Disentangling environmental effects in microbial association networks

Background Ecological interactions among microorganisms are fundamental for ecosystem function, yet they are mostly unknown or poorly understood. High-throughput-omics can indicate microbial interactions through associations across time and space, which can be represented as association networks. Associations could result from either ecological interactions between microorganisms, or from environmental selection, where the association is environmentally driven. Therefore, before downstream analysis and interpretation, we need to distinguish the nature of the association, particularly if it is due to environmental selection or not. Results We present EnDED (environmentally driven edge detection), an implementation of four approaches as well as their combination to predict which links between microorganisms in an association network are environmentally driven. The four approaches are sign pattern, overlap, interaction information, and data processing inequality. We tested EnDED on networks from simulated data of 50 microorganisms. The networks contained on average 50 nodes and 1087 edges, of which 60 were true interactions but 1026 false associations (i.e., environmentally driven or due to chance). Applying each method individually, we detected a moderate to high number of environmentally driven edges—87% sign pattern and overlap, 67% interaction information, and 44% data processing inequality. Combining these methods in an intersection approach resulted in retaining more interactions, both true and false (32% of environmentally driven associations). After validation with the simulated datasets, we applied EnDED on a marine microbial network inferred from 10 years of monthly observations of microbial-plankton abundance. The intersection combination predicted that 8.3% of the associations were environmentally driven, while individual methods predicted 24.8% (data processing inequality), 25.7% (interaction information), and up to 84.6% (sign pattern as well as overlap). The fraction of environmentally driven edges among negative microbial associations in the real network increased rapidly with the number of environmental factors. Conclusions To reach accurate hypotheses about ecological interactions, it is important to determine, quantify, and remove environmentally driven associations in marine microbial association networks. For that, EnDED offers up to four individual methods as well as their combination. However, especially for the intersection combination, we suggest using EnDED with other strategies to reduce the number of false associations and consequently the number of potential interaction hypotheses.

Detecting Sparse Microbial Association Signals Adaptively From Longitudinal Microbiome Data Based on Generalized Estimating Equations

Background: The relationship between the compositions of microbial communities and various host phenotypes is an important research topic. Microbiome association research addresses multiple domains, such as human disease, diet and medicine. Statistical methods for testing microbiome-phenotype associations have been studied recently to determine their ability to assess longitudinal microbiome data. However, existing methods fail to detect sparse association signals in longitudinal microbiome data. Methods: In this paper, we developed a novel method, namely, aGEEMiHC, which is a data-driven adaptive microbiome higher criticism analysis based on generalized estimating equations, to detect sparse microbial association signals from longitudinal microbiome data. aGEEMiHC adopts a generalized estimating equations framework that fully considers the correlation among different observations from the same cluster (individuals) in longitudinal data, and it integrates multiple microbiome higher criticism analyses based on generalized estimating equations by setting different working correlation structures. Thus, the proposed method is robust to diverse correlation structures for longitudinal data.Results: The proposed method shows a stable performance for diverse association patterns in both sparsity levels and phylogenetic relevance. Extensive simulation experiments demonstrate that it can control the type I error correctly and achieve superior performance according to a statistical power comparison. In our simulation, we applied aGEEMiHC to longitudinal microbiome data with various types of host phenotypes to demonstrate the stability of our method. aGEEMiHC is also utilized for real longitudinal microbiome data, and we found a significant association between the gut microbiome and Crohn's disease. Conclusions: aGEEMiHC is a statistical method that facilitates association testing for sparse microbial association signals from longitudinal microbiome data, and it can be applied to situations in which the true underlying correlations among different observations from the same cluster in longitudinal data are unknown. It is worth noting that our method also ranks the significant factors associated with the host phenotype to provide potential biomarkers. The R package GEEMiHC is available at https://github.com/xpjiang-ccnu/GEEMiHC.

