitans required 50 fewer genes than in monoinfection, demonstrating that some allopatric microbes can drastically alleviate gene essentialities. These results expand our understanding of how diverse microbes alter growth and gene essentiality within polymicrobial infections.
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Shelomi, Matan, and Ming-Ju Chen. "Culturing-Enriched Metabarcoding Analysis of the Oryctes rhinoceros Gut Microbiome." Insects 11, no. 11 (November 11, 2020): 782. http://dx.doi.org/10.3390/insects11110782.
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Wood-feeding insects should have a source of enzymes like cellulases to digest their food. These enzymes can be produced by the insect, or by microbes living in the wood and/or inside the insect gut. The coconut rhinoceros beetle, Oryctes rhinoceros, is a pest whose digestive microbes are of considerable interest. This study describes the compartments of the O. rhinoceros gut and compares their microbiomes using culturing-enriched metabarcoding. Beetle larvae were collected from a coconut grove in southern Taiwan. Gut contents from the midgut and hindgut were plated on nutrient agar and selective carboxymethylcellulose agar plates. DNA was extracted from gut and fat body samples and 16S rDNA metabarcoding performed to identify unculturable bacteria. Cellulase activity tests were performed on gut fluids and microbe isolates. The midgut and hindgut both showed cellulolytic activity. Bacillus cereus, Citrobacter koseri, and the cellulolytic fungus Candida xylanilytica were cultured from both gut sections in most larvae. Metabarcoding did not find Bacillus cereus, and found that either Citrobacter koseri or Paracoccus sp. were the dominant gut microbes in any given larva. No significant differences were found between midgut and hindgut microbiomes. Bacillus cereus and Citrobacter koseri are common animal gut microbes frequently found in Oryctes rhinoceros studies while Candida xylanilytica and the uncultured Paracoccus sp. had not been identified in this insect before. Some or all of these may well have digestive functions for the beetle, and are most likely acquired from the diet, meaning they may be transient commensalists rather than obligate mutualists. Broader collection efforts and tests with antibiotics will resolve ambiguities in the beetle–microbe interactions.
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Hill, Vincent R., Amy L. Polaczyk, Donghyun Hahn, Jothikumar Narayanan, Theresa L. Cromeans, Jacquelin M. Roberts, and James E. Amburgey. "Development of a Rapid Method for Simultaneous Recovery of Diverse Microbes in Drinking Water by Ultrafiltration with Sodium Polyphosphate and Surfactants." Applied and Environmental Microbiology 71, no. 11 (November 2005): 6878–84. http://dx.doi.org/10.1128/aem.71.11.6878-6884.2005.
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ABSTRACT The ability to simultaneously concentrate diverse microbes is an important consideration for sample collection methods that are used for emergency response and environmental monitoring when drinking water may be contaminated with an array of unknown microbes. This study focused on developing a concentration method using ultrafilters and different combinations of a chemical dispersant (sodium polyphosphate [NaPP]) and surfactants. Tap water samples were seeded with bacteriophage MS2, Escherichia coli, Enterococcus faecalis, Cryptosporidium parvum, 4.5-μm microspheres, Salmonella enterica serovar Typhimurium, Bacillus globigii endospores, and echovirus 1. Ten-liter tap water samples were concentrated to ∼250 ml in 12 to 42 min, depending on the experimental condition. Initial experiments indicated that pretreating filters with fetal bovine serum or NaPP resulted in an increase in microbe recovery. The addition of NaPP to the tap water samples resulted in significantly higher microbe and microsphere recovery efficiencies. Backflushing of the ultrafilter was found to significantly improve recovery efficiencies. The effectiveness of backflushing was improved further with the addition of Tween 80 to the backflush solution. The ultrafiltration method developed in this study, incorporating the use of NaPP pretreatment and surfactant solution backflushing, was found to recover MS2, C. parvum, microspheres, and several bacterial species with mean recovery efficiencies of 70 to 93%. The mean recovery efficiency for echovirus 1 (49%) was the lowest of the microbes studied for this method. This research demonstrates that ultrafiltration can be effective for recovering diverse microbes simultaneously in tap water and that chemical dispersants and surfactants can be beneficial for improving microbial recovery using this technique.
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Gnanasekar, Aditi, Neil Shende, Jaideep Chakladar, Wei T. Li, Lindsay M. Wong, Michael Karin, and Weg M. Ongkeko. "Abstract 3528: Influence of obesity-associated intra-tumor microbes on exacerbating cancer severity." Cancer Research 82, no. 12_Supplement (June 15, 2022): 3528. http://dx.doi.org/10.1158/1538-7445.am2022-3528.
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Abstract Background: Despite there being a well-established connection between the gut microbiome and metabolic disease in humans, intra-tumor microbes and the mechanisms by which they regulate cell signaling, inflammation, and adipocyte growth to exacerbate disease severity in cancer patients also suffering from obesity remains largely unclear. In this study, we identified microbes to be distinctly abundant in cancer patients who are obese and correlated microbe abundance to patient survival, clinical variables, and immunological genes and pathways, in order to mechanistically explain how differential microbe abundance may influence clinical outcome. Methods: Microbial reads were aligned and extracted from raw whole-transcriptome RNA-sequencing data of cancer patient samples using Pathoscope 2.0 software. The Kruskal-Wallis test was used to correlate body mass index (BMI)-associated microbes to clinical variables. Reactome FIViz and Gene Set Enrichment Analysis were used to calculate pathway enrichment. Results: We identified specific microbes, including Pseudomonas fluorescens SBW25 and Enterobacter cloacae, and chemokine and interleukin-related genes to be potential determining factors of disease severity among cancer patients in BMI-associated groups. Gene set enrichment analysis revealed that microbes abundant in cancer tissue in obese patient samples, including Pseudomonas baetica in liver cancer patients, were significantly associated with the upregulation oncogenic, cell migration-related signaling pathways. Intra-tumor microbes from obese patient samples were also found to correlate with chemokine signaling and TFR2/NFkB-related genes, both of which have well-established roles in inflammatory activity. Conclusions: Our study significantly advances the understanding of the microbiome composition of the tumor microenvironment in patients who are obese and microbes’ relationship with clinical and immunologic variables, particularly inflammatory-related genes and pathways. We uncovered unknown mechanisms of the microbiome-immune interaction and obtained definitive data on microbiome dysbiosis in patients with obesity as a key determinant of severity of cancer, including microbe regulation of inflammasome activity. While deeper sequencing, more rigorous contamination correction, and in vitro and in vivo experiments are necessary to fully elucidate how microbe species can effectively act as therapeutic agents in probiotic and prebiotic therapies to reduce insulin resistance, inflammation, and glucose levels, our results are essential for guiding this future research. Citation Format: Aditi Gnanasekar, Neil Shende, Jaideep Chakladar, Wei T. Li, Lindsay M. Wong, Michael Karin, Weg M. Ongkeko. Influence of obesity-associated intra-tumor microbes on exacerbating cancer severity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3528.
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Jheeta, Sohan. "Molecules to Microbes." Sci 2, no. 4 (November 27, 2020): 86. http://dx.doi.org/10.3390/sci2040086.
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How did life begin on Earth? And is there life elsewhere in the Cosmos? Challenging questions, indeed. The series of conferences established by NoR CEL in 2013 addresses these very questions. This paper comprises a summary report of oral presentations that were delivered by NoR CEL’s network members during the 2018 Athens conference and, as such, disseminates the latest research which they have put forward. More in depth material can be found by consulting the contributors referenced papers. Overall, the outcome of this conspectus on the conference demonstrates a case for the existence of “probable chemistry” during the prebiotic epoch.
