Interactions-based classification of a single microbial sample

To address the limitation of overlooking crucial ecological interactions due to relying on single time point samples, we developed a computational approach that analyzes individual samples based on the interspecific microbial relationships. We verify, using both numerical simulations as well as real and shuffled microbial profiles from the human oral cavity, that the method can classify single samples based on their interspecific interactions. By analyzing the gut microbiome of people with autistic spectrum disorder, we found that our interaction-based method can improve the classification of individual subjects based on a single microbial sample. These results demonstrate that the underlying ecological interactions can be practically utilized to facilitate microbiome-based diagnosis and precision medicine.

Microbial Dynamics during labneh Ambaris Production in Earthenware Jars

The responses of various microbial populations to modifications in the physicochemical properties of a food matrix, as well as interactions between these populations already present, are the main factors that shape microbial dynamics in that matrix. This work focused on the study of microbial dynamics during labneh Ambaris production, a traditional Lebanese concentrated fermented goat milk made in jars during 3 months. This was assessed in two earthenware jars at a production facility. DNA metabarcoding of the ITS2 region as well as the V3-V4 region of the 16S rRNA gene was used to characterize the fungal and bacterial communities, respectively. Viable bacterial isolates were also identified by Sanger sequencing of the V1-V4 region of the 16S rRNA gene. Our results showed that the dominant microorganisms identified within labneh Ambaris (Lactobacillus kefiranofaciens, Lentilactobacillus kefiri, Lactococcus lactis, Geotrichum candidum, Pichia kudriavzevii and Starmerella sp.) settle early in the product and remain until the end of maturation with varying abundances throughout fermentation. Microbial counts increased during early fermentation stage, and remained stable during mid-fermentation, then declined during maturation. While microbial compositions were globally comparable between the two jars during mid-fermentation and maturation stages, differences between the two jars were mainly detected during early fermentation stage (D0 until D10). No significant sensorial differences were observed between the final products made in the two jars. Neither coliforms nor Enterobacteriaceae were detected in their viable state, starting D7 in both jars, suggesting the antimicrobial properties of the product.

Defining the Benefits of Antibiotic Resistance in Commensals and the Scope for Resistance Optimization

Antibiotic resistance is a major medical and public health challenge, characterized by global increases in the prevalence of resistant strains. The conventional view is that all antibiotic resistance is problematic, even when not in pathogens. Resistance in commensal bacteria poses risks, as resistant organisms can provide a reservoir of resistance genes that can be horizontally transferred to pathogens or may themselves cause opportunistic infections in the future. While these risks are real, we propose that commensal resistance can also generate benefits during antibiotic treatment of human infection, by promoting continued ecological suppression of pathogens. To define and illustrate this alternative conceptual perspective, we use a two-species mathematical model to identify the necessary and sufficient ecological conditions for beneficial resistance. We show that the benefits are limited to species (or strain) interactions where commensals suppress pathogen growth and are maximized when commensals compete with, rather than prey on or otherwise exploit pathogens. By identifying benefits of commensal resistance, we propose that rather than strictly minimizing all resistance, resistance management may be better viewed as an optimization problem. We discuss implications in two applied contexts: bystander (nontarget) selection within commensal microbiomes and pathogen treatment given polymicrobial infections. IMPORTANCE Antibiotic resistance is commonly viewed as universally costly, regardless of which bacterial cells express resistance. Here, we derive an opposing logic, where resistance in commensal bacteria can lead to reductions in pathogen density and improved outcomes on both the patient and public health scales. We use a mathematical model of commensal-pathogen interactions to define the necessary and sufficient conditions for beneficial resistance, highlighting the importance of reciprocal ecological inhibition to maximize the benefits of resistance. More broadly, we argue that determining the benefits as well as the costs of resistances in human microbiomes can transform resistance management from a minimization to an optimization problem. We discuss applied contexts and close with a review of key resistance optimization dimensions, including the magnitude, spectrum, and mechanism of resistance.

Microbial Dynamics of a Specialty Italian Raw Ewe's Milk Cheese Curdled with Extracts from Spontaneous and Cultivated Onopordum tauricum Willd

Milk coagulants prepared by maceration of flowers harvested from both spontaneous and cultivated Onopordum tauricum Willd. and a commercially available coagulant obtained from Cynara cardunculus L. (control) were assayed for small-scale manufacturing of Caciofiore, an Italian specialty raw ewe's milk cheese produced in a family run dairy farm located in the Marche region (Central Italy). The microbiota of the three thistle-based milk coagulants and their effect on the microbial dynamics of raw milk cheeses during fermentation and maturation (from day 0 up until day 60) were investigated through a combined approach based on viable counting and Illumina DNA sequencing. In both the control and experimental cheeses, despite the slight differences emerged depending on the coagulant used, Lactococcus lactis and Debaryomyces hansenii were the prevalent species among bacteria and fungi, respectively. Moreover, raw ewe's milk was the main factor affecting the evolution of both the bacterial and fungal microbiota in all cheeses. The overall similarities between control and experimental cheeses herein analyzed supports the exploitation of Onopordum tauricum Willd. as an alternative milk coagulating agent for production of Caciofiore and, more in general, raw ewe's milk cheeses.

