Metataxonomic Analysis Research Articles

Journey to the morpho-textural traits, microbiota, and volatilome of Ciauscolo PGI salami

Two independent manufacturing batches of naturally fermented Ciauscolo PGI salami were studied from the day of production to the end of ripening (20 days). The microbiota compositional shift of samples was studied through culture-dependent and metataxonomic analysis. Analyses of physico-chemical, morpho-textural, and volatilome traits were also carried out. Latilacobacillussakei was the dominant species from t5, together with Dellaglioa algida and Leuconostoc carnosum. Among eumycetes, Cladosporium cladosporioides, Debaryomyces hansenii, Kurtzmaniella zeylanoides, and Malassezia restricta/globosa were the most abundant taxa occurring in all samples. Candidate starter or adjunct cultures of Lat. sakei were isolated and characterized for: i) acidification performance; ii) enzymatic activity; iii) production of exopolysaccharides; iv) production of bacteriocins; v) quantification of the hdcA gene of Gram-positive bacteria. The 44 Lat. sakei cultures showed a suitable acid production capacity, together with the capability to cope with the main environmental stresses occurring in fermented sausages. For most of the isolates, strong aminopeptidase activity (leucine arylamidase and the valine arylamidase) was observed. Moreover, the majority of isolates showed the in vitro production of sucrose-dependent exopolysaccharides. No Lat. sakei isolates positive for the hdcA gene were observed. Based on these evidences, a few candidate starter or adjunct cultures, with potential use for product safety and quality improvement, were highlighted, namely Lat. sakei C5, C7, C11, C31, C45, C48, C53, C55, and C60. In the analyzed Ciauscolo PGI samples, 53 volatile substances were fully or tentatively identified; among these, spices-derived components (black pepper and garlic cloves) were constantly detected throughout the whole ripening time.

The Microbial Terroir of the Nemea Zone Agiorgitiko cv.: A First Metataxonomic Approach

Vitis vinifera L. cv. Agiorgitiko is one of the most popular indigenous wine grape varieties in Greece, cultivated almost exclusively in the Nemea Protected Designation of Origin (PDO) zone. Here, the microbiota of soil, grapes, and wine, during controlled (CF) and spontaneous (SF) fermentations of Agiorgitko cv. from three vineyards in the PDO Nemea zone were explored, using both classical microbiological analysis and metataxonomics to get evidence about the microbial terroir of the PDO Nemea zone. The classical microbiological analysis revealed higher total mesophilic counts in soil, while in both grapes and wine samples, yeasts prevailed. Lactic acid bacteria and acetic acid bacteria counts were lower in grapes compared to wine and soil. Metataxonomic analysis revealed that, regarding yeasts/fungi, genera Fusarium, Sarea, and Alternaria dominated in soil; Aureobasidium, Cladosporium, and Penicillium in grapes; Saccharomyces in wine during CF; and Hanseniaspora and Saccharomyces in wine during SF. Regarding bacteria, genera Skermanella, Acidobacterium, and Ohtaekwangia dominated in soil, Sphingomonas, Micrococcus, and Rubrobacter in grapes, while Tatumella, Alcanivorax, and Komagateibacter in wine during both CF and SF. Finally, the factors that significantly influence the microbiota of soil, grapes, and wine samples were assessed, and potential microbial biomarkers were identified for the first time in a Greek grape variety.

Bacillus subtilis KM0 Impacts gut Microbiota Profile and Transcription of Genes Related to Transcellular Transport in Zebrafish (Danio rerio).