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Jheeta, Sohan. "Molecules to Microbes." Sci 1, no. 2 (July 25, 2019): 42. http://dx.doi.org/10.3390/sci1020042.
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How did life begin on Earth? And is there life elsewhere in the Cosmos? Challenging questions, indeed. The series of conferences established by NoR CEL in 2013, addresses these very same questions. The basis for this paper is the summary report of oral presentations that were delivered by NoR CEL’s network members during the 2018 Athens conference and, as such, disseminates the latest research which they have put forward. More in depth material can be found by consulting the contributors referenced papers. Overall, the outcome of this conspectus on the conference demonstrates a case for the existence of “probable chemistry” during the prebiotic epoch.
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Jheeta, Sohan. "Molecules to Microbes." Sci 2, no. 2 (March 28, 2020): 20. http://dx.doi.org/10.3390/sci2020020.
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How did life begin on Earth? And is there life elsewhere in the Cosmos? Challenging questions, indeed. The series of conferences established by NoR CEL in 2013, addresses these very same questions. The basis for this paper is the summary report of oral presentations that were delivered by NoR CEL’s network members during the 2018 Athens conference and, as such, disseminates the latest research which they have put forward. More in depth material can be found by consulting the contributors referenced papers. Overall, the outcome of this conspectus on the conference demonstrates a case for the existence of “probable chemistry” during the prebiotic epoch.
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Aivelo, Tuomas, Anna Norberg, and Barbara Tschirren. "Bacterial microbiota composition of Ixodes ricinus ticks: the role of environmental variation, tick characteristics and microbial interactions." PeerJ 7 (December 19, 2019): e8217. http://dx.doi.org/10.7717/peerj.8217.
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Ecological factors, host characteristics and/or interactions among microbes may all shape the occurrence of microbes and the structure of microbial communities within organisms. In the past, disentangling these factors and determining their relative importance in shaping within-host microbiota communities has been hampered by analytical limitations to account for (dis)similar environmental preferences (‘environmental filtering’). Here we used a joint species distribution modelling (JSDM) approach to characterize the bacterial microbiota of one of the most important disease vectors in Europe, the sheep tick Ixodes ricinus, along ecological gradients in the Swiss Alps. Although our study captured extensive environmental variation along elevational clines, the explanatory power of such large-scale ecological factors was comparably weak, suggesting that tick-specific traits and behaviours, microhabitat and -climate experienced by ticks, and interactions among microbes play an important role in shaping tick microbial communities. Indeed, when accounting for shared environmental preferences, evidence for significant patterns of positive or negative co-occurrence among microbes was found, which is indicative of competition or facilitation processes. Signals of facilitation were observed primarily among human pathogens, leading to co-infection within ticks, whereas signals of competition were observed between the tick endosymbiont Spiroplasma and human pathogens. These findings highlight the important role of small-scale ecological variation and microbe-microbe interactions in shaping tick microbial communities and the dynamics of tick-borne disease.
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Ali, Alimuddin, and Herlina Rante. "Karakterisasi Mikrobia Rizosfer asal Tanaman Ginseng Jawa (Talinum triangulare) berdasarkan Gen Ribosomal 16S rRNA dan 18S rRNA." JURNAL BIOLOGI PAPUA 3, no. 2 (October 20, 2018): 74–81. http://dx.doi.org/10.31957/jbp.552.
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The rhizosphere is a biologically active zone of the soil around plant roots that contains soil-borne microbes including bacteria and fungi. The microbes were isolated from rhizosphere soil roots of Java ginseng. The population of microbes was estimated by plate count method. The isolates were identified based on a great variety of morphological, and cultural characteristics. The total of rhizosphere soil microbe population were 20.91(106 cfu.g−1soils) and showed that 12 isolates of bacteria, 15 isolates of actinomycetes, and 10 isolates of fungi which were found in all of soil samples. The molecular analysis of the ribosomal genes showed that the bacterial isolate, actinomycetes and fungi were closely related to of Staphylococcus sp. DGM (JF923460), Streptomyces avidinii (EU593640) and fungi Aspergillus niger (HQ379853), respectively. Key words: rhizosphere, Java ginseng, 16S rRNA gene, 18S rRNA gene
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Tang, J. Y., and W. J. Riley. "A total quasi-steady-state formulation of substrate uptake kinetics in complex networks and an example application to microbial litter decomposition." Biogeosciences 10, no. 12 (December 16, 2013): 8329–51. http://dx.doi.org/10.5194/bg-10-8329-2013.
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Abstract. We demonstrate that substrate uptake kinetics in any consumer–substrate network subject to the total quasi-steady-state assumption can be formulated as an equilibrium chemistry (EC) problem. If the consumer-substrate complexes equilibrate much faster than other metabolic processes, then the relationships between consumers, substrates, and consumer-substrate complexes are in quasi-equilibrium and the change of a given total substrate (free plus consumer-bounded) is determined by the degradation of all its consumer-substrate complexes. In this EC formulation, the corresponding equilibrium reaction constants are the conventional Michaelis–Menten (MM) substrate affinity constants. When all of the elements in a given network are either consumer or substrate (but not both), we derived a first-order accurate EC approximation (ECA). The ECA kinetics is compatible with almost every existing extension of MM kinetics. In particular, for microbial organic matter decomposition modeling, ECA kinetics explicitly predicts a specific microbe's uptake for a specific substrate as a function of the microbe's affinity for the substrate, other microbes' affinity for the substrate, and the shielding effect on substrate uptake by environmental factors, such as mineral surface adsorption. By taking the EC solution as a reference, we evaluated MM and ECA kinetics for their abilities to represent several differently configured enzyme-substrate reaction networks. In applying the ECA and MM kinetics to microbial models of different complexities, we found (i) both the ECA and MM kinetics accurately reproduced the EC solution when multiple microbes are competing for a single substrate; (ii) ECA outperformed MM kinetics in reproducing the EC solution when a single microbe is feeding on multiple substrates; (iii) the MM kinetics failed, while the ECA kinetics succeeded, in reproducing the EC solution when multiple consumers (i.e., microbes and mineral surfaces) were competing for multiple substrates. We then applied the EC and ECA kinetics to a guild based C-only microbial litter decomposition model and found that both approaches successfully simulated the commonly observed (i) two-phase temporal evolution of the decomposition dynamics; (ii) final asymptotic convergence of the lignocellulose index to a constant that depends on initial litter chemistry and microbial community structure; and (iii) microbial biomass proportion of total organic biomass (litter plus microbes). In contrast, the MM kinetics failed to realistically predict these metrics. We therefore conclude that the ECA kinetics are more robust than the MM kinetics in representing complex microbial, C substrate, and mineral surface interactions. Finally, we discuss how these concepts can be applied to other consumer–substrate networks.
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Tang, J. Y., and W. J. Riley. "A total quasi-steady-state formulation of substrate uptake kinetics in complex networks and an example application to microbial litter decomposition." Biogeosciences Discussions 10, no. 6 (June 28, 2013): 10615–83. http://dx.doi.org/10.5194/bgd-10-10615-2013.