To Other Planets With Upgraded Millennial Kombucha in Rhythms of Sustainability and Health Support

Humankind has entered a new era of space exploration: settlements on other planetary bodies are foreseen in the near future. Advanced technologies are being developed to support the adaptation to extraterrestrial environments and, with a view on the longer term, to support the viability of an independent economy. Biological processes will likely play a key role and lead to the production of life-support consumables, and other commodities, in a way that is cheaper and more sustainable than exclusively abiotic processes. Microbial communities could be used to sustain the crews’ health as well as for the production of consumables, for waste recycling, and for biomining. They can self-renew with little resources from Earth, be highly productive on a per-volume basis, and be highly versatile—all of which will be critical in planetary outposts. Well-defined, semi-open, and stress-resistant microecosystems are particularly promising. An instance of it is kombucha, known worldwide as a microbial association that produces an eponymous, widespread soft drink that could be valuable for sustaining crews’ health or as a synbiotic (i.e., probiotic and prebiotic) after a rational assemblage of defined probiotic bacteria and yeasts with endemic or engineered cellulose producers. Bacterial cellulose products offer a wide spectrum of possible functions, from leather-like to innovative smart materials during long-term missions and future activities in extraterrestrial settlements. Cellulose production by kombucha is zero-waste and could be linked to bioregenerative life support system (BLSS) loops. Another advantage of kombucha lies in its ability to mobilize inorganic ions from rocks, which may help feed BLSS from local resources. Besides outlining those applications and others, we discuss needs for knowledge and other obstacles, among which is the biosafety of microbial producers.

Massive cryptic microbe-sponge deposits in a Devonian fore-reef slope (Elbingerode Reef Complex, Harz Mts., Germany)

A massive occurrence of microbial carbonates, including abundant sponge remains, within the Devonian Elbingerode Reef Complex was likely deposited in a former cavity of the fore-reef slope during the early Frasnian. It is suggested that the formation of microbial carbonate was to a large part favored by the activity of heterotrophic, i.e., sulfate-reducing bacteria, in analogy to Quaternary coral reef microbialites. The Elbingerode Reef Complex is an example of an oceanic or Darwinian barrier reef system. In modern barrier reef settings, microbialite formation is commonly further facilitated by weathering products from the central volcanic islands. The Devonian microbialites of the Elbingerode Reef Complex occur in the form of reticulate and laminated frameworks. Reticulate framework is rich in hexactinellid glass sponges, the tissue decay of which led to the formation of abundant micrite as well as peloidal and stromatactis textures. Supposed calcimicrobes such as Angusticellularia (formerly Angulocellularia) and Frutexites, also known from cryptic habitats, were part of the microbial association. The microbial degradation of sponge tissue likely also contributed to the laminated framework accretion as evidenced by the occurrence of remains of so-called “keratose” demosponges. Further typical textures in the microbialite of the Elbingerode Reef Complex include zebra limestone, i.e., the more or less regular intercalation of microbial carbonate and cement. Elevated concentrations of magnesium in the microbialite as compared to the surrounding metazoan (stromatoporoid-coral) reef limestone suggests that the microbialite of the Elbingerode Reef Complex was initially rich in high-magnesium calcite, which would be yet another parallel to modern, cryptic coral reef microbial carbonates. Deposition and accretion of the microbialite largely occurred in oxygenated seawater with suboxic episodes as indicated by the trace element (REE + Y) data.

The state of the resident intestinal microbial association and its relationship with concentrations of dioxins in blood lipids of firefighters

Relevance. Career firefighters are involved in extreme activities, and their functional reserves are probabilistically disturbed. Toxic products of combustion can significantly affect their health state.Intention – To analyze and evaluate effects of blood lipid dioxins on the microbiome of the parietal intestinal flora in firefighters of the Federal Fire Service of the Emercom of Russia.Methodology. Relationships between the microbiota composition and concentrations of blood lipid dioxins were analyzed in firefighters vs Emercom employees not involved in firefighting (control group).Results and Discussion. Microbiota concentrations in firefighters were associated with levels of blood lipid dioxins. In firefighters with dioxins > 350 pg/g lipids in the blood, normal microflora concentrations significantly decreased and conditionally pathogenic microflora concentrations significantly increased compared to firefighters with lower concentrations of dioxins and the control group.Conclusion. Disturbances in the microbiome of the parietal intestinal flora in the examined firefighters are related to exposure to toxic products of combustion, including dioxins, during firefighting. The microbiome disorders detected in firefighters can predict development of the digestive tract pathology, thus necessitating control and targeted correction of the somatic state and microecological status of this contingent.