It is known that probiotic microorganisms play important roles in the composition of the intestinal microbiota. Also, probiotics can affect the paracellular and transcellular transport mechanisms performed by intestinal cells. The aim of this work was to evaluate the effect of the potential probiotic Bacillus subtilis KM0 on the profile of the gut microbiota and transcription of genes related to intestinal transport of zebrafish (Danio rerio). Zebrafish was exposed by immersion to B. subtilis KM0 for 48h, and the intestines were collected for metataxonomic analysis and transcription of genes related to transcellular and paracellular transports. Although exposure to B. subtilis changed the intestinal microbiota profile of zebrafish, the diversity indices were not altered. A decrease in the number of genera of potentially pathogenic bacteria (Flavobacterium, Plesiomonas, and Pseudomonas) and downregulation in transcription of transcellular transport genes (cubn and amn) were observed. B. subtilis KM0 strain had the expected probiotic effect, by interfering with the proliferation of potentially pathogenic bacteria and decreasing the transcription of genes codifying for signals involved with a mechanism that can be used for invasion by pathogens. The present study demonstrated that, even with a short-term exposure, a bacterium with probiotic potential such as the KM0 strain of B. subtilis can modify the profile of the host's intestinal microbiota, with an impact on the regulation of intestinal genes related to mechanisms that can be used for invasion by pathogenic bacteria.

Lactobacillus gasseri LG-G12 Restores Gut Microbiota and Intestinal Health in Obesity Mice on Ceftriaxone Therapy

Gut microbiota imbalance is associated with the occurrence of metabolic diseases such as obesity. Thus, its modulation is a promising strategy to restore gut microbiota and improve intestinal health in the obese. This paper examines the role of probiotics, antimicrobials, and diet in modulating gut microbiota and improving intestinal health. Accordingly, obesity was induced in C57BL/6J mice, after which they were redistributed and fed with an obesogenic diet (intervention A) or standard AIN-93 diet (intervention B). Concomitantly, all the groups underwent a treatment phase with Lactobacillus gasseri LG-G12, ceftriaxone, or ceftriaxone followed by L. gasseri LG-G12. At the end of the experimental period, the following analysis was conducted: metataxonomic analysis, functional profiling of gut microbiota, intestinal permeability, and caecal concentration of short-chain fatty acids. High-fat diet impaired bacterial diversity/richness, which was counteracted in association with L. gasseri LG-G12 and the AIN-93 diet. Additionally, SCFA-producing bacteria were negatively correlated with high intestinal permeability parameters, which was further confirmed via functional profile prediction of the gut microbiota. A novel perspective on anti-obesity probiotics is presented by these findings based on the improvement of intestinal health irrespective of undergoing antimicrobial therapy or not.

First insights into the gut microbiome of Diatraea saccharalis: From a sugarcane pest to a reservoir of new bacteria with biotechnological potential

A country’s biodiversity is a key resource for the development of a sustainable bioeconomy. However, often the most biodiverse countries on the planet hardly profit from their biological diversity. On the contrary, occasionally components of that biodiversity become a threat to society and its food sustainability. That is the case of the sugarcane borer Diatraea saccharalis. Here, the analysis of the bacteria associated with the digestive tract of D. saccharalis reveals a rich and diverse microbiota. Two types of diets were analyzed under laboratory conditions. The metataxonomic analysis revealed a number of taxa common to most of the larval pools analyzed with relative abundances exceeding 5%, and five families of bacteria which have also been reported in the gut of another Lepidoptera. A large fraction of microorganisms detected by amplicon sequencing were considered to be rare and difficult to cultivate. However, among the cultivable microorganisms, 12 strains with relevant biotechnological features were identified. The strain that showed the highest cellulolytic activity (GCEP-101) was genome sequenced. The analysis of the GCEP-101 complete genome revealed that the values of 16S rRNA identity, the Average Nucleotide Identity, and the digital DNA–DNA hybridization place the strain as a candidate for a new species within the genus Pseudomonas. Moreover, the genome annotation of the putative new species evidenced the presence of genes associated with cellulose degradation, revealing the hidden potential of the pest as a reservoir of biotechnologically relevant microorganisms.

Lactic acid bacteria in cow raw milk for cheese production: Which and how many?