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Abstract. We demonstrate that substrate uptake kinetics in any consumer-substrate network subject to the total quasi-steady-state assumption can be formulated as an equilibrium chemistry (EC) problem. If the consumer-substrate complexes equilibrate much faster than other metabolic processes, then the relationships between consumers, substrates, and consumer-substrate complexes are in quasi-equilibrium and the change of a given total substrate (free plus consumer-bounded) is determined by the degradation of all its consumer-substrate complexes. In this EC formulation, the corresponding equilibrium reaction constants are the conventional Michaelis–Menten (MM) substrate affinity constants. When all of the elements in a given network are either consumer or substrate (but not both), we derived a first-order accurate EC approximation (ECA). The ECA kinetics is compatible with almost every existing extension of MM kinetics. In particular, for microbial organic matter decomposition modeling, ECA kinetics explicitly predicts a specific microbe's uptake for a specific substrate as a function of the microbe's affinity for the substrate, other microbes' affinity for the substrate, and the shielding effect on substrate uptake by environmental factors, such as mineral surface adsorption. By taking the EC solution as a reference, we evaluated MM and ECA kinetics for their abilities to represent several differently configured enzyme-substrate reaction networks. In applying the ECA and MM kinetics to microbial models of different complexities, we found (i) both the ECA and MM kinetics accurately reproduced the EC solution when multiple microbes are competing for a single substrate; (ii) ECA outperformed MM kinetics in reproducing the EC solution when a single microbe is feeding on multiple substrates; (iii) the MM kinetics failed, while the ECA kinetics succeeded, in reproducing the EC solution when multiple consumers (i.e., microbes and mineral surfaces) were competing for multiple substrates. We then applied the EC and ECA kinetics to a guild based C-only microbial litter decomposition model and found that both approaches successfully simulated the commonly observed (i) two-phase temporal evolution of the decomposition dynamics; (ii) final asymptotic convergence of the lignocellulose index to a constant that depends on initial litter chemistry and microbial community structure; and (iii) microbial biomass proportion of total organic biomass (litter plus microbes). In contrast, the MM kinetics failed to realistically predict these metrics. We therefore conclude that the ECA kinetics is more robust than the MM kinetics in representing complex microbial, C substrate, and mineral surface interactions. Finally, we discuss how these concepts can be applied to other consumer-substrate networks.
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Lee, Hye-Yeon, Shin-Hae Lee, and Kyung-Jin Min. "The Increased Abundance of Commensal Microbes Decreases Drosophila melanogaster Lifespan through an Age-Related Intestinal Barrier Dysfunction." Insects 13, no. 2 (February 21, 2022): 219. http://dx.doi.org/10.3390/insects13020219.
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Background: Commensal microbiota live in their host with a symbiotic relationship that affects the host’s health and physiology. Many studies showed that microbial load and composition were changed by aging and observed that increasing the abundance and changing the composition of commensal microbes had detrimental effects on host lifespan. We hypothesized that dysbiosis of the intestinal microbiota leads to systemic effects in aging flies as a result of the increased intestinal permeability. Methods: We used the fruit fly, Drosophila melanogaster, laboratory strains w1118, as a model system with many advantages for microbe–host studies. Results: The incidence of intestinal dysfunction was increased with age, and intestinal dysfunction increased the permeability of the fly intestine to resident microbes. The lifespan of flies with an intestinal barrier dysfunction was increased by removal of the microbes. Interestingly, some bacteria were also found in the hemolymph of flies with intestinal barrier dysfunction. Conclusion: Our findings suggest the possibility that, as the host ages, there is an increase in intestinal permeability, which leads to an increased intestinal microbial load and a reduction in the host lifespan. Our data therefore indicate a connection between commensal microbes and host lifespan.
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Dereschuk, Kypros, Lauren Apostol, Ishan Ranjan, Jaideep Chakladar, Wei Tse Li, Mahadevan Rajasekaran, Eric Y. Chang, and Weg M. Ongkeko. "Identification of Lung and Blood Microbiota Implicated in COVID-19 Prognosis." Cells 10, no. 6 (June 10, 2021): 1452. http://dx.doi.org/10.3390/cells10061452.
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The implications of the microbiome on Coronavirus disease 2019 (COVID-19) prognosis has not been thoroughly studied. In this study we aimed to characterize the lung and blood microbiome and their implication on COVID-19 prognosis through analysis of peripheral blood mononuclear cell (PBMC) samples, lung biopsy samples, and bronchoalveolar lavage fluid (BALF) samples. In all three tissue types, we found panels of microbes differentially abundant between COVID-19 and normal samples correlated to immune dysregulation and upregulation of inflammatory pathways, including key cytokine pathways such as interleukin (IL)-2, 3, 5-10 and 23 signaling pathways and downregulation of anti-inflammatory pathways including IL-4 signaling. In the PBMC samples, six microbes were correlated with worse COVID-19 severity, and one microbe was correlated with improved COVID-19 severity. Collectively, our findings contribute to the understanding of the human microbiome and suggest interplay between our identified microbes and key inflammatory pathways which may be leveraged in the development of immune therapies for treating COVID-19 patients.
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Nandan, Parmar Keshri, and Anshita Nagar. "ISOLATION AND IDENTIFICATION OF BACTERIOCIN PRODUCING MICROBES USING BIOCHEMICAL AND MOLECULAR TOOLS AND ANALYSIS OF ITS BIOPRESERVATION POTENTIAL." Asian Journal of Pharmaceutical and Clinical Research 9, no. 9 (December 1, 2016): 278. http://dx.doi.org/10.22159/ajpcr.2016.v9s3.15043.
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ABSTRACTObjective: Food safety is a matter of utmost importance in developing countries as well as in developed countries, so keeping this in mind this researchwork deals with the identification and characterization of bacteriocin producing microbes by using biochemical and molecular characterization. This study has also covered the biopreservation potential of bacteriocin produced by these microbes against sapodilla, tomato and banana as well.Methods: For the purpose of sample collection and isolation, samples of milk, curd and gangajal water were taken and bacteriocin producing microbes were isolated by using serial dilution method. Screening of bacteriocin producing microbe was done by antibacterial sensitivity test using agar well diffusion method against Bacillus amyloliquefaciens, Escherichia Coli, Staphylococcus aureus and Pseudomonas aeruginosa by determining their zone of inhibition. Biochemical characterization was done by using different tests, such as, catalase test, mannitol test, citrate test, gelatin test, maltose test, indole test, urease test, lactose test etc. Molecular characterization was done by using 16S rRNA gene sequencing. Preservative action of bacteriocinwas observed on fruits that comprise sapodilla, tomato and banana by spraying bacteriocin on them and analyzing their activities shows for at least10 days.Results: Microbes were found to be Enterococcus faecalis (Accession number KX011874) and Bacillus cereus (Accession number KX011875). Periodicobservatory studies reflect that using bacteriocin, banana can be preserved for nearly 6-7 days while sapodilla for 8-9 days and tomato for 9-10 days.Conclusion: From present study we would like to conclude that bacteriocins produced by microbes which is found in milk or curd can also be used asbiopreservatives for these defined fruits that is sapodilla, tomato and banana.Keywords: Bacteriocin, Biopreservation, 16S rRNA analysis.
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Rozen, D. E., D. J. P. Engelmoer, and P. T. Smiseth. "Antimicrobial strategies in burying beetles breeding on carrion." Proceedings of the National Academy of Sciences 105, no. 46 (November 10, 2008): 17890–95. http://dx.doi.org/10.1073/pnas.0805403105.
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Rich and ephemeral resources, such as carrion, are a source of intense interspecific competition among animal scavengers and microbial decomposers. Janzen [Janzen DH (1977) Am Nat 111:691–713] hypothesized that microbes should be selected to defend such resources by rendering them unpalatable or toxic to animals, and that animals should evolve counterstrategies of avoidance or detoxification. Despite the ubiquity of animal-microbe competition, there are few tests of Janzen's hypothesis, in particular with respect to antimicrobial strategies in animals. Here, we use the burying beetle Nicrophorus vespilloides, a species that obligately breeds on carcasses of small vertebrates, to investigate the role of parental care and avoidance as antimicrobial strategies. We manipulated competition between beetle larvae and microbes by providing beetles with either fresh carcasses or old ones that had reached advanced putrefaction. We found evidence for a strong detrimental effect of microbial competition on beetle reproductive success and larval growth. We also found that parental care can largely compensate for these negative effects, and that when given a choice between old and fresh carcasses, parents tended to choose to rear their broods on the latter. We conclude that parental care and carcass avoidance can function as antimicrobial strategies in this species. Our findings extend the range of behavioral counterstrategies used by animals during competition with microbes, and generalize the work of Janzen to include competition between microbes and insects that rely on carrion as an obligate resource for breeding and not just as an opportunistic meal.
