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Kombucha is a fermented tea with a combination of yeast and bacteria. Kombucha teas may have a variable microbiota based on geographic origin and cultural conditions. The microbial flora of kombucha has been studied with culture-dependent methods. But, the improvement of the metataxonomic approach has broadened our perspective on fermented foods. In this study, a kombucha mother was procured from an artisanal supplier in Türkiye. High-throughput new-generation sequencing (16S rRNA and Internal Transcribed Spacer (ITS)) was carried out to investigate the microbial communities of kombucha after 7 days of fermentation in both liquid tea (L) and pellicle (P). Microbial counts, pH (4.42 ± 0.01 and 3.50 ± 0.02), and TA% (0.26 ± 0.02 and 0.60 ± 0.04) were also detected on the first and 7th days of fermentation. According to metataxonomic results, the dominant bacteria were Komagataeibacter obediens (%21.13), an acetic acid-producing bacteria, and the dominant fungal genus was Pichia kudriavzevii (64.35%) in L while Romboutsia sp. CE17 was the dominant bacteria (7%) and Pichia kudriavzevii was also the dominant yeast in P. This study also revealed different species which were not common in kombucha including propionic acid and butyric acid-producing bacteria such as Anaerotignum propionicum and Butyrivibrio fibrisolvens, a butyrivibriocin producing bacteria. Accordingly, different yeast species were detected such as Tetrapisispora phaffii and Ogataea polimorpha. [ABSTRACT FROM AUTHOR]

The human body immune system, metabolism and homeostasis are affected by microbes. Dysbiosis occurs when the homeostatic equilibrium is disrupted due to an alteration in the normal microbiota of the intestine. Dysbiosis can cause cancer, and also affect a patient's ability to respond to treatment. Metataxonomics seeks to identify the bacteria present in a biological sample, based on the sequencing of the 16S rRNA genetic marker. Precision medicine attempts to find relationships between the microbiota and the risk of acquiring cancer, and design new therapies targeting bacteria. Flexible and portable bioinformatic pipelines are necessary to be able to bring metataxonomics to the clinical field, which allow groups of biological samples to be classified according to their diversity in the microbiota. With this aim we implemented Metatax, a new pipeline to analyze biological samples based on 16S rRNA gene sequencing. The results obtained with our pipeline should complement those obtained by sequencing a patient's DNA and RNA, in addition to clinical data, to improve knowledge of the possible reasons for a disease or a worse response to treatment. [ABSTRACT FROM AUTHOR]

Purpose: To compare bacteria recovered by standard cultures and metataxonomics, particularly with regard to ventilator-associated pneumonia (VAP) pathogens, and to determine if the presence of particular bacteria or microbiota in tracheal and oropharyngeal secretions during the course of intubation was associated with the development of VAP.Methods: In this case-control study, oropharyngeal secretions and endotracheal aspirate were collected daily in mechanically ventilated patients. Culture and metataxonomics (16S rRNA gene-based taxonomic profiling of bacterial communities) were performed on serial upper respiratory samples from patients with late-onset definite VAP and their respective controls.Results: Metataxonomic analyses showed that a low relative abundance of Bacilli at the time of intubation in the oropharyngeal secretions was strongly associated with the subsequent development of VAP. On the day of VAP, the quantity of human and bacterial DNA in both tracheal and oropharyngeal secretions was significantly higher in patients with VAP than in matched controls with similar ventilation times. Molecular techniques identified the pathogen(s) of VAP found by culture, but also many more bacteria, classically difficult to culture, such as Mycoplasma spp. and anaerobes.Conclusions: Molecular analyses of respiratory specimens identified markers associated with the development of VAP, as well as important differences in the taxa abundance between VAP and controls. Further prospective trials are needed to test the predictive value of these markers, as well as the relevance of uncultured bacteria in the pathogenesis of VAP. [ABSTRACT FROM AUTHOR]

Although the diversity of microbial communities (microbiota) inhabiting body niches are of proven importance to health in both humans and non-human animals, the functional importance of these collective genomes (microbiome) to the adaptive potential of their hosts has only recently been considered within a conservation framework. If loss of gut biodiversity threatens the health (and therefore the fitness of individuals), and this loss can be correlated with the adaptive potential of a species in changing environments, measuring functional composition of the microbiota from non-invasive samples, such as faeces and skin swabs, could provide a useful and practical tool for determining conservation priorities. This article reviews the evidence for adaptive potential of microbiota in wild species, and proposes future directions. While there is ample indication of inter- and intra-specific variation in microbiota diversity, there is little evidence that diversity per se confers fitness. However, there are convincing examples showing that microbiota flexibility, composition and function may well be sources of adaptive potential, although case studies are relatively few, and the analytical approaches needed to demonstrate the mechanisms underlying host-microbiota interactions have only recently been developed. [ABSTRACT FROM AUTHOR]

One benefit of animal-mediated seed dispersal is that dispersers may deposit the seeds in protected or enriched microhabitats favorable for seedling survival. Ants are a common seed disperser, and seeds deposited in soils occupied by ant colonies have higher germination and survival rates, benefits attributed to enriched soil conditions and protection from seed predators and fire. Fungal pathogens also devastate young plants, and fungal protection may be an additional benefit of ant-mediated seed dispersal. Ants secrete anti-microbial compounds that appear to suppress the spread of fungal and bacterial diseases in ant colonies, and they confer fungal pathogen protection to the seeds they handle. If fungal protection is a potential benefit of ant-mediated dispersal, we expected that ant-occupied soil (soils inhabited by ants for colony nesting) would contain fewer phytopathogenic fungi than proximate soils without ant nests. We tested this hypothesis with ant soils from the Aphaenogaster rudis complex; the dominant seed-dispersing ants in eastern deciduous forests. We investigated published Aphaenogaster soil fungi data and conducted our own metataxonomic analysis of ant-occupied and unoccupied soils to identify phytopathogenic fungi and investigate whether ant colony presence corresponds with reduced plant fungal pathogens in the soil. We found reduced phytopathogenic fungi presence and richness in soils containing ant colonies as compared to nearby control soils indicating that the presence of ant colonies was concomitant with a reduction in plant pathogens. Ant chemical secretions protect colonies from microbial pathogens in the crowded, moist nest conditions. Plant seeds also thrive in these locations and environments, where they are subject to phytopathogenic fungi. Multiple hypotheses explain the benefits ant-mediated seed dispersal provides plants, but heretofore, fungal protection has been suggested, but not tested. Soil occupation by ants corresponds to phytopathogenic fungi declines, which have the potential to benefit plants. [ABSTRACT FROM AUTHOR]

The study of the food microbiome has gained considerable interest in recent years, mainly due to the wide range of applications that can be derived from the analysis of metagenomes. Among these applications, it is worth mentioning the possibility of using metagenomic analyses to determine food authenticity, to assess the microbiological safety of foods thanks to the detection and tracking of pathogens, antibiotic resistance genes and other undesirable traits, as well to identify the microorganisms responsible for food processing defects. Metataxonomics and metagenomics are currently the gold standard methodologies to explore the full potential of metagenomes in the food industry. However, there are still a number of challenges that must be solved in order to implement these methods routinely in food chain monitoring, and for the regulatory agencies to take them into account in their opinions. These challenges include the difficulties of analysing foods and food-related environments with a low microbial load, the lack of validated bioinformatics pipelines adapted to food microbiomes and the difficulty of assessing the viability of the detected microorganisms. This review summarizes the methods of microbiome analysis that have been used, so far, in foods and food-related environments, with a specific focus on those involving Next-Generation Sequencing technologies., (© 2021. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)