Lactic Acid Bacteria (LAB) exert a fundamental activity in cheese production, as starter LAB in curd acidification, or non-starter LAB (NSLAB) during ripening, in particular in flavor formation. NSLAB originate from the farm and dairy environment, becoming natural contaminants of raw milk where they are present in very low concentrations. Afterward, throughout the different cheesemaking processes, they withstand chemical and physical stresses becoming dominant in ripened cheeses. However, despite a great body of knowledge is available in the literature about NSLAB effect on cheese ripening, the investigations regarding their presence and abundance in raw milk are still poor. With the aim to answer the initial question: "which and how many LAB are present in cow raw milk used for cheese production?," this review has been divided in two main parts. The first one gives an overview of LAB presence in the complex microbiota of raw milk through the meta-analysis of recent taxonomic studies. In the second part, we present a collection of data about LAB quantification in raw milk by culture-dependent analysis, retrieved through a systematic review. Essentially, the revision of data obtained by plate counts on selective agar media showed an average higher concentration of coccoid LAB than lactobacilli, which was found to be consistent with meta-taxonomic analysis. The advantages of the impedometric technique applied to the quantification of LAB in raw milk were also briefly discussed with a focus on the statistical significance of the obtainable data. Furthermore, this approach was also found to be more accurate in highlighting that microorganisms other than LAB are the major component of raw milk. Nevertheless, the variability of the results observed in the studies based on the same counting methodology, highlights that different sampling methods, as well as the "history" of milk before analysis, are variables of great importance that need to be considered in raw milk analysis.

Beehives possess their own distinct microbiomes

BackgroundHoneybees use plant material to manufacture their own food. These insect pollinators visit flowers repeatedly to collect nectar and pollen, which are shared with other hive bees to produce honey and beebread. While producing these products, beehives accumulate a considerable number of microbes, including bacteria that derive from plants and different parts of the honeybees’ body. Whether bacteria form similar communities amongst beehives, even if located in close proximity, is an ecologically important question that has been addressed in this study. Specific ecological factors such as the surrounding environment and the beekeeping methods used can shape the microbiome of the beehive as a whole, and eventually influence the health of the honeybees and their ecosystem.ResultsWe conducted 16S rRNA meta-taxonomic analysis on honey and beebread samples that were collected from 15 apiaries in the southeast of England to quantify the bacteria associated with different beehives. We observed that honeybee products carry a significant variety of bacterial groups that comprise bee commensals, environmental bacteria and symbionts and pathogens of plants and animals. Remarkably, this bacterial diversity differs not only amongst apiaries, but also between the beehives of the same apiary. In particular, the levels of the bee commensals varied significantly, and their fluctuations correlated with the presence of different environmental bacteria and various apiculture practices.ConclusionsOur results show that every hive possesses their own distinct microbiome and that this very defined fingerprint is affected by multiple factors such as the nectar and pollen gathered from local plants, the management of the apiaries and the bacterial communities living around the beehives. Based on our findings, we suggest that the microbiome of beehives could be used as a valuable biosensor informing of the health of the honeybees and their surrounding environment.

Queijo Serra da Estrela PDO Cheese: Investigation into Its Morpho-Textural Traits, Microbiota, and Volatilome.

Queijo Serra da Estrela is a PDO Portuguese cheese produced through coagulation of raw ewe’s milk using cardoon (Cynara cardunculus L.) flowers. The present research was aimed at depicting an up-to-date and comprehensive overview of the microbiota of Queijo Serra da Estrela cheese. To this end, viable counting and metataxonomic analysis were carried out on cheeses sampled from four Portuguese artisan producers. Physico-chemical and morpho-textural analyses were also performed, together with the analysis of volatile organic compounds (VOCs). Finally, non-starter lactic acid bacteria (NSLAB) isolated from the cheeses were characterized for their enzymatic activities using a semi-quantitative method. According to the metataxonomic analysis, Lactococcus lactis and Lactococcus piscium were the species occurring at the highest relative abundance. The isolates collected from the cheeses were assigned to Enterococcus durans, Enterococcus faecalis, Enterococcus faecium, Enterococcus lactis, Levilactobacillus brevis, Latilactobacillus graminis, Leuconostoc mesenteroides, and the Lacticaseibacillus casei group. The enzymatic characterization of these cultures highlighted esterase, aminopeptidase, acid phosphatase, beta-galactosidase, alpha-glucosidase, and beta-glucosidase among the major enzymatic activities. Fungal populations were dominated by Debaryomyces hansenii and Kurtzmaniella zeylanoides; however, species rarely found in cheese (e.g., Candida boidinii, Vishniacozyma victoriae, and Starmerella) were also detected. The volatile compounds characterizing the analyzed cheeses were carboxylic acids and esters, followed by carbonyl compounds and alcohols.