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Surana, Neil, and Dennis L. Kasper. "Moving beyond microbiome-wide associations to causal microbe identification." Journal of Immunology 200, no. 1_Supplement (May 1, 2018): 53.7. http://dx.doi.org/10.4049/jimmunol.200.supp.53.7.
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Abstract Microbiome-wide association studies have established that numerous diseases are associated with changes in the microbiota. These studies typically generate a long list of commensals implicated as biomarkers of disease, with no clear relevance to disease pathogenesis. If the field is to move beyond correlations and begin to address causation, an effective system is needed for refining this catalog of differentially abundant microbes and allow for mechanistic studies. We demonstrate that triangulation of microbe–phenotype relationships is an effective method for reducing the noise in microbiota studies and enabling identification of causal microbes. We found that gnotobiotic mice harboring different microbial communities exhibited differential survival in a colitis model. Co-housing of these mice generated animals that had hybrid microbiotas and displayed intermediate susceptibility to colitis. Mapping of microbe–phenotype relationships in parental mouse strains and in mice with hybrid microbiotas identified the bacterial family Lachnospiraceae as a correlate for protection from disease. Using directed microbial culture techniques, we discovered Clostridium immunis, a novel bacterial species, that—when administered to colitis-prone mice—protected them against colitis-associated death. To demonstrate its generalizability, we used our approach to identify 2 bacteria that induce intestinal expression of an antimicrobial peptide. Thus, we have used microbe–phenotype triangulation to move beyond the standard correlative microbiome study and identify causal microbes for 2 distinct phenotypes. Identification of disease-modulating commensals by our approach may also be applicable to human microbiome studies.
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Lawrence O. Flowers. "Phytomicrobiome systems affect plant health and crop production." International Journal of Science and Research Archive 8, no. 1 (February 28, 2023): 1024–29. http://dx.doi.org/10.30574/ijsra.2023.8.1.0195.
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The sustainability of plant life is intimately connected to its evolution with microbial life. Based on experimental evidence, microbial assemblages benefit plants on molecular, cellular, and ecological levels. The plant microbiome or phytomicrobiome are the microbes closely associated with a particular plant species. Distinct plant microbial ecosystems are in the phyllosphere, rhizosphere, soil, and endosphere. Plant-associated microbes affect plants in numerous ways and participate in various physiological functions essential for the plant, including nutrient recycling, the breakdown and synthesis of critical molecules, and other phytoprotective functions. While studying plant-microbe interactions is not new, recent developments in metagenomic sequencing and high-throughput pathway identification techniques have allowed scientists to explore unculturable microbes associated with plants. This review primarily focuses on the significant role of the phytomicrobiome and describes the prevalent taxonomic units found in association with plants. Plants are suitable tractable model systems to study plant-microbe interactions and can be grown under different experimental conditions to examine other characteristics of the phytomicrobiome. This article also provides a systematic review of the current research on the phytomicrobiome. It explores the extent to which the phytomicrobiome participates in an essential process that promotes plant fitness and sustainabilityand reviews research that focuses on microbiome community shifts in response to abiotic and biotic stress. Genetic engineering of plant-associated microbes to enhance plant growth and protection is addressed. The use of nanofertilizers and phytomicrobiome transplantation to restore plant health and improve the success of agriculturally beneficial crops is also discussed.
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Ganesan, Balasubramanian, Silvana Martini, Jonathan Solorio, and Marie K. Walsh. "Determining the Effects of High Intensity Ultrasound on the Reduction of Microbes in Milk and Orange Juice Using Response Surface Methodology." International Journal of Food Science 2015 (2015): 1–7. http://dx.doi.org/10.1155/2015/350719.
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This study investigated the effects of high intensity ultrasound (temperature, amplitude, and time) on the inactivation of indigenous bacteria in pasteurized milk,Bacillus atrophaeusspores inoculated into sterile milk, andSaccharomyces cerevisiaeinoculated into sterile orange juice using response surface methodology. The variables investigated were sonication temperature (range from 0 to 84°C), amplitude (range from 0 to 216 μm), and time (range from 0.17 to 5 min) on the response, log microbe reduction. Data were analyzed by statistical analysis system software and three models were developed, each for bacteria, spore, and yeast reduction. Regression analysis identified sonication temperature and amplitude to be significant variables on microbe reduction. Optimization of the inactivation of microbes was found to be at 84.8°C, 216 μm amplitude, and 5.8 min. In addition, the predicted log reductions of microbes at common processing conditions (72°C for 20 sec) using 216 μm amplitude were computed. The experimental responses for bacteria, spore, and yeast reductions fell within the predicted levels, confirming the accuracy of the models.
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Heitmann, Sabrina, Gillian E. Bergmann, Edward Barge, Mary Ridout, George Newcombe, and Posy E. Busby. "Culturable Seed Microbiota of Populus trichocarpa." Pathogens 10, no. 6 (May 24, 2021): 653. http://dx.doi.org/10.3390/pathogens10060653.
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Plants harbor a diverse community of microbes, whose interactions with their host and each other can influence plant health and fitness. While microbiota in plant vegetative tissues has been extensively studied, less is known about members of the seed microbiota. We used culture-based surveys to identify bacteria and fungi found in the seeds of the model tree, Populus trichocarpa, collected from different sites. We found that individual P. trichocarpa seeds typically contained zero or one microbe, with common taxa including species of Cladosporium, Aureobasidium, Diaporthe, Alternaria, and Pseudomonas, a bacterium. Pseudomonas isolates were associated with seed mortality and were negatively associated with the occurrence of fungal isolates within Epicoccum, Alternaria, and Aureobasidium from the same seed. Next, we conducted an inoculation experiment with one of the isolated seed microbes, Pseudomonas syringae pv. syringae, and found that it reduced seed germination and increased seedling mortality for P. trichocarpa. Our findings highlight common fungi and bacteria in the seeds of P. trichocarpa, prompting further study of their functional consequences. Moreover, our study confirms that P. syringae pv. syringae is a seed pathogen of P. trichocarpa and is the first report that P. syringae pv. syringae is a lethal seedling pathogen of P. trichocarpa, allowing for future work on the pathogenicity of this bacterium in seedlings and potential antagonism with other seed microbes.
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Londonkar, Ramesh, and Maithilee Kesralikar. "Microbes in Cancer." International Journal of Current Microbiology and Applied Sciences 10, no. 12 (December 10, 2021): 251–57. http://dx.doi.org/10.20546/ijcmas.2021.1012.029.
