Kefir, a traditional probiotic beverage with significant cultural, social, and health relevance, has garnered increasing scientific interest for its functional properties. Here, we synthesized findings from 14 studies investigating the bacterial and fungal diversity in artisanal cow’s milk kefir through metagenomic analysis. Following the PRISMA guidelines (Preferred Reporting Items for Systematic Reviews and Meta-Analyses), a comprehensive search was conducted in databases including Portal BVS, Scopus, Scielo, and Web of Science. From an initial pool of 522 articles, 14 were selected based on stringent inclusion and exclusion criteria, focusing on English-written studies. Key terms such as “kefir milk”, “artisanal kefir”, “milk”, “metagenomics”, and “cow” were identified through Boolean searches over the last five years. This review addresses the growing need for research on the microbial diversity of artisanal cow’s milk kefir from various global regions. The results indicate a remarkable diversity in microbial communities, primarily dominated by bacteria from the phylum Firmicutes (notably Lactobacillus) and yeasts from the genera Saccharomyces and Kluyveromyces. These microbial compositions are shaped by factors such as milk type, production methods, and grain handling practices, reflecting regional adaptations and influencing kefir’s sensory, probiotic, and functional properties. We argue that a full understanding of these microbial dynamics is critical for standardizing production processes and enhancing quality control measures, ultimately ensuring artisanal kefir’s consistency and health benefits.

Intestinal microbiota perform important functions for the health of fishes. Knowing the microbial composition and evaluating the possible effects caused by anthropogenic pollution in the intestinal microbiota of fish populations might represent an important step in defining microbial biomarkers for water pollution. This study evaluated the impact of environmental contamination on the gut microbiota of the livebearer killifish Phalloceros caudimaculatus. The 16S survey using the V4 region of the 16S rRNA gene was used to characterize and compare the microbiota of two P. caudimaculatus populations from streams with different levels of environmental contamination in Rio Grande, RS, Brazil. Twelve bacterial operational taxonomic units (OTUs) (around one-third of the total) were shared between both fish populations. They represent the core microbiota of the gut in this species. The dominant phyla were Protebacteria and Firmicutes, with more than 80% of relative abundance. The dominant genus was Burkholderia with more than 35% of the relative abundance irrespective of the environmental condition. We detected a lower microbial diversity (Shannon index and observed OTUs) in fish from the polluted stream compared to the reference stream. The PERMANOVA analysis showed that the intestinal microbial communities from fish living in the polluted stream were distinct from those found in the reference stream (p < 0.05). Finally, we identified Luteolibacter, Methylocaldum and Rhodobacter genera, which correlated strongly with the polluted stream. These taxa might represent potential microbial biomarkers of exposure to environmental contaminants in the guts of fish. Confirmation of these findings in other polluted environments might allow the development of a microbiota-based screening approach for environmental evaluation in ecotoxicological studies in aquatic ecosystems.

Introduction: Deforestation of areas for agriculture and cattle breeding is the leading cause of ecological degradation and loss of biodiversity. The solution to mitigate these damages relies on techniques that improve soil health and the microbial quality of these degraded areas. Here, we demonstrate that the high nutrient and microbiological contents of Amazonian Dark Earths (ADE) can promote the development of trees used in ecological restoration projects.Methods: We used degraded soil from crops as control and ADE from the Central Amazon to conduct the experiment, using 20% of ADE as inoculum in degraded agricultural soil. Our goal was to assess whether a small amount of ADE could promote changes that improve plant development similar to its growth under a 100%ADE. We simulated conversion from pasture to forest restoration area by plantingU. brizanthain all pots. After 60 days, we removed it and plantedCecropia pachystachya,Peltophorum dubium, andCedrela fissilis.Results: Our results demonstrated that both 20%ADE and 100%ADE treatments increased pasture productivity and, consequently, soil carbon stock. Also, in these treatments,P. dubiumandC. fissilishad better growth and development, with 20%ADE plants showing a performance similar to those planted in 100%ADE. Both 20%ADE and 100%ADE showed similar numbers of taxa, being significantly higher than in the control soil.Discussion: The 20%ADE was sufficient to increase significantly the microbial richness in the soil, providing several beneficial microorganisms to all tree species such asPedomicrobium,Candidatus Nitrososphaera, and members of Paenebacillaceae. Nevertheless,C. pachystachya, a common pioneer tree in the Amazonian Forest showed a small response even to 100%ADE with a corresponding lower taxa number than the other two species. In conclusion, we point out that microbial structure remains very similar among plants but dissimilar among treatments, highlighting the role of ADE as an enhancer of plant development and beneficial microbiota enrichment in the rhizosphere. The use of 20%ADE was sufficient to alter the microbial community. Therefore, we believe our data could contribute to speeding up forest restoration programs by adopting new biotechnological approaches for forest restoration ecology.

Preterm birth remains the main contributor to early childhood mortality. The vaginal environment, including microbiota composition, might contribute to the risk of preterm delivery. Alterations in the vaginal microbial community structure might represent a risk factor for preterm birth. Here, we aimed to (a) investigate the association between preterm birth and the vaginal microbial community and (b) identify microbial biomarkers for risk of preterm birth. Microbial DNA was isolated from vaginal swabs in a cohort of 69 women enrolled at hospital admission for their delivery. Microbiota was analyzed by high-throughput 16S rRNA sequencing. While no differences in microbial diversity measures appeared associated with the spontaneous preterm and full-term outcomes, the microbial composition was distinct for these groups. Differential abundance analysis showed Lactobacillus species to be associated with full-term birth whereas an unknown Prevotella species was more abundant in the spontaneous preterm group. Although we studied a very miscegenated population from Brazil, our findings were similar to evidence pointed by other studies in different countries. The role of Lactobacillus species as a protector in the vaginal microbiome is demonstrated to be also a protector of spontaneous preterm outcome whereas the presence of pathogenic species, such as Prevotella spp., is endorsed as a factor of risk for spontaneous preterm delivery.

Artisanal kefir is produced by fermenting milk with kefir grains, resulting in a lightly carbonated drink with health-promoting bioactive compounds. However, sensory variability and fermentation conditions challenge its standardization, limiting commercialization in Brazil due to regulatory requirements. This study evaluated the physicochemical properties, volatile compounds, and microbiological stability of artisanal kefir produced in southern Brazil during 30 days of storage. Metabarcoding analysis, carried out by