Metataxonomic and metaproteomic profiling of the oral microbiome in oral lichen planus - a pilot study

ABSTRACT Background A growing body of evidence demonstrates a different bacterial composition in the oral cavity of patients with oral lichen planus (OLP). Patients and methods Buccal swab samples were collected from affected and non-affected sites of six patients with reticular OLP and the healthy oral mucosa of six control subjects. 16S rRNA gene MiSeq sequencing and mass spectrometry-based proteomics were utilised to identify the metataxonomic and metaproteomic profiles of the oral microbiome in both groups. Results From the metataxonomic analysis, the most abundant species in the three subgroups were Streptococcus oralis and Pseudomonas aeruginosa, accounting for up to 70% of the total population. Principal Coordinates Analysis showed differential clustering of samples from the healthy and OLP groups. ANCOM-BC compositional analysis revealed multiple species (including P. aeruginosa and several species of Veillonella, Prevotella, Streptococcus and Neisseria) significantly over-represented in the control group and several (including Granulicatella elegans, Gemella haemolysans and G. parahaemolysans) in patients with OLP. The metaproteomic data were generally congruent and revealed that several Gemella haemolysans-belonging peptidases and other proteins with inflammatory and virulence potential were present in OLP lesions. Conclusion Our data suggest that several bacterial species are associated with OLP. Future studies with larger cohorts should be conducted to determine their role in the aetiology of OLP and evaluate their potential as disease biomarkers.

Administration of Ligilactobacillus salivarius CECT 30632 to elderly during the COVID-19 pandemic: Nasal and fecal metataxonomic analysis and fatty acid profiling.

Elderly was the most affected population during the first COVID-19 and those living in nursing homes represented the most vulnerable group, with high mortality rates, until vaccines became available. In a previous article, we presented an open-label trial showing the beneficial effect of the strain Ligilactobacillus salivarius CECT 30632 (previously known as L. salivarius MP101) on the functional and nutritional status, and on the nasal and fecal inflammatory profiles of elderly residing in a nursing home highly affected by the pandemic. The objective of this post-hoc analysis was to elucidate if there were changes in the nasal and fecal bacteriomes of a subset of these patients as a result of the administration of the strain for 4 months and, also, its impact on their fecal fatty acids profiles. Culture-based methods showed that, while L. salivarius (species level) could not be detected in any of the fecal samples at day 0, L. salivarius CECT 30632 (strain level) was present in all the recruited people at day 120. Paradoxically, the increase in the L. salivarius counts was not reflected in changes in the metataxonomic analysis of the nasal and fecal samples or in changes in the fatty acid profiles in the fecal samples of the recruited people. Overall, our results indicate that L. salivarius CECT 30632 colonized, at least temporarily, the intestinal tract of the recruited elderly and may have contributed to improvements in their functional, nutritional, and immunological status, without changing the general structure of their nasal and fecal bacteriomes when assessed at the genus level. They also suggest the ability of low abundance bacteria to train immunity.