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Cancer is the uncontrolled growth of abnormal cells anywhere in a body. There are different types of cancers involves uncontrolled cell division and metastasis forming neoplasm and mass of undifferentiated cells that is tumor is a group of cells that have undergone unregulated growth which will often form a mass of tissue, but may be distributed slowly. Recent studies indicate that, the gut micro biome has emerged as an important mediating factor of health and disease. Interactions between microbes and human cells play very important roles in human metabolism including digestion of biomolecules like carbohydrates, production of essential amino acids, beneficial fatty acid synthesis and vitamin compounds. During cancer progression, these metabolic interactions between microbes and human cells may shift from one that support health to another that threatens it, as microbes begin interacting with cancer cells rather than healthy human cells. Indeed, microbial dysbiosis (disruption to the gut microbiota homeostasis caused by an imbalance in the microflora, changes in their functional composition and metabolic activities, or a shift in their local distribution) has been found to contribute to gastrointestinal cancer development. The mechanisms of action and these microbes appear to be diverse, with some activating the immune system, others inducing cell death via apoptosis and others inhibiting the growth of new blood vessels thereby depriving tumors of resources. It is the need of the hour for researchers where Future work should investigate the metabolic and ecological interactions between tumor cells and microbes that underlie this effect in order to discover new microbes that can be used in cancer treatments.
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Dwivedi, Harinath, Kusum Agrawal, and Shubhini A. Saraf. "Evaluation of Factors Affecting Uricase Production by the Screened Wild/Natural Microbes." E-Journal of Chemistry 9, no. 4 (2012): 2287–96. http://dx.doi.org/10.1155/2012/976242.
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Gout is a metabolic disorder due to the deposition of uric acid crystals within articular or periarticular tissues. Uricase (urate oxidase) catalyzes the oxidation of less water soluble uric acid (7 mg/dl) to a compound allantoin which is more water soluble(11g/L at 40°C) resulting into the ease of excretion of uric acid. The objective of the work was to develop a new method for screening of microbes for uricase production and estimation of uricase thereof. This was achieved by utilizing the fact that uric acid dissolves on being acted upon by uricase. The proposed method is a novel, inexpensive, simple and sensitive technique for screening and estimation of uricase. Biomass and uricase production at different stages of microbial growth curve for the uricase producing microbe was studied. Effects of different medium components affecting uricase production by microbes were studied using Placket Burman statistical design. Addition of uric acid in the nutrient medium was found to be effective in increasing the uricase production by microbes growing in the medium.
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Sebayang, N. U. W., T. Sabrina, and R. M. Sari. "Analysis the nutrient of bio-vermicompost with different techniques applications of some microbes and earthworms." IOP Conference Series: Earth and Environmental Science 1059, no. 1 (July 1, 2022): 012024. http://dx.doi.org/10.1088/1755-1315/1059/1/012024.
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Abstract Vermicompost is an organic fertilizer resulting from the decomposition of organic materials by utilizing earthworms. The presence of these microorganisms means that vermicompost contains compounds that are needed to increase soil fertility or for plant growth. This study aims to analyze the nutrients of bio-vermicompost with a combination of application techniques of beneficial microbes and earthworms. This study used a factorial Completely Randomized Design (CRD). The first factor is the application of microbes and earthworms with 4 treatments, T0: without earthworm, T1: application microbe followed (one week) by earthworm, T2: application microbe and earthworm in same time, T3: application earthworm followed (one week) by microbe. The second factor is the type of microbe with 4 treatments, M1: Azospirillum sp, M2: Azotobacter chroococum, M3: Trichoderma asperellum, M4: Talaromyces pinophilus. The results showed that the application technique had a significant effect on C-organic, C/N ratio, pH, P2O5, and K2O. The combination of both treatments significantly affect to the water content. The highest N was found in A3M1 (earthworm application followed by Azospirillum) which was 2.19%. The combination of A2M2 (Application of earthworms and Azotobacter at the same time) is the best combination in increasing the content of P2O5 (1.225%) and K2O5 (2.245%).
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Armstrong, H., R. Dickner, A. Rieger, I. K. Mander, J. Jerasi, D. Santer, R. Valcheva, et al. "A15 MICROBES MEDIATE FIBER-INDUCED INFLAMMATION IN IBD." Journal of the Canadian Association of Gastroenterology 3, Supplement_1 (February 2020): 17–19. http://dx.doi.org/10.1093/jcag/gwz047.014.
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Abstract Background The etiology of inflammatory bowel diseases (IBD) remains unknown, although gut microorganisms and diet have been implicated. Dietary fibers pass through the bowel undigested and are fermented within the intestine by microbes, promoting gut health. However, many IBD patients describe experiencing sensitivity to fibres. Interestingly, fiber receptors on immune cells are able to interact with fibers typically found on the surface of fungal cells (which share properties with dietary fibers), for example, resulting in a paradoxical pro-inflammatory response. Aims As an altered microbial composition is a hallmark of IBD, we hypothesized that the loss of fiber fermenting-microbes populating the IBD gut could lead to dietary fibers not being efficiently broken down into their beneficial biproducts, resulting in binding of intact fibers to pro-inflammatory host cell receptors. This can ultimately drive pro-inflammatory responses and a microenvironment that promotes continued dysbiosis and increased pathogenicity of select microbes, as observed in IBD. Methods Fiber receptor expression gut was examined using immunohistochemistry and flow cytometry and demonstrated elevated receptor expression due to increased presence of immune cells in IBD patient biopsies. Cytokine secretion, in response to fiber (5mg/mL) or pre-fermented fibers, cultured with microbes of interest, was measured by ELISAs in cell lines in vitro and biopsy tissues cultured ex vivo. Results Whole-fibers induced pro-inflammatory cytokine production in macrophage, monocytes, and neutrophils. Specific microbes were capable of fermenting fiber, measured by gas chromatography. Pre-fermentation of fibers by these microbes reduced inflammatory cytokine production. The fiber oligofructose increased IL-1β in pediatric CD (n=44) and UC (n=29) biopsies cultured ex vivo but not in non-IBD (n=25). The increase was greater in patients with more severe disease. Pre-fermentation of oligofructose by bacteria reduced this secretion of IL-1β. Whole-microbe intestinal washes from severe IBD patients were unable to ferment oligofructose or reduce fiber-associated inflammation in macrophage cells compared to remission or non-IBD children. Statistical analysis of food frequency questionnaire (FFQ) data on fiber consumption demonstrated that fiber-associated inflammation in patient biopsies cultured ex vivo (ELISA and qPCR) correlated with fiber avoidance (FFQ). Conclusions Comparing in vitro findings to our patient FFQs, intestinal washes (microbe abundance), and detailed patient history will better define the relationship between microbes, dietary fibers, and gut inflammation in IBD. This will allow for tailored dietary intervention through dietary recommendations, prebiotic, and/or probiotic therapies. Funding Agencies CCCWeston Foundation, WCHRI
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Russak, Julie E., and Darrell S. Rigel. "Tanning bed hygiene: Microbes found on tanning beds present a potential health risk." Journal of the American Academy of Dermatology 62, no. 1 (January 2010): 155–57. http://dx.doi.org/10.1016/j.jaad.2009.05.034.
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Wang, Shengqin, Na Li, Nan Li, Huixi Zou, and Mingjiang Wu. "A Comparative Analysis of Biosynthetic Gene Clusters in Lean and Obese Humans." BioMed Research International 2019 (June 12, 2019): 1–7. http://dx.doi.org/10.1155/2019/6361320.
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Obesity is intrinsically linked with the gut microbiome, and studies have identified several obesity-associated microbes. The microbe-microbe interactions can alter the composition of the microbial community and influence host health by producing secondary metabolites (SMs). However, the contribution of these SMs in the prevention and treatment of obesity has been largely ignored. We identified several SM-encoding biosynthetic gene clusters (BGCs) from the metagenomic data of lean and obese individuals and found significant association between some BGCs, including those that produce hitherto unknown SM, and obesity. In addition, the mean abundance of BGCs was positively correlated with obesity, consistent with the lower taxonomic diversity in the gut microbiota of obese individuals. By comparing the BGCs of known SM between obese and nonobese samples, we found that menaquinone produced by Enterobacter cloacae showed the highest correlation with BMI, in agreement with a recent study on human adipose tissue composition. Furthermore, an obesity-related nonribosomal peptide synthetase (NRPS) was negatively associated with Bacteroidetes, indicating that the SMs produced by intestinal microbes in obese individuals can change the microbiome structure. This is the first systemic study of the association between gut microbiome BGCs and obesity and provides new insights into the causes of obesity.