Raw goat's milk fermented Anbaris from Lebanon: insights into the microbial dynamics and chemical changes occurring during artisanal production, with a focus on yeasts

Anbaris is a raw goat milk product naturally fermented in terracotta jars. The aim of this research paper was to follow the dynamics underlying an artisanal production to understand the concomitant evolution of the microbial populations in relation to the chemical changes occurring within the product, make sure of the sanitary conditions prevailing during the production and uncover for the first time its culturable yeast populations. Throughout the fermentation process, Anbaris was endowed with high acidity and included high microbial populations counts of LAB and yeasts that were rapidly installed within the product and maintained as regular new milk additions were made, contributing to lipolytic and proteolytic activities. Salt content varied according to the arbitrary salt additions made during the process but was high in the end product while protein and fat contents varied inversely to moisture. Frequent additions of Enterobacteriaceae and Coliforms contaminated milk samples seemingly fueled a contamination of the product during its manufacturing and in the final fresh Anbaris. Seven species of culturable yeasts, Pichia kudriavzevii, Kluyveromyces marxianus, Rhodotorula mucilaginosa, Saccharomyces cerevisiae, Debaryomyces hansenii, Candida parapsilosis and Kazachstania exigua were found during the production. The first two dominated the process in terms of frequency of occurrence and abundance at the different stages and might be signature species of the product. The same lineage of K. marxianus isolates was maintained throughout the fermentation and sample specific patterns were observed. Strains of this species exhibited low diversity within our product, and more globally in the Lebanese dairy products we studied.

Dynamics of Bacterial Composition and Association with Quality Formation and Biogenic Amines Accumulation during Fish Sauce Spontaneous Fermentation

High-throughput sequencing and high-pressure liquid chromatography (HPLC) methods were used to investigate the influences of microbial dynamics on the quality and biogenic amine (BA) content during fish sauce fermentation. The homogeneity of total viable bacteria and lactic acid bacteria in fish sauce becomes higher as fermentation progresses. Tetragenococcus was the key genus of fish sauce fermentation. Carnobacterium (38.43%) and Lentibacillus (41.01%) were the dominant genera in the samples fermented for 3 months and 18 months, respectively. These three bacterial genera were significantly related to the physicochemical characteristics and characteristic flavors of the sauces. Tetragenococcus was significantly positively correlated with nitrogen oxides, the main characteristic flavor components in fish sauce. The BA content in fish sauce fermentation increased from 106.88 to 376.03 mg/kg, and the content of histamine reached 115.30 mg/kg at the end of fermentation, indicating that fish sauce has health risks. About 66.67% of Lentibacillus isolates were able to produce a large amount of BA, suggesting that Lentibacillus was the key genus for BA accumulation in fish sauce fermentation. Research on reducing the content of BA in fish sauce by intervening with regard to the fermentation temperature showed that a safe fish sauce product could be obtained at the fermentation temperature of about 25°C. These results help us to understand the contribution of microbial community composition to fish sauce fermentation and provide a basis for improving the quality and safety of fermented fish sauce. IMPORTANCE Traditional fermentation of fish sauce is mainly carried out by complex microbial communities from raw anchovies and processing environments. However, it is still unclear how the environmental microbiota influences the quality and the safety of fish sauce products. Therefore, this study comprehensively explained the influence of microorganisms on the quality and safety of fish sauce during the fermentation process in terms of physicochemical characters, flavors, and BA. Additionally, the accumulation of BA in fish sauce fermentation was controlled by intervening in the fermentation temperature. This finding contributes to a deeper understanding of the role of environmental microbiota during fermentation and provides data support for improving the safety of fish sauce.

Seasonality of Glacial Snow and Ice Microbial Communities

Blooms of microalgae on glaciers and ice sheets are amplifying surface ice melting rates, which are already affected by climate change. Most studies on glacial microorganisms (including snow and glacier ice algae) have so far focused on the spring and summer melt season, leading to a temporal bias, and a knowledge gap in our understanding of the variations in microbial diversity, productivity, and physiology on glacier surfaces year-round. Here, we investigated the microbial communities from Icelandic glacier surface snow and bare ice habitats, with sampling spanning two consecutive years and carried out in both winter and two summer seasons. We evaluated the seasonal differences in microbial community composition using Illumina sequencing of the 16S rRNA, 18S rRNA, and ITS marker genes and correlating them with geochemical signals in the snow and ice. During summer, Chloromonas, Chlainomonas, Raphidonema, and Hydrurus dominated surface snow algal communities, while Ancylonema and Mesotaenium dominated the surface bare ice habitats. In winter, algae could not be detected, and the community composition was dominated by bacteria and fungi. The dominant bacterial taxa found in both winter and summer samples were Bacteriodetes, Actinobacteria, Alphaproteobacteria, and Gammaproteobacteria. The winter bacterial communities showed high similarities to airborne and fresh snow bacteria reported in other studies. This points toward the importance of dry and wet deposition as a wintertime source of microorganisms to the glacier surface. Winter samples were also richer in nutrients than summer samples, except for dissolved organic carbon-which was highest in summer snow and ice samples with blooming microalgae, suggesting that nutrients are accumulated during winter but primarily used by the microbial communities in the summer. Overall, our study shows that glacial snow and ice microbial communities are highly variable on a seasonal basis.