Investigating of the microbial communities in a red circle disease of sea cucumber based on metagenomic sequencing

Diseases in aquaculture restrict the survival and development of Apostichopus japonicus, one of the most important Chinese marine culture species. A novel disease, named "red circle" disease, is frequently observed in sea cucumber seedling ponds and results in the death of sea cucumbers. No information about this disease in A. japonicus is available. In this study, we investigated the whole microbial community structure and predicted microbial functional profiles in "red circle" disease affecting sea cucumbers through metagenomics. Metataxonomic analysis of "red circle" samples showed different domains, namely, bacteria (71.39%), virus (5.11%), archaea (0.15%), eukaryotes (0.06%), and some unclassified microbiota (23.29%). Proteobacteria was the most abundant phylum (42.88%), followed by Bacteroidetes (3.30%), Viruses_noname (3.12%), Verrucomicrobia (2.99%), Planctomycetes (2.67%), and Viruses_unclassified (1.99%). The species belong to genus Vibrio, which accounted for 4.51% of the microbiota. Vibrio alginolyticus was the most abundant species of genus Vibrio in the "red circle" samples, followed by Vibrio diabolicus, Vibrio parahaemolyticus, Vibrio cholerae, and Vibrio tubiashii. Functional analysis of "red circle" samples metagenome revealed the genes for the metabolism and environmental information processing of a wide range of bioactive compounds, including amino acids and carbohydrates. Results of our study provides insight into the "red circle" disease and microbial community in A. japonicus seedling ponds and widens our understanding of this new disease.

Microbiota profile of filleted gilthead seabream (Sparus aurata) during storage at various conditions by 16S rRNA metabarcoding analysis

The aim of the present work was to study the microbiota profile of gilthead seabream (Sparus aurata) fillets stored either aerobically or under Modified Atmosphere Packaging (MAP) conditions at 0, 4, 8 and 12 °C, via 16S rRNA metabarcoding sequencing. Throughout storage, sensory assessment was also applied to estimate fillets’ end of shelf-life. Results indicated that storage conditions strongly influenced the shelf-life of the fillets, since the sensorial attributes of air-stored samples deteriorated earlier than that of MAP-stored fillets, while higher temperatures also contributed to a more rapid products’ end of shelf-life. Metataxonomic analysis indicated that Pseudomonas was by far the dominant genus at the end of fillet’s shelf-life, in the vast majority of treatments, even though a sporadic but noteworthy presence of other genera (e.g, Shewanella, Carnobacterium, Brochothrix etc.) at the middle stages of MAP-stored fillets is also worth mentioning. On the other hand, a completely different profile as well as a more abundant bacterial diversity was observed at the end of shelf-life of MAP-stored fillets at 12 °C, in which Serratia was the most dominant bacterium, followed by Kluyvera, Hafnia, Rahnella and Raoultella, while Pseudomonas was detected in traces. The findings of the present work are very important, providing useful information about the spoilage status of gilthead seabream fillets during several storage conditions, triggering in parallel the need for further studies to enrich the current knowledge and help stakeholders develop innovative strategies that delay the growth of key spoiler players and consequently, retard spoilage course.

Impact of Lactobacillus-originated metabolites on enterohemorrhagic E. coli in rumen fluid.

Rumen is one of the richest microbial ecosystems naturally harboring many zoonotic pathogens. Controlling the colonization of cattle originated zoonotic pathogens in rumen, particularly enterohemorrhagic Escherichia coli (EHEC), is critical in reducing foodborne enteric diseases in humans. In this study, we aimed to inhibit the growth of EHEC in a simulated rumen system with collected rumen fluids (RFs) using live probiotics, synbiotics, and their metabolites. EHEC inoculated RF was treated with live wild type Lactobacillus casei (LCwt), LCwt with 0.5% peanut flour (LCwt+PF), an engineered LC capable of overexpressing linoleate isomerase (LCCLA), and their metabolites collected in cell-free culture supernatants (CFCSwt, CFCSwt+PF, and CFCSCLA) at various time points. A growth stimulatory effect toward Lactobacillus spp. was exerted by all CFCS, while the EHEC was suppressed. Among other treatments only LCwt+PF reduced EHEC by 2.68 logs after 72h. This observation was also supported by metataxonomic analysis. A reduction in Bacteroidetes and Proteobacteria while increase in Firmicutes was observed at 48h by the presence of CFCSs as compared to the control. Our observation implies probiotic-originated metabolites modulate rumen microbiota positively which can be deployed to control the transmission of cattle-borne pathogens specifically EHEC.