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Liddle, Kaylin, Terence McGonigle, and Alexander Koiter. "Microbe Biomass in Relation to Organic Carbon and Clay in Soil." Soil Systems 4, no. 3 (July 8, 2020): 41. http://dx.doi.org/10.3390/soilsystems4030041.
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Soil microbes are key to nutrient cycling and soil formation, yet the impact of soil properties on microbe biomass remains unclear. Using 240 soil cores of 0–15 cm depth, taken at random points across six cattle-grazed pastures on an undulating landscape, we evaluated the biomass of microbes in soil as affected by naturally occurring variation in soil organic carbon (SOC), clay content, and local topography. The study pastures varied in historic land-use for crops or forage seeding. SOC was found to be greater in topographically low areas. In contrast, clay content was not related to topography, and clay deposition possibly varies with glaciation legacy. Microbial biomass carbon (MBC) was correlated positively with SOC, increasing from 700 mg kg−1 MBC at 25 g kg−1 SOC to 2240 mg kg−1 MBC at 90 g kg−1 SOC. Most likely, SOC promotes MBC through the release of water-soluble organic carbon. However, the response of MBC to clay content was negative, decreasing from 1340 mg kg−1 MBC at 5% clay to 880 mg kg−1 MBC at 30% clay. Small voids in association with clay particles likely restrict the access of microbes to SOC. The relationship between SOC and MBC illustrates the important role of SOC for soil function, in terms of nutrient availability and development of soil structure via the contribution of microbes. Lastly, there was considerable spatial variability in MBC across the 65 ha site, highlighting the importance of land-use histories and gradients in environmental variables, to determine the biomass of microbes in soil.
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Pappas, Maria L., Konstantinos Samaras, Ioannis Koufakis, and George D. Broufas. "Beneficial Soil Microbes Negatively Affect Spider Mites and Aphids in Pepper." Agronomy 11, no. 9 (September 13, 2021): 1831. http://dx.doi.org/10.3390/agronomy11091831.
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Beneficial soil microbes have long been recognized for their ability to improve plant growth, to antagonize pathogens and to prime plants against biotic stressors. Nevertheless, their ability to enhance plant resistance against arthropod pests remains largely unexplored, especially in crop plants such as pepper. Herein, we assessed the effects of several fungal and bacterial species/strains applied in the soil on the performance of key pests of pepper plants. Specifically, we recorded the impact of pepper inoculation with commercial strains of beneficial bacteria (Bacillus amyloliquefaciens and Pseudomonas spp.) as well as fungi (Trichoderma spp. and Cordyceps fumosorosea) on the population growth of the green peach aphid, Myzus persicae, and the two-spotted spider mite, Tetranychus urticae. Furthermore, we recorded the effects of microbial inoculation on plant growth parameters, such as stem and root weight. We found that both pests can be negatively affected by microbial inoculation: spider mites laid up to 40% fewer eggs, and the number of aphids were up to 50% less on pepper-inoculated plants, depending on the microbe. We also recorded a variation among the tested microbes in their impact on herbivore performance, but no significant effects were found on plant biomass. Our results add to the growing literature that beneficial soil microbes may be capable of exerting biocontrol capabilities against aboveground herbivorous pests possibly, among other means, via the elicitation of plant defense responses.
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Jufri, Rhezqy Furwati. "Microbial Isolation." Journal La Lifesci 1, no. 1 (January 30, 2020): 18–23. http://dx.doi.org/10.37899/journallalifesci.v1i1.33.
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The importance of isolating a microbe from the environment, such as food (solid substrate), drinks (liquid substrate), and yourself because of the many microbes that are difficult to observe or distinguish directly using the five senses. A sample can contain bacteria or fungi. By isolating, the shape of the colonies and the contents in a sample can be observed. Bacteria from the air and normal flora form colonies with lobate-shaped edges, whereas bacteria found in well water samples form colonies with irregular edges and there are also fungi found in the well water samples.
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Harrison, Peter J., Teresa M. Dunn, and Dominic J. Campopiano. "Sphingolipid biosynthesis in man and microbes." Natural Product Reports 35, no. 9 (2018): 921–54. http://dx.doi.org/10.1039/c8np00019k.
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Sphingolipids are found in nearly all domains of life where they play a myriad of essential roles in structure and signalling. This review covers recent highlights from studies of the structures, mechanisms and inhibitors of key enzymes from the sphingolipid biosynthetic enzymes of prokaryotes and eukaryotes.
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Sarkar, Satyajit, and S. E. Kabir. "Studies on the impact of commonly used herbicides on beneficial soil microbes in Terai tea plantation, West Bengal, India." Annals of Plant Sciences 5, no. 01 (February 5, 2016): 1254. http://dx.doi.org/10.21746/aps.2016.01.002.
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The harmful effect of commonly used herbicides on the beneficial soil microbes in Terai tea plantation was investigated. It was found that almost all the herbicides had adverse effect on the population of beneficial microbes. 2,4-Dichlorophenoxy acetic acid was found to be most damaging herbicide.
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Wang, Jianping, Lin Lin, Bin Li, Feike Zhang, and Ning Liu. "Dietary Artemisia vulgaris meal improved growth performance, gut microbes, and immunity of growing Rex rabbits." Czech Journal of Animal Science 64, No. 4 (April 9, 2019): 174–79. http://dx.doi.org/10.17221/162/2018-cjas.
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Artemisia vulgaris (A. vulgaris) is an edible plant showing antioxidant and antibacterial effects, but its effect as a feed additive or forage source on the herbivore growth and health is unclear. This study aimed to investigate the effect of A. vulgaris meal supplementation on the growth performance, gut microbes, and immune function in rabbits. A total of 120 growing Rex rabbits were randomly allocated into 4 treatments with 6 replicates per 5 rabbits each. There were four experimental diets containing A. vulgaris meal at doses of 0, 3.0, 6.0 or 9.0%, respectively. The experiment lasted for 70 days. The results showed that diets supplemented with A. vulgaris meal improved the rabbits’ feed intake, body weight gain, and decreased feed conversion ratio (P < 0.05). Linear and quadratic responses were found between the growth parameters and the herbal meal doses (P ≤ 0.002). A. vulgaris meal also improved gut microbe populations by increasing Lactobacilli and Bifidobacteria, and decreasing E. coli, C. perfringens, Salmonella, and Gram-negative bacteria (P < 0.05), and linear and quadratic dose-dependent advantages were exhibited for these microbes (P ≤ 0.013). Furthermore, blood levels of IgA, IgM, and lymphocytes of bursale, thymus, CD4 and CD8 were increased by the treatments containing A. vulgaris meal (P < 0.05), and linear dose-dependent effect was found on these immune indexes (P < 0.001). Diet supplemented with A. vulgaris meal is effective in improving growth, gut microbes, and immunity of Rex rabbits.
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Malalur, Pannaga G., Xiaokui Mo, Rebecca Hoyd, John L. Hays, David Paul Carbone, and Daniel Spakowicz. "Investigating intra-tumor microbes, blood microbes, and CEA for development of non-invasive biomarkers in colorectal cancer." Journal of Clinical Oncology 39, no. 15_suppl (May 20, 2021): 3551. http://dx.doi.org/10.1200/jco.2021.39.15_suppl.3551.