Metatranscriptomic Analyses Unravel Dynamic Changes in the Microbial and Metabolic Transcriptional Profiles in Artisanal Austrian Hard-Cheeses During Ripening

Vorarlberger Bergkäse (VB) is an artisanal Austrian washed-rind hard cheese produced from alpine cows' raw milk without the addition of ripening cultures. Ripening time is a key factor in VB, as it strongly influences the microbial communities present in the cheeses and the organoleptic properties of the product. In this study, the microbial and metabolic transcriptional profiles in VB rinds at different ripening times were investigated. VB products before (30 days of ripening) and after (90 days of ripening) selling were selected, RNA was extracted and subjected to shotgun metatranscriptomic sequencing. The analysis revealed some of the previously described abundant bacterial taxa of Brevibacterium, Corynebacterium, Halomonas, Psychrobacter, and Staphylococcus to be highly active in VB rinds. Additionally, the investigation of most important metabolic pathways in cheese ripening clearly showed differences in the gene transcription profiles and the active microbiota between the two ripening points investigated. At 30 days of ripening, metabolic events related with the degradation of residual lactose, lactate, citrate, proteolysis, and lipolysis were significantly more transcribed and mainly associated with Staphylococcus. On the other hand, genes involved in the degradation of smaller compounds derived from previous metabolism (i.e., metabolism of free amino acids and fatty acids) were significantly more expressed in VB rinds with 90 of ripening, and mainly associated with Brevibacterium and Corynebacterium. These latter metabolic activities are responsible of the generation of compounds, such as methanethiol and 2,3-butanediol, that are very important for the flavor and aroma characteristics of cheeses. This study shows the dynamic changes in the gene transcriptional profiles associated with energy substrates metabolism and the generation of organoleptic compounds during VB ripening and uncovers bacterial taxa as key drivers of the ripening process. These taxa might be the target for future studies toward an accelerated cheese ripening and the enhancement of its organoleptic properties.

Variability of ecosystem carbon source from microbial respiration is controlled by rainfall dynamics

Soil heterotrophic respiration (R _h) represents an important component of the terrestrial carbon cycle that affects whether ecosystems function as carbon sources or sinks. Due to the complex interactions between biological and physical factors controlling microbial growth, R _h is uncertain and difficult to predict, limiting our ability to anticipate future climate trajectories. Here we analyze the global FLUXNET 2015 database aided by a probabilistic model of microbial growth to examine the ecosystem-scale dynamics of R _h and identify primary predictors of its variability. We find that the temporal variability in R _h is consistently distributed according to a Gamma distribution, with shape and scale parameters controlled only by rainfall characteristics and vegetation productivity. This distribution originates from the propagation of fast hydrologic fluctuations on the slower biological dynamics of microbial growth and is independent of biome, soil type, and microbial physiology. This finding allows us to readily provide accurate estimates of the mean R _h and its variance, as confirmed by a comparison with an independent global dataset. Our results suggest that future changes in rainfall regime and net primary productivity will significantly alter the dynamics of R _h and the global carbon budget. In regions that are becoming wetter, R _h may increase faster than net primary productivity, thereby reducing the carbon storage capacity of terrestrial ecosystems.

The Microbiota of Grana Padano Cheese. A Review

Grana Padano (GP) is the most appreciated and marketed cheese with Protected Designation of Origin in the world. The use of raw milk, the addition of undefined cultures (defined as 'sieroinnesto naturale'), the peculiar manufacturing proces, and the long ripening make the cheese microbiota play a decisive role in defining the quality and the organoleptic properties of the product. The knowledge on the microbial diversity associated with GP has been the subject, in recent years, of several studies aimed at understanding its composition and characteristics in order, on the one hand, to improve its technological performances and, on the other hand, to indirectly enhance the nutritional quality of the product. This review aims to briefly illustrate the main available knowledge on the composition and properties of the GP microbiota, inferred from dozens of studies carried out by both classical microbiology techniques and metagenomic analysis. The paper will essentially, but not exclusively, be focused on the lactic acid bacteria (LAB) derived from starter (SLAB) and the non-starter bacteria, both lactic (NSLAB) and non-lactic, of milk origin.

Microbial Interactions between Amylolytic and Non-Amylolytic Lactic Acid Bacteria Strains Isolated during the Fermentation of Pozol

Pozol is a Mexican beverage prepared from fermented nixtamalized maize dough. To contribute to understanding its complex microbial ecology, the effect of inoculating on MRS-starch pure and mixed cultures of amylolytic Sii-25124 and non-amylolytic W. confusa 17, isolated from pozol, were studied on their interactions and fermentation parameters. These were compared with L. plantarum A6, an amylolytic strain isolated from cassava. Microbial growth, kinetic parameters, amylolytic activity, lactic acid production, and hydrolysis products from starch fermentation were measured. The population dynamics were followed by qPCR. L. plantarum A6 showed higher enzymatic activity, lactic acid, biomass production, and kinetic parameters than pozol LAB in pure cultures. Mixed culture of each pozol LAB with L. plantarum A6 showed a significant decrease in amylolytic activity, lactic acid yield, specific growth rate, and specific rate of amylase production. The interaction between Sii-25124 and W. confusa 17 increased the global maximum specific growth rate (µ), the lactic acid yield from starch (Y_lac/s), lactic acid yield from biomass (Y_lac/x), and specific rate of lactic acid production (q_lac) by 15, 30, 30, and 40%, respectively, compared with the pure culture of Sii-25124. Interactions between the two strains are essential for this fermentation.

Bacterial Dynamics in the Accessory Nidamental Gland of Sepioteuthis lessoniana throughout Maturation

The accessory nidamental gland (ANG) is part of the reproduction organ in the majority of female cephalopods, including the bigfin reef squid Sepioteuthis lessoniana, an economically important fishery product. Microbes in Alphaproteobacteria, Gammaproteobacteria, and Verrucomicrobia have been suggested to play a role in the maturation of the S. lessoniana ANG and are responsible for its color. However, the bacterial composition and dynamics of the different maturation stages of the ANG remain unclear. In the present study, we surveyed ANG-associated bacterial dynamics in wild-caught S. lessoniana at various developmental stages in different populations over 3 years. The results obtained showed that the ANG bacterial community shifted gradually and decreased in diversity throughout maturation. Verrucomicrobia occupied the ANG during the early stages in large numbers, and was replaced by Bacteroidia, Alphaproteobacteria, and Gammaproteobacteria in the later stages. Flavobacteriales and Alphaproteobacteria both appeared to contribute to pigmentation, while Bacteroidia, Alphaproteobacteria, and Gammaproteobacteria may be involved in enriching the heme biosynthesis pathway in the ANG with the maturation of S. lessoniana. The present results provide an open question of whether S. lessoniana actively selects the bacterial community in the ANG to adjust to its surrounding environment.