Consumers and food safety: Application of metataxonomic analyses and multivariate statistics in order to identify behaviours affecting microbial contaminations in household kitchens

Microbial contamination of the domestic environment can lead to food spoilage, food waste and food-borne illness generating public health concern. The present study was aimed at evaluating: microbiological contamination of domestic refrigerators using both traditional microbiological and metataxonomic methods, linking these results with consumers' characteristics, observed/stated practices in food handling and storage in households. Data were collected by means of an online survey focused on consumer habits and characteristics, and by direct observation of practices, through consumers' kitchens inspections where surface samples from refrigerators (n = 64). Microbiological and metataxononimc analyses on those samples allowed the evaluation of microbial contamination and its composition. Multivariate analysis was applied to the core Amplicon Sequence Variants composition in order to highlight relations between contamination agents and consumer practices. Consumer analysis evaluated correlation among stated/observed practices with respondents' objective knowledge of hygiene practices. Finally, multivariate dimensions derived by genera analysis were used to evaluate the role of consumer characteristics and habits in domestic contamination. The results indicated a low level of contamination. Metataxonomic analysis provided a set of microbial genera, of which, 12 were the main responsible for fridge contaminations. The respondents' objective knowledge of hygiene practices was found to be significantly related to stated practices, whereas there was no significant result in combination with observed ones. Therefore, with limited sample dimension, theoretical knowledge showed a stronger relation to stated practices, whereas it did not always reflect real-life habits. However, the direction of correlations suggests that improving consumer knowledge of good hygiene practices through more practical awareness-raising actions, could reduce food contamination and the risk of food-borne illnesses. Finally, the application of the multivariate analyses allowed the observation of two clusters with different characteristics in terms of genera composition and consumers habits (such as refrigerator's temperature checking and food arrangement in it). Thus, such an innovative approach led to identifying the putative factors which are the most in relation with microbial contamination/general composition of fridges. Nonetheless, the combination of microbiological methods with the social evaluation of consumers could provide useful insights to tackle the causes of food contamination.

Staphylococcus aureus artificially inoculated in mealworm larvae rearing chain for human consumption: Long-term investigation into survival and toxin production

The present research reports the results of a long-term study (70 days) of the dynamics of Staphylococcus aureus artificially inoculated in a Tenebrio molitor rearing chain for human consumption. To this end, a rearing substrate consisting of organic wheat middlings was spiked with S. aureus to obtain three initial contamination levels, namely 1 (low level), 5 (medium level) and 7 (high level) Log colony forming unit per gram. Microbial viable counting coupled with metataxonomic analysis were performed to evaluate: i) the persistence and growth of S. aureus in the rearing substrate; ii) the colonization and growth of S. aureus in the insect larvae; iii) the occurrence and load of S. aureus in the frass (excrement from larvae mixed with substrate residues); iv) the presence of S. aureus enterotoxins in the rearing substrate, frass, and larvae. The results of the present study highlighted that wheat middlings contaminated with S. aureus do not represent a suitable environment for the multiplication of the pathogen, irrespective of the initial contamination level. Of note, frass originated from the larvae reared on contaminated wheat middlings might potentially represent a source of S. aureus, with cell loads depending on the initial contamination level. A complex resident microbiota was revealed by metataxonomic analysis. Interestingly, co-occurrence/co-exclusions analysis did not reveal associations between the target microorganism and the microbiota of wheat middlings, larvae, or frass. Considering safety aspects of larvae, the results overall collected suggested that, under the applied conditions, T. molitor represents an inhospitable or even hostile environment for S. aureus, with this latter showing counts below the detection limit in the larvae at the end of the 70-day rearing trial, irrespective of the initial contamination level. The results also suggested that a combination of bactericidal factors, including unfavorable environmental conditions (such as low aw of wheat middlings and frass), might have established in the rearing chain. Finally, the absence of staphylococcal toxins suggests that, even when S. aureus is present at high contamination levels, it is not able to produce toxins in wheat middlings, larvae, or frass.