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3551 Background: The development of non-invasive biomarkers has the potential to revolutionize clinical care for colorectal cancer (CRC) patients. The presence of bacteria in CRC tumor biopsies has been shown to contribute to CRC development. In a previous study, our group showed some intra-tumor microbes in CRC tumor biopsies correlated with overall survival in CRC patients. However, the correlations between microbes in tumor vs blood, and between non-invasive serum marker carcinoembryonic antigen (CEA) and microbes are unknown. We hypothesize that tumor microbes will also be found in blood, and that CEA will correlate with certain microbes. Methods: We obtained RNA-seq data from CRC tumor biopsies from patients treated at The Ohio State University Comprehensive Cancer Center as part of the Oncology Research Information Exchange Network (ORIEN). Reads were aligned to human and exogenous genomes using TopHat2 and Kraken2/Bracken, respectively. RNA-seq from CRC tumor biopsies as well as peripheral blood at the Cancer Genome Atlas (TCGA) consortium were processed by the same method. Results: The analyzed ORIEN cohort included 93 CRC patients with an age range from 30-83 years, 60.2% male, 87.1% adenocarcinoma, and 47.3% with metastatic CRC. The TGCA cohort included 495 CRC patients with an age range from 31-90 years, 53.3% male, 85.1% adenocarcinoma, and 15.5% with metastatic CRC. Over fifteen exogenous phyla (including bacteria, viruses, fungi) were observed in both ORIEN and TCGA cohorts. Several of the samples were dominated by viral sequences while others by bacteria, suggesting considerable tumor microbiome heterogeneity. Evaluation of the fraction of microbes in tumor and blood showed that nearly all the microbes found in blood (97.6%) were also observable in tumor in the TCGA cohort. Microbial abundances of various taxa, including Fusobacterium, significantly correlated between blood and tumor. Several bacteria including members of the genera Bacillus and Staphylococcus were positively associated with tumor stage (metastatic vs non-metastatic), but microbial relative abundances were not correlated with the location of tumor in colon (right, left, transverse colon). Certain microbial species from the ORIEN cohort were found to positively correlate with CEA, (including from the genera Fusobacterium, Lactobacillus, Pseudomonas, Vibrio, Clostridium) and these associations remained when adjusted for alcohol and smoking by multivariate analysis. Conclusions: Nearly all the microbes found in blood were found in tumor and abundances of various taxa were significantly correlated, suggesting that blood-based cancer microbiome analysis has great potential. Serum CEA has a low diagnostic ability when used alone, but combining this with blood microbiome could improve diagnostic/prognostic utility as a non-invasive biomarker.
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Anand, Priya, and Phulan Rani. "Wood Degrading Enzymes and their Decay Strength: A Review." International Journal of Plant & Soil Science 36, no. 5 (March 26, 2024): 253–65. http://dx.doi.org/10.9734/ijpss/2024/v36i54523.
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The degradation of wood is a major point of concern in the economy. The microbes that degrade the wood release various enzymes that decay the wood. In the present review article, we have collected the data for various decay strengths of different decay enzymes released by the various microbes from several peer-reviewed articles. The fungus basidiomycetes and some wood-degrading bacteria are responsible for the degradation of wood. The degraded wood is a major loss to the economy timber decay and many more. The degradation of wood or wood decay is also a major loss to the ecosystem by losing some precious plant species. Various data mining techniques have been used in this review to collect the data from the publications. The data in this article covers the various fields, the Name of the plant being degraded, the name of the wood degrading microbe, the Enzyme released by the microbe, the Decay strength of that enzyme, and the total loss to the economy by that decay. The unwanted decay of plant wood can be minimized if the causative agent and the enzyme released by it are found.
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Pelttari, Eila, Eliisa Karhumäki, Jane Langshaw, Hannu Peräkylä, and Hannu Elo. "Antimicrobial Properties of Substituted Salicylaldehydes and Related Compounds." Zeitschrift für Naturforschung C 62, no. 7-8 (August 1, 2007): 487–97. http://dx.doi.org/10.1515/znc-2007-7-806.
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A systematic survey of the antimicrobial properties of substituted salicylaldehydes and some related aromatic aldehydes is reported. A total of 23 different compounds, each at four different concentrations, were studied using a panel of seven microbes (Aspergillus niger, Bacillus cereus, Candida albicans, Escherichia coli, Pseudomonas aeruginosa, Saccharomyces cerevisiae and Staphylococcus epidermidis) and employing the paper disc agar diffusion method. Several aldehydes, most notably halogenated, nitro-substituted and hydroxylated salicylaldehydes, displayed highly potent activity against the microbes studied, giving inhibitory zones up to 49 mm in diameter (paper disc diameter 6 mm), while unsubstituted benzaldehyde and salicylaldehyde had minimal activity. Further, 4,6-dimethoxysalicylaldehyde had considerable activity against C. albicans and slight activity against S. cerevisiae, while displaying minimal activity against bacteria. Also two aromatic dialdehydes had interesting activity. In general, P. aeruginosa was the least sensitive microbe, a result that is in line with observations from a large screening project, in which this microbe was the one against which the least number of active substances was found. Interestingly, the structure-activity relationships of the aldehydes studied were clearly different for different microbes. Many of the aldehydes tested had such high antimicrobial activity that they are noteworthy candidates for practical applications as well as interesting lead compounds for the development of novel antimicrobial drugs and disinfectants. The structure-activity relationships are discussed in detail. For high activity, substituents are required in benzaldehyde as well as in its 2-hydroxy derivative salicylaldehyde. One hydroxy group alone (at the 2-position) is not enough, but further hydroxylation may produce high activity. The effects of substituents are in some cases dramatic. Halogenation, hydroxylation and nitro substitution may produce highly active compounds, but the effects are not easily predicted nor can they be extrapolated from one microbe to another
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Martin-Cuadrado, Ana-Belen, Rohit Ghai, Aitor Gonzaga, and Francisco Rodriguez-Valera. "CO Dehydrogenase Genes Found in Metagenomic Fosmid Clones from the Deep Mediterranean Sea." Applied and Environmental Microbiology 75, no. 23 (October 2, 2009): 7436–44. http://dx.doi.org/10.1128/aem.01283-09.
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ABSTRACT The use of carbon monoxide (CO) as a biological energy source is widespread in microbes. In recent years, the role of CO oxidation in superficial ocean waters has been shown to be an important energy supplement for heterotrophs (carboxydovores). The key enzyme CO dehydrogenase was found in both isolates and metagenomes from the ocean's photic zone, where CO is continuously generated by organic matter photolysis. We have also found genes that code for both forms I (low affinity) and II (high affinity) in fosmids from a metagenomic library generated from a 3,000-m depth in the Mediterranean Sea. Analysis of other metagenomic databases indicates that similar genes are also found in the mesopelagic and bathypelagic North Pacific and on the surfaces of this and other oceanic locations (in lower proportions and similarities). The frequency with which this gene was found indicates that this energy-generating metabolism would be at least as important in the bathypelagic habitat as it is in the photic zone. Although there are no data about CO concentrations or origins deep in the ocean, it could have a geothermal origin or be associated with anaerobic metabolism of organic matter. The identities of the microbes that carry out these processes were not established, but they seem to be representatives of either Bacteroidetes or Chloroflexi.
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Rothman, Jason A., Diana L. Cox-Foster, Corey Andrikopoulos, and Quinn S. McFrederick. "Diet Breadth Affects Bacterial Identity but Not Diversity in the Pollen Provisions of Closely Related Polylectic and Oligolectic Bees." Insects 11, no. 9 (September 20, 2020): 645. http://dx.doi.org/10.3390/insects11090645.