Microbial Dynamics and In Vitro Degradation of Plant Secondary Metabolites in Hanwoo Steer Rumen Fluids

Plant secondary metabolite (PSM) degradations and feed breakdown into small particles may occur primarily in the rumen. It is possible to predict the rate and extent of feed disappearance in the rumen during incubation by different in vitro techniques, which differ based on the PSM structures, including phenolics, and flavonoids. However, PSM degradation and conversion efficiency in the rumen remains unclear. This study's objective was to evaluate the in vitro degradation of a group of PSMs in the rumen fluid, collected from Hanwoo steer samples. PSMs including rutin, vitexin, myricetin, p-coumaric acid, ferulic acid, caffeic acid, quercetin, luteolin, propyl gallate, and kaempferol were used in their pure forms at 1mg/250 mL in a rumen fluid buffer system. The mixture of selected PSMs and buffer was incubated at 39 °C for 12-72 h, and samples were collected every 12 h and analyzed by a high-performance liquid chromatography-diode array detector (HPLC-DAD) to determine the biotransformation of the polyphenolics. The results revealed that the luteolin, ferulic acid, caffeic acid, coumaric acid, rutin, myricetin, vitexin, kaempferol, and quercetin were decreased after 12 h of incubation in the rumen fluid (p ≤ 0.05) and were more than 70% decreased at 72 h. In contrast, the propyl gallate concentrations were not significantly changed after 24 h of incubation in rumen fluid compared to other metabolites. Finally, microbial dynamics study showed that the Firmicutes, Bacterodetes, Actinobacteria, and Syngergistetes were the dominant phyla found in rumen fluids. The data suggest that most polyphenolic compounds may degrade or reform new complex structures in the rumen.

A snapshot study of the microbial community dynamics in naturally fermented cow's milk

Natural fermentation of milk is a prerequisite in the production of traditional dairy products and is considered a bioresource of fermentative microorganisms and probiotics. To understand the microbial dynamics during distinct fermentative phases, the roles of different microbes, and the relationship between bacteria and fungi, microbial community dynamics was investigated by culture-dependent and culture-independent approaches. Natural, static fermentation of milk induces the formation of the underlying curds and the superficial sour cream (Zuohe in the Mongolian language). From an overall perspective, viable LAB increased remarkably. Yeast showed an initial increase in their abundance (from 0 hr to 24 hr), which was followed by a decrease, and mold was detected at the later stages of fermentation (after 68 hr). The observed trends in microbiota variation suggest an antagonistic interaction between bacteria (LAB) and fungi (yeast and mold). The beneficial bacterial and fungal genus and species (e.g., Lactococcus, Streptococcus, Leuconostoc, Dipodascus, Lactococcus lacti, Dipodascus australiensis) are gradually increased in concentration, and the potentially detrimental microbial genus and species (e.g., Acinetobacter, Pseudomonas, Fusarium, Aspergillus, Mortierella, Acinetobacter johnsonii, Fusarium solani) decrease during the decline of bacterial and fungi diversity from natural fermentation. The study of microbial community dynamics could make a great contribution to understand the mechanism of natural fermentation of milk and the formation of curds and Zuohe, and to discover the potentially fermentative microbes for industrial starter cultures.

Microbial dynamics, metabolomic profiles, and the correlation between them during fermentation of serofluid dish

BACKGROUND

Serofluid dish, a traditional Chinese fermented food, possesses unique flavors and health beneficial effects. These properties are likely due to the sophisticated metabolic networks during fermentation, which are mainly driven by microbiota. However, the exact roles of metabolic pathways and the microbial community during this process remain equivocal.

RESULTS

Here, we investigated the microbial dynamics by next-generation sequencing, and outlined a differential non-targeted metabolite profiling in the process of serofluid dish fermentation using the method of hydrophilic interaction liquid chromatography column with ultra-high-performance liquid chromatography-quadruple time-of-flight mass spectrometry. Lactobacillus was the leading genus of bacteria, while Pichia and Issatchenkia were the dominant fungi. They all accumulated during fermentation. In total, 218 differential metabolites were identified, of which organic acids, amino acids, sugar and sugar alcohols, fatty acids, and esters comprised the majority. The constructed metabolic network showed that tricarboxylic acid cycle, urea cycle, sugar metabolism, amino acids metabolism, choline metabolism, and flavonoid metabolism were regulated by the fermentation. Furthermore, correlation analysis revealed that the leading fungi, Pichia and Issatchenkia, were linked to organic acids, amino acid and sugar metabolism, flavonoids, and several other flavor and functional components. Antibacterial tests indicated the antibacterial effect of serofluid soup against Salmonella and Staphylococcus.

CONCLUSION

This work provides new insights into the complex microbial and metabolic networks during serofluid dish fermentation, and a theoretical basis for the optimization of its industrial production. © 2020 Society of Chemical Industry.