An observational investigation of the faecal microbiota and metabonome of gastrostomy fed children, on blended and formula diets

ABSTRACT Gastrostomy fed children traditionally have a Formulae diet (FD), which fulfills nutritional requirements; however, many families are adopting Blended diets (BD), which are what the whole family would eat. We undertook an observational investigation of the colonic microbiota and metabonome in a small group of gastrostomy fed children, who were either on an FD or BD, and compared, where possible to their siblings (17 FD, 28 BD, 19 HS). There was no increase in complications in tube blockage or infection rates, but a significant improvement in the prevalence of bowel problems, a reduction in medication and an increase in quality of life. Metataxonomic analysis showed that the FD group was significantly different to the Sibling group, and that families did not cluster together. Whole sample metabonomics showed no differences between groups; however, univariate analysis of biologically important metabolites did differ. Changing to a BD resulted in no increase in complications or risks, but improved the overall quality of life for the children and families.

Impact of Physicochemical Parameters on the Diversity and Distribution of Microbial Communities Associated with Three South African Peatlands.

Peatlands are complex wetland-like ecosystems that harbor diverse microbial communities. In this study, the microbial communities (fungal and actinobacterial) associated with an unimpacted peatland (Vankervelsvlei; VV), an impacted peatland (Goukou River system; GK), and a developing peatland (Nuwejaars River system; NR) were determined through ITS and 16S rRNA metataxonomic analyses. Unidentified Acidimicrobiales dominated in GK and NR, unidentified Intrasporangiaceae and Solirubobacterales in NR, and Corynebacterium, Propionibacterium, and Streptomyces species in VV. The fungal phyla, Ascomycota and Basidiomycota, dominated all three sites, and harbored unique fungal taxa belonging to a wide range of fungal guilds. Physicochemical properties of the peat collected from the three sites were analyzed in association with microbial community structures in order to determine which parameters acted as the main drivers for microbial diversity. BEST analysis (linking microbial diversity patterns to environmental variables) showed that nitrogen (N), aluminum (Al), phosphorus (P), and potassium (K) were the most significant physicochemical drivers of actinobacterial community structure, while iron (Fe) and humification were the environmental parameters that affected the fungal communities the most. In conclusion, this study has provided some insight into the fungal and actinobacterial communities associated with three South African peatlands and the main environmental drivers that influence these communities.

Dynamics of Microbiota in Three Backslopped Liquid Sourdoughs That Were Triggered with the Same Starter Strains

The preparation of sourdough may include the use of starter microorganisms to address the fermentation process toward specific conditions. The aim of this work was to study the dynamics of the microbial ecosystem in three liquid sourdoughs (SD1, SD2 and SD3) triggered with the same microbial strains. Lactiplantibacillus plantarum (formerly known as Lactobacillus plantarum), Saccharomyces cerevisiae and Candida lambica strains were inoculated as starters, and sourdoughs were differentiated for the fermentation conditions and for the method of starter inoculation. The analyses were performed on the three sourdoughs propagated in the laboratory for 22 days and on the sample SD1, which was transferred to a bakery and refreshed over many months. The dynamics of microbial communities were studied by plate-count analysis and metataxonomic approach. The acidity of sourdough was evaluated over time. Metataxonomic analysis highlighted a large heterogeneity of fungi microbiota in all sourdough preparations, many of them probably originated from the flour, being pathogens of plants. Few yeast species were found, and S. cerevisiae was plentiful but did not predominate over the other species, whereas the C. lambica species decreased over time and then disappeared in all preparations. The bacterial microbiota was less heterogeneous than the fungi microbiota; the species L. plantarum, Leuconostoc citreum and Levilactobacillus brevis (formerly known as Lactobacillus brevis) were always present in all sourdoughs, whereas Fructilactobacillus sanfranciscensis (formerly known as Lactobacillus sanfranciscensis) became the dominant species in bakery-propagated SD1 and in SD2 at the end of the propagation period.