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Mounting evidence suggests that microbes found in the pollen provisions of wild and solitary bees are important drivers of larval development. As these microbes are also known to be transmitted via the environment, most likely from flowers, the diet breadth of a bee may affect the diversity and identity of the microbes that occur in its pollen provisions. Here, we tested the hypothesis that, due to the importance of floral transmission of microbes, diet breadth affects pollen provision microbial community composition. We collected pollen provisions at four sites from the polylectic bee Osmia lignaria and the oligolectic bee Osmia ribifloris. We used high-throughput sequencing of the bacterial 16S rRNA gene to characterize the bacteria found in these provisions. We found minimal overlap in the specific bacterial variants in pollen provisions across the host species, even when the bees were constrained to foraging from the same flowers in cages at one site. Similarly, there was minimal overlap in the specific bacterial variants across sites, even within the same host species. Together, these findings highlight the importance of environmental transmission and host specific sorting influenced by diet breadth for microbes found in pollen provisions. Future studies addressing the functional consequences of this filtering, along with tests for differences between more species of oligoletic and polylectic bees will provide rich insights into the microbial ecology of solitary bees.
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Arjomand Fard, N., H. Armstrong, M. W. Carroll, H. Q. Huynh, and E. Wine. "A41 LINKING THE APPENDIX MICROBIOME WITH INFLAMMATORY BOWEL DISEASES." Journal of the Canadian Association of Gastroenterology 4, Supplement_1 (March 1, 2021): 270–71. http://dx.doi.org/10.1093/jcag/gwab002.039.
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Abstract Background The appendix has been shown to be associated with the pathogenesis and health outcomes in inflammatory bowel diseases (IBD). Specifically, post appendectomy patients are found to be protective for development of ulcerative colitis (UC); however, mechanisms of appendix involvement remain unclear. Aims Our aim is to examine the microbes associated with the appendix of IBD patients by identifying changes in microbe abundance and interactions with the host in patient cecum luminal washes, collected from close to the neck of the appendix during colonoscopy. We hypothesize that microbes originating in the appendix of IBD patients, through interactions with host-cells in a disrupted microenvironment in the appendix, could contribute to the pathogenesis of UC. Methods Shotgun metagenomics was performed on cecum luminal washes of IBD patients and non-IBD controls. Guided by the metagenomic results, we performed gentamicin protection assays to determine virulence of microbes of interest using Caco2 intestinal epithelial cells. Co-culturing them with human host cells in vitro will identify relevant disease-related factors secreted by microbes and/or host cells using disease models and multiomic approaches. Results Shotgun metagenomics results showed that among numerous microbes, several bacterial taxa demonstrated differences in abundance between IBD and non-IBD patients: Flavonifractor, Bacteroide fragilis, and Alistipes represented 8%, 10%, and 21% abundance respectively in non-IBD patients, while in IBD patients they were present below 0.1%. In contrast, Bacteroide vulgatus and Escherichia coli were about 9% and 69% respectively, in IBD patients, whilst they were present at 1.7% and 1.2% in non-IBD patients, respectively. Following our recent method for validating pathobionts (Armstrong, 2019), we used the gentamicin protection assays to assess the ability of these bacteria to invade Caco2 cells, demonstrating a correlation between invasive potential of these microbes and cecal abundance. Mechanistic experiments, aimed at identifying factors impacting invasion, are in progress. Conclusions These results provide preliminary, but promising findings suggesting mechanisms by which microbiota possibly originating in the appendix may show altered virulence, which may be related to changes in the appendix microenvironment in IBD. With plans in place to increase our patient cohort we will validate these findings. Identifying and profiling these microbes in IBD patients can help improve the understanding of mechanisms underlying microenvironment changes within the appendix and the gut, which could shed light on the role of the appendix in IBD pathogenesis and clarify how microbes drive inflammation in IBD. Funding Agencies CIHR
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Hanif, Marwa Irfan, Delianis Pringgenies, and Gunawan Widi Santosa. "Potential Application of Consortium Microbe from Sea Cucumber Intestinal Symbiont as Preservatives for Vaname Shrimp." Indonesian Journal of Environmental Management and Sustainability 3, no. 3 (September 30, 2019): 106–11. http://dx.doi.org/10.26554/ijems.2019.3.3.93-99.
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Vaname shrimp is one of the most profitable export commodities in Indonesia. However, the shrimp meat undergoes rapid quality degradation when shipped without any preservatives. This is an issue since the preservatives commonly found on the market are formalin-based. This study aims to discover a natural preservative solution by utilizing microbes. The objective of the study is to discover natural preservatives made of symbiont microbe in sea cucumber's intestinal organ by antimicrobial activity screening. Sea cucumber samples were collected from Bandengan waters of Jepara. There are 3 symbiotic microbe form intestinal cucumber that can inhibit the growth from Bacillus cereus and Pseudomonas aeruginosa. These three microbes are Listeria sp., Staphylococcus sp., and Rothia sp. Consequently, tested microbial samples were prepared into a consortium microbe and were tested further as a preservative agent for shrimp with a positive control parameter (cooling). The observations conducted in this study include organoleptic properties, acidity, total colony, proximate test (protein, water, ash, fat, and carbohydrate contents), and Total Volatile Base-Nitrogen (TVBN). The results found 3 active isolates are synergic one to each other as a bacterial consortium. Acidity test of sample extract treatment measured a pH of 7.44, compared to the non-treatment result of 7.14. Organoleptic test results of the shrimp indicated that the shrimp was acceptable for consumption. Proximate test of the treatment did not show a significant difference compared to the positive control treatment. Total colony and TVBN test on treated samples resulted in 48 x 105 CFU/ml and 39.62 mgN% respectively, whereas a similar test on non-treatment sample showed 119 x 105 CFU/ml and 45.31 mgN% respectively. It was concluded that the extract of sea cucumber symbiont microbe consortium showed potency in preventing meat quality degradation in shrimp, although treatment by freezing still produces a better result.
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Yuan, Shunling, Jialun Yang, Ye Jian, Yong Lei, Sisi Yao, Zelin Hu, Xia Liu, Changfa Tang, and Wenfeng Liu. "Treadmill Exercise Modulates Intestinal Microbes and Suppresses LPS Displacement to Alleviate Neuroinflammation in the Brains of APP/PS1 Mice." Nutrients 14, no. 19 (October 5, 2022): 4134. http://dx.doi.org/10.3390/nu14194134.
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Neuroinflammation occurs throughout the pathogenesis of Alzheimer’s disease (AD). Here, we investigated the effects of treadmill exercise on neuroinflammation in APP/PS1 transgenic AD mice and the potential involvement of microbe–gut–brain axis (MGB) mechanisms based on growing evidence that AD’s pathogenesis is correlated with a deterioration in the function of gut microbiota. APP/PS1 transgenic AD mice were subjected to 12 weeks of treadmill exercise, followed by spatial memory tests. After the behavioral study, the amyloid (Aβ) pathology, gut microbes and metabolites, bacterial lipopolysaccharide (LPS) displacement, and degree of neuroinflammation were analyzed. We found that this strategy of exercise enriched gut microbial diversity and alleviated neuroinflammation in the brain. Notably, exercise led to reductions in pathogenic bacteria such as intestinal Allobaculum, increases in probiotic bacteria such as Akkermansia, increased levels of intestine–brain barrier proteins, and attenuated LPS displacement. These results suggest that prolonged exercise can effectively modulate gut microbes and the intestinal barrier and thereby reduce LPS displacement and ultimately alleviate AD-related neuroinflammation.