Developing a Functional Poly(dimethylsiloxane)-Based Microbial Nanoculture System Using Dimethylallylamine

Here, a novel poly(dimethylsiloxane) (PDMS)-based microbial culture system was investigated. Bacteria were encapsulated in functional and semipermeable membranes, mimicking the cell microenvironment and facilitating mass transport for interrogating microbial dynamics, thereby overcoming one of the major challenges associated with commercially available PDMS such as Sylgard 184. The hydrophobic nature and lack of control in the polymer network in Sylgard 184 significantly impede the the tunability of the transport and mechanical properties of the material as well as its usage as an isolation chamber for culturing and delivering microbes. Therefore, a novel PDMS composition was developed and functionalized with dimethylallylamine (DMAA) to alter its hydrophobicity and modify the polymer network. Characterization techniques including NMR spectroscopy, contact angle measurements, and sol-gel process were utilized to evaluate the physical and chemical properties of the newly fabricated membranes. Furthermore, the DMAA-containing polymer mixture was used as a proof of concept to generate hydrodynamically stable microcapsules and cultivate Escherichia coli cells in the functionalized capsules. The membrane exhibited a selective permeability to tetracycline, which diffused into the capsules to inhibit the growth of the encapsulated microbes. The functionality achieved here with the addition of DMAA, coupled with the high-throughput encapsulation technique, could prove to be an effective testing and diagnostic tool to evaluate microbial resistance, growth dynamics, and interspecies interaction and lays the foundation for in vivo models.

Microbial Dynamics in Traditional and Modern Sour Beer Production

Traditional sour beers are produced by spontaneous fermentations involving numerous yeast and bacterial species. One of the traits that separates sour beers from ales and lagers is the high concentration of organic acids such as lactic acid and acetic acid, which results in reduced pH and increased acidic taste. Several challenges complicate the production of sour beers through traditional methods. These include poor process control, lack of consistency in product quality, and lengthy fermentation times. This review summarizes the methods for traditional sour beer production with a focus on the use of lactobacilli to generate this beverage. In addition, the review describes the use of selected pure cultures of microorganisms with desirable properties in conjunction with careful application of processing steps. Together, this facilitates the production of sour beer with a higher level of process control and more rapid fermentation compared to traditional methods.

Fine Resolution Analysis of Microbial Communities Provides Insights Into the Variability of Cocoa Bean Fermentation

Cocoa bean fermentation is an important microbial process, where most metabolites that affect chocolate quality and aroma are generated. Production of reproducible high-quality beans is a major challenge because most fermentations occur in open containers with a lack of variable control. Here we present a study that aims to identify the effect of farm protocols, climate, and bean mass exposure, in the dynamics and composition of microbial communities. Using high-throughput sequencing of molecular markers for bacteria and yeasts, complemented with culture-based methods, we evaluated the microbial diversity and dynamics associated to spontaneous cocoa fermentation in two distinct agro-ecological zones in Colombia. The bacterial communities were classified at two levels of evolutionary relationship, at a coarse resolution (OTU-level) and at a finer resolution (oligotype-level). A total of six bacterial OTUs were present in both farms, following a microbial succession that starts with the Enterobacteraceae family (one OTU), transitioning to the Lactobacillaceae family (three OTUs), and finishing with Acetobacteraceae family (two OTUs). When undesirable practices were done, OTUs were observed at unexpected moments during the fermentation. At a finer taxonomic resolution, 48 oligotypes were identified, with 46 present in both farms. These oligotypes have different patterns of prevalence. In the case of Lactobacillaceae a high evenness was observed among oligotypes. In contrast, for Enterobacteraceae and Acetobacteraceae a high dominance of one or two oligotypes was observed, these oligotypes were the same for both farms, despite geographic location and season of sampling. When the overall fermentations were compared using correlations matrices of oligotypes abundance, they show a clear clustering by farm, suggesting that farm protocols generate a unique fingerprint in the dynamics and interactions of the microbial communities. The comparison between the upper and middle layers of the bean mass showed that environmental exposure affects the paces at which ecological successions occur, and therefore, is an important source of cocoa quality heterogeneity. In conclusion, the results presented here showed that the dynamics of microbial fermentation can be used to identify the sources of variability and evidence the need for better fermentation technologies that favor the production of reproducible high-quality cocoa beans.

Bacterial and Eukaryotic Small-Subunit Amplicon Data Do Not Provide a Quantitative Picture of Microbial Communities, but They Are Reliable in the Context of Ecological Interpretations

High-throughput sequencing (HTS) of amplified fragments of rRNA genes provides unprecedented insight into the diversity of prokaryotic and eukaryotic microorganisms. Unfortunately, HTS data are prone to quantitative biases, which may lead to an erroneous picture of microbial community composition and thwart efforts to advance its understanding. These concerns motivated us to investigate how accurately HTS data characterize the variability of microbial communities, the relative abundances of specific phylotypes, and their relationships with environmental factors in comparison to an established microscopy-based method. We compared results obtained by HTS and catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) from three independent aquatic time series for both prokaryotic and eukaryotic microorganisms (almost 900 data points, the largest obtained with both methods so far). HTS and CARD-FISH data disagree with regard to relative abundances of bacterial and eukaryotic phylotypes but identify similar environmental drivers shaping bacterial and eukaryotic communities.

High-throughput sequencing (HTS) of gene amplicons is a preferred method of assessing microbial community composition, because it rapidly provides information from a large number of samples at high taxonomic resolution and low costs. However, mock community studies show that HTS data poorly reflect the actual relative abundances of individual phylotypes, casting doubt on the reliability of subsequent statistical analysis and data interpretation. We investigated how accurately HTS data reflect the variability of bacterial and eukaryotic community composition and their relationship with environmental factors in natural samples. For this, we compared results of HTS from three independent aquatic time series (n = 883) with those from an established, quantitative microscopic method (catalyzed reporter deposition-fluorescence in situ hybridization [CARD-FISH]). Relative abundances obtained by CARD-FISH and HTS disagreed for most bacterial and eukaryotic phylotypes. Nevertheless, the two methods identified the same environmental drivers to shape bacterial and eukaryotic communities. Our results show that amplicon data do provide reliable information for their ecological interpretations. Yet, when studying specific phylogenetic groups, it is advisable to combine HTS with quantification using microscopy and/or the addition of internal standards.