Microbiological, morpho-textural, and volatile characterization of Portuguese Queijo de Nisa PDO cheese

Queijo de Nisa PDO (Protected Designation of Origin) is a semi-hard cheese obtained from raw ewe's milk clotted with cardoon (Cynara cardunculus, L.) rennet. The aim of the present study was to characterize the bacterial communities naturally occurring in Queijo de Nisa PDO cheese samples through viable counting and metataxonomic analysis. Moreover, physico-chemical and morpho-textural analyses were also performed, together with the analysis of volatile organic compounds (VOCs) through solid-phase microextraction (SPME) coupled with gas chromatography-mass spectrometry (GC–MS). In the analyzed samples, pH values were comprised between 4.84 and 5.74. As for lactic acid, the concentration varied between 0.83 and 2.10 g 100 g-1. Water activity varied between 0.942 and 0.960. Lightness of the samples ranged from 107.82 to 119.16, whereas hardness ranged between 34.45 N and 126.05 N. As for microbiological analyses, lactococci and lactobacilli counts were up to 9.01 Log CFU g-1. Coagulase-negative cocci and enterococci counts were up to 7 Log CFU g-1. Metataxonomic analysis revealed that Lactococcus lactis and Leuconostoc mesenteroides occurred at high frequency in all the analyzed samples. Moreover, Lactiplantibacillus plantarum, Lactococcus piscium, and Lacticaseibacillus zeae were also detected. The most represented VOCs were carboxylic acids, carbonyl compounds, alcohols, and esters. In the analyzed cheese samples, significant relationships between bacteria and VOCs were also evidenced. Of note, research on the microbiological and chemical features, as well as on morpho-textural characteristics, of Queijo de Nisa PDO cheese can increase the knowledge on the interactions between raw materials, environment, and autochthonous microorganisms, thus enabling protection of biodiversity and tradition.

Microbial dynamics and key sensory traits of laboratory-scale co-fermented green olives (Olea europaea L. cv. Ascolana tenera) and sea fennel (Crithmum maritimum L.)

Table olives (Olea europaea L.) are one of the most important fermented vegetables worldwide, whereas sea fennel (Crithmum maritimum L.) represents an emerging food crop, characterized by interesting nutritional and sensory qualities. Both are characterized by a high concentration of bioactive compounds with health beneficial effects. Thanks to these features, table olives and sea fennel undoubtedly represent two valuable ingredients for the manufacture of innovative vegetable preserves. Given these premises, the present study was aimed at exploring the co-fermentation of green olives and sea fennel to produce laboratory-scale prototypes of innovative high value preserves. To this end, the effects of two recipes, two standard methods for production of table olives, and two fermentation microbiota (resident or inoculated) were assessed. The prototypes were evaluated for their microbial dynamics as well as for key sensory traits by a panel of trained assessors. During the fermentation, all the prototypes showed a progressive pH reduction. Mesophilic lactobacilli, mesophilic lactococci, and yeasts were the main microbial groups at the end of the fermentation, while Enterobacteriaceae decreased during fermentation. Metataxonomic analysis revealed an evolution of the microbiota, with Lactiplantibacillus plantarum dominating in all the prototypes in the late stage of fermentation, irrespective of the recipe, processing method, and starter inoculation. A greater crunchiness and lower fibrousness were perceived in the Greek style prototypes, which were preferred than Spanish style prototypes by trained panelists.