POSSIBILITIES OF TREATMENT OF I NFECTED ULCERS OF THE LOWER EXTREMITIES IN CHRONIC VENOUS INSUFFICIENCY WITHOUT THE USE OF ANTIBIOTICS

Summary. Introduction. Purulent diseases and purulent complications in modern medicine remain a complex and not always a positive problem, because in the development of such diseases is quite prominent microbial factor. Overcoming the latter is getting harder every year. The urgency of the problem. The fact is that before our eyes, almost exponentially, the number of microorganisms resistant to existing antibiotics is increasing. Not to mention the toxic effects of many of them on certain organs due to their natural tropism, we note allergic effects, individual intolerance and dysbacterial effects, we note that the cost of some drugs for 1–2 days of use is equal to pension (monthly «income» of most retirees). Given this, you need to look for an opportunity to do without the use of antibiotics, which determines the urgency of the problem. Goal. Explore the possibility of treating infected lower extremity ulcers without the use of antibiotics. Materials and methods. The possibility of treating purulent ulcers of the lower extremities on the background of chronic venous insufficiency by using apatite polymeric drainage bandage based on hydroxyapatite supplemented with zinc oxide has been studied. Results and discussion. Polyvalent microbial association was established in 100 % of patients, staphylococcal colonization prevailed in 75 % of them. On 3–4 days of treatment, a decrease in inflammation, regression of symptoms, reduction of microbial insemination, the appearance of signs of repair, improvement of foot function were recorded. Conclusions. 1) The possibility of treating infected wounds by using apatite polymer drainage bandage has been confirmed; 2) On 3–4 days of application of the drainage bandage there is a regression of the inflammatory process in the area of the ulcer; 3) Microbial contamination of the wound surface for 4 days is reduced from 108 to 73.5 CFU/ml; 4) Subjective sensation and foot function improve by 3–4 days of treatment.

Microbial association networks in cheese: a meta-analysis

Interactions among starter and non-starter microorganisms (starter bacteria, naturally occurring or intentionally added non-starter bacteria, yeasts and filamentous fungi, spoilage and pathogenic microorganisms and, finally bacteriophages and even arthropods) deeply affect the dynamics of cheese microbial communities and, as a consequence, multiple aspects of cheese quality, from metabolites affecting the taste, aroma and flavor, to body, texture and color. Understanding and exploiting microbial interactions is therefore key to managing cheese quality. This is true for the simplest systems (fresh cheeses produced from pasteurized milk using defined starters composed solely of Lactic Acid Bacteria) and the more so for complex, dynamic systems, like surface ripened cheese produced from raw milk, in which a dynamic succession of diverse microorganisms is essential for obtained the desired combination of sensory properties while guaranteeing safety. Positive (commensalism, protocooperation) and negative (competition, amensalism, predation and parasitism) among members of the cheese biota have been reviewed multiple times. Although the complex, multidimensional datasets generated by multi-omic approaches to cheese microbiology and biochemistry are ideally suited for the representation of biotic and metabolic interactions as networks, network science concepts and approaches are rarely applied to cheese microbiology. In this review we first illustrate concepts relevant to the description of microbial interaction networks using network science concepts. Then, we briefly review methods used for the inference and analysis of microbial association networks and their potential use in the interpretation of the cheese interactome. Since these methods can only be used for mining microbial associations, a review of the experimental methods used to confirm the nature of microbial interactions among cheese microbes. Finally, we demonstrate the potential of microbial association network inference by mining metataxonomic data stored in the public database DairyFMBN, a specialized version of FoodMicrobionet which collates data on 74 metataxonomic studies on dairy products. Microbial association networks were inferred from 34 studies on cheese with up to 4 different methods and the results discussed to evaluate several aspects (choice of method, level of taxonomic resolution for the analysis, network, node and edge properties) which provide insight on the usefulness of this approach as explorative tool in the detection of microbial interactions in cheese.