IMPORTANCE High-throughput sequencing (HTS) of amplified fragments of rRNA genes provides unprecedented insight into the diversity of prokaryotic and eukaryotic microorganisms. Unfortunately, HTS data are prone to quantitative biases, which may lead to an erroneous picture of microbial community composition and thwart efforts to advance its understanding. These concerns motivated us to investigate how accurately HTS data characterize the variability of microbial communities, the relative abundances of specific phylotypes, and their relationships with environmental factors in comparison to an established microscopy-based method. We compared results obtained by HTS and catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) from three independent aquatic time series for both prokaryotic and eukaryotic microorganisms (almost 900 data points, the largest obtained with both methods so far). HTS and CARD-FISH data disagree with regard to relative abundances of bacterial and eukaryotic phylotypes but identify similar environmental drivers shaping bacterial and eukaryotic communities.

Cropping With Slag to Address Soil, Environment, and Food Security

The effective utilization of slag fertilizer in agriculture to neutralize soil acidity, improve crop productivity, mitigate greenhouse gas emissions, and stabilize heavy metals in contaminated soils turns it into a high value added product in sustainable agriculture. These effects could be due to the shift in microbial metabolism and/or modification of microbial habitats. At the system level, soil microorganisms play an integral role in virtually all ecosystem processes. There is a growing interest to reveal the underlying mechanisms of slag-microbe interactions and the contribution of soil biota to ecosystem functioning. In this perspective, we discuss the possible driving mechanisms of slag-microbe interactions in soil and how these slag-microbe interactions can affect crop yield, greenhouse gas emissions, soil carbon sequestration, and heavy metal stabilization in contaminated soils. In addition, we discuss the problems and environmental concerns in using slag in agriculture. Emphasis has been given for further research to validate the proposed mechanisms associated with slag-microbe interactions for increasing soil quality, crop productivity, and mitigating environmental consequences. While evaluating the slag amendment, effects on agriculture and environment, the potential risks, socio-economics, techno-economics, and ethics should be assessed.

The gut virome: the 'missing link' between gut bacteria and host immunity?

The human gut virome includes a diverse collection of viruses that infect our own cells as well as other commensal organisms, directly impacting on our well-being. Despite its predominance, the virome remains one of the least understood components of the gut microbiota, with appropriate analysis toolkits still in development. Based on its interconnectivity with all living cells, it is clear that the virome cannot be studied in isolation. Here we review the current understanding of the human gut virome, specifically in relation to other constituents of the microbiome, its evolution and life-long association with its host, and our current understanding in the context of inflammatory bowel disease and associated therapies. We propose that the gut virome and the gut bacterial microbiome share similar trajectories and interact in both health and disease and that future microbiota studies should in parallel characterize the gut virome to uncover its role in health and disease.

Postharvest Supply Chain with Microbial Travelers: a Farm-to-Retail Microbial Simulation and Visualization Framework

Fresh produce supply chains present variable and diverse conditions that are relevant to food quality and safety because they may favor microbial growth and survival following contamination. This study presents the development of a simulation and visualization framework to model microbial dynamics on fresh produce moving through postharvest supply chain processes. The postharvest supply chain with microbial travelers (PSCMT) tool provides a modular process modeling approach and graphical user interface to visualize microbial populations and evaluate practices specific to any fresh produce supply chain. The resulting modeling tool was validated with empirical data from an observed tomato supply chain from Mexico to the United States, including the packinghouse, distribution center, and supermarket locations, as an illustrative case study. Due to data limitations, a model-fitting exercise was conducted to demonstrate the calibration of model parameter ranges for microbial indicator populations, i.e., mesophilic aerobic microorganisms (quantified by aerobic plate count and here termed APC) and total coliforms (TC). Exploration and analysis of the parameter space refined appropriate parameter ranges and revealed influential parameters for supermarket indicator microorganism levels on tomatoes. Partial rank correlation coefficient analysis determined that APC levels in supermarkets were most influenced by removal due to spray water washing and microbial growth on the tomato surface at postharvest locations, while TC levels were most influenced by growth on the tomato surface at postharvest locations. Overall, this detailed mechanistic dynamic model of microbial behavior is a unique modeling tool that complements empirical data and visualizes how postharvest supply chain practices influence the fate of microbial contamination on fresh produce.IMPORTANCE Preventing the contamination of fresh produce with foodborne pathogens present in the environment during production and postharvest handling is an important food safety goal. Since studying foodborne pathogens in the environment is a complex and costly endeavor, computer simulation models can help to understand and visualize microorganism behavior resulting from supply chain activities. The postharvest supply chain with microbial travelers (PSCMT) model, presented here, provides a unique tool for postharvest supply chain simulations to evaluate microbial contamination. The tool was validated through modeling an observed tomato supply chain. Visualization of dynamic contamination levels from harvest to the supermarket and analysis of the model parameters highlighted critical points where intervention may prevent microbial levels sufficient to cause foodborne illness. The PSCMT model framework and simulation results support ongoing postharvest research and interventions to improve understanding and control of fresh produce contamination.

Microbial Dynamics during Industrial Rearing, Processing, and Storage of Tropical House Crickets (Gryllodes sigillatus) for Human Consumption

In this study, the microbiota during industrial rearing, processing, and storage of the edible tropical house cricket, Gryllodes sigillatus, was investigated. To this end, we analyzed samples from the cricket feed, obtained before feeding as well as from the cages, and from the crickets during rearing, after harvest, and after processing into frozen, oven-dried, and smoked and oven-dried (smoked/dried) end products. Although the feed contained lower microbial numbers than the crickets, both were dominated by the same species-level operational taxonomic units, as determined by Illumina MiSeq sequencing. They corresponded, among others, to members of Porphyromonadaceae, Fusobacterium, Parabacteroides, and Erwinia The harvested crickets contained high microbial numbers, but none of the investigated food pathogens Salmonella spp., Listeria monocytogenes, Bacillus cereus, or coagulase-positive staphylococci. However, some possible mycotoxin-producing fungi were isolated from the crickets. A postharvest heat treatment, shortly boiling the crickets, reduced microbial numbers, but an endospore load of 2.4 log CFU/g remained. After processing, an increase in microbial counts was observed for the dried and smoked/dried crickets. Additionally, in the smoked/dried crickets, a high abundance of a Bacillus sp. was observed. Considering the possible occurrence of food-pathogenic species from this genus, it is advised to apply a heat treatment which is sufficient to eliminate spores. Nevertheless, the microbial numbers remained constant over a 6-month storage period, whether frozen (frozen end product) or at ambient temperature (oven-dried and smoked/dried end products).IMPORTANCE The need for sustainable protein sources has led to the emergence of a new food sector, producing and processing edible insects into foods. However, insight into the microbial quality of this new food and into the microbial dynamics during rearing, processing, and storage of edible insects is still limited. Samples monitored for their microbiota were obtained in this study from an industrial rearing and processing cycle. The results lead first to the identification of process steps which are critical for microbial food safety. Second, they can be used in the construction of a Hazard Analysis and Critical Control Points (HACCP) plan and of a Novel Food dossier, which is required in Europe for edible insects. Finally, they confirm the shelf-life period which was determined by the rearer.

Evaluating Monitoring Strategies to Detect Precipitation-Induced Microbial Contamination Events in Karstic Springs Used for Drinking Water

Monitoring of microbial drinking water quality is a key component for ensuring safety and understanding risk, but conventional monitoring strategies are typically based on low sampling frequencies (e.g., quarterly or monthly). This is of concern because many drinking water sources, such as karstic springs are often subject to changes in bacterial concentrations on much shorter time scales (e.g., hours to days), for example after precipitation events. Microbial contamination events are crucial from a risk assessment perspective and should therefore be targeted by monitoring strategies to establish both the frequency of their occurrence and the magnitude of bacterial peak concentrations. In this study we used monitoring data from two specific karstic springs. We assessed the performance of conventional monitoring based on historical records and tested a number of alternative strategies based on a high-resolution data set of bacterial concentrations in spring water collected with online flow cytometry (FCM). We quantified the effect of increasing sampling frequency and found that for the specific case studied, at least bi-weekly sampling would be needed to detect precipitation events with a probability of >90%. We then proposed an optimized monitoring strategy with three targeted samples per event, triggered by precipitation measurements. This approach is more effective and efficient than simply increasing overall sampling frequency. It would enable the water utility to (1) analyze any relevant event and (2) limit median underestimation of peak concentrations to approximately 10%. We conclude with a generalized perspective on sampling optimization and argue that the assessment of short-term dynamics causing microbial peak loads initially requires increased sampling/analysis efforts, but can be optimized subsequently to account for limited resources. This offers water utilities and public health authorities systematic ways to evaluate and optimize their current monitoring strategies.

Microbes and Diet-Induced Obesity: Fast, Cheap, and Out of Control

Here I revisit our early experiments published in Cell Host & Microbe (Turnbaugh et al., 2008) showing that a diet rich in fat and simple sugars alters the gut microbiome in a manner that contributes to host adiposity, and reflect upon the remarkable advances and remaining challenges in this field.

The Biodiversity of the Microbiota Producing Heat-Resistant Enzymes Responsible for Spoilage in Processed Bovine Milk and Dairy Products

Raw bovine milk is highly nutritious as well as pH-neutral, providing the ideal conditions for microbial growth. The microbiota of raw milk is diverse and originates from several sources of contamination including the external udder surface, milking equipment, air, water, feed, grass, feces, and soil. Many bacterial and fungal species can be found in raw milk. The autochthonous microbiota of raw milk immediately after milking generally comprises lactic acid bacteria such as Lactococcus, Lactobacillus, Streptococcus, and Leuconostoc species, which are technologically important for the dairy industry, although they do occasionally cause spoilage of dairy products. Differences in milking practices and storage conditions on each continent, country and region result in variable microbial population structures in raw milk. Raw milk is usually stored at cold temperatures, e.g., about 4°C before processing to reduce the growth of most bacteria. However, psychrotrophic bacteria can proliferate and contribute to spoilage of ultra-high temperature (UHT) treated and sterilized milk and other dairy products with a long shelf life due to their ability to produce extracellular heat resistant enzymes such as peptidases and lipases. Worldwide, species of Pseudomonas, with the ability to produce these spoilage enzymes, are the most common contaminants isolated from cold raw milk although other genera such as Serratia are also reported as important milk spoilers, while for others more research is needed on the heat resistance of the spoilage enzymes produced. The residual activity of extracellular enzymes after high heat treatment may lead to technological problems (off flavors, physico-chemical instability) during the shelf life of milk and dairy products. This review covers the contamination patterns of cold raw milk in several parts of the world, the growth potential of psychrotrophic bacteria, their ability to produce extracellular heat-resistant enzymes and the consequences for dairy products with a long shelf life. This problem is of increasing importance because of the large worldwide trade in fluid milk and milk powder.

Seasonal dynamics of extremely halophilic microbial communities in three Argentinian salterns

Seasonal sampling was carried out at three Argentinian salterns, Salitral Negro (SN), Colorada Grande (CG) and Guatraché (G), to analyze abiotic parameters and microbial diversity and dynamics. Microbial assemblages were correlated to environmental factors by statistical analyses. Principal component analysis of the environmental data grouped SN and CG samples separately from G samples owing to G's higher pH values and sulfate concentration. Differences in microbial assemblages were also found. Many archaeal sequences belonged to uncultured members of Haloquadratum and Haloquadratum-related genera, with different environmental optima. Notably, nearly half of the archaeal sequences were affiliated to the recently described 'Candidatus Haloredividus' (phylum Nanohaloarchaeota), not previously detected in salt-saturated environments. Most bacterial sequences belonged to Salinibacter representatives, while sequences affiliated to the recently described genus Spiribacter were also found. Seasonal analysis showed at least 40% of the microbiota from the three salterns was prevalent through the year, indicating they are well adapted to environmental fluctuations. On the other hand, a minority of archaeal and bacterial sequences were found to be seasonally distributed. Five viral morphotypes and also eukaryal predators were detected, suggesting different mechanisms for controlling prokaryotic numbers. Notably, Guatraché was the saltern that harbored the highest virus-to-cell ratios reported to date for hypersaline environments.

Chemical dispersants can suppress the activity of natural oil-degrading microorganisms

During the Deepwater Horizon oil well blowout in the Gulf of Mexico, the application of 7 million liters of chemical dispersants aimed to stimulate microbial crude oil degradation by increasing the bioavailability of oil compounds. However, the effects of dispersants on oil biodegradation rates are debated. In laboratory experiments, we simulated environmental conditions comparable to the hydrocarbon-rich, 1,100 m deep plume that formed during the Deepwater Horizon discharge. The presence of dispersant significantly altered the microbial community composition through selection for potential dispersant-degrading Colwellia, which also bloomed in situ in Gulf deep waters during the discharge. In contrast, oil addition to deepwater samples in the absence of dispersant stimulated growth of natural hydrocarbon-degrading Marinobacter. In these deepwater microcosm experiments, dispersants did not enhance heterotrophic microbial activity or hydrocarbon oxidation rates. An experiment with surface seawater from an anthropogenically derived oil slick corroborated the deepwater microcosm results as inhibition of hydrocarbon turnover was observed in the presence of dispersants, suggesting that the microcosm findings are broadly applicable across marine habitats. Extrapolating this comprehensive dataset to real world scenarios questions whether dispersants stimulate microbial oil degradation in deep ocean waters and instead highlights that dispersants can exert a negative effect on microbial hydrocarbon degradation rates.

Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life

BACKGROUND

The premature infant gut has low individual but high inter-individual microbial diversity compared with adults. Based on prior 16S rRNA gene surveys, many species from this environment are expected to be similar to those previously detected in the human microbiota. However, the level of genomic novelty and metabolic variation of strains found in the infant gut remains relatively unexplored.

RESULTS

To study the stability and function of early microbial colonizers of the premature infant gut, nine stool samples were taken during the third week of life of a premature male infant delivered via Caesarean section. Metagenomic sequences were assembled and binned into near-complete and partial genomes, enabling strain-level genomic analysis of the microbial community.We reconstructed eleven near-complete and six partial bacterial genomes representative of the key members of the microbial community. Twelve of these genomes share >90% putative ortholog amino acid identity with reference genomes. Manual curation of the assembly of one particularly novel genome resulted in the first essentially complete genome sequence (in three pieces, the order of which could not be determined due to a repeat) for Varibaculum cambriense (strain Dora), a medically relevant species that has been implicated in abscess formation.During the period studied, the microbial community undergoes a compositional shift, in which obligate anaerobes (fermenters) overtake Escherichia coli as the most abundant species. Other species remain stable, probably due to their ability to either respire anaerobically or grow by fermentation, and their capacity to tolerate fluctuating levels of oxygen. Metabolic predictions for V. cambriense suggest that, like other members of the microbial community, this organism is able to process various sugar substrates and make use of multiple different electron acceptors during anaerobic respiration. Genome comparisons within the family Actinomycetaceae reveal important differences related to respiratory metabolism and motility.

CONCLUSIONS

Genome-based analysis provided direct insight into strain-specific potential for anaerobic respiration and yielded the first genome for the genus Varibaculum. Importantly, comparison of these de novo assembled genomes with closely related isolate genomes supported the accuracy of the metagenomic methodology. Over a one-week period, the early gut microbial community transitioned to a community with a higher representation of obligate anaerobes, emphasizing both taxonomic and metabolic instability during colonization.

Long-term effect of mineral fertilizers and amendments on microbial dynamics in an alfisol of Western Himalayas

The microbial dynamics expressed in terms of culturable microbial populations i.e. bacteria, fungi, actinomycetes and Azotobacter were measured after 33 years of continuous application of mineral fertilizers and amendments to an acid alfisol. The bacterial, fungal and Azotobacter populations were maximum in plots treated with mineral fertilizers and FYM (100%NPK+FYM) while actinomycetes population was maximum in mineral fertilizes and lime treated plots (100%NPK+Lime). The bacterial population decreased and fungal population increased with increasing levels of NPK i.e. from 50% to 150%NPK. Bacillus species of bacteria and Gliocladium, Aspergillus and Rhizopus species of fungi were the main dominating culturable microorganisms in all the treatments. The FYM and lime amended plots sustained crop productivity and microbial populations at higher levels than rest of the mineral fertilizer treatments. The nitrogenous fertilizers alone had the most deleterious effect on crop productivity and the biological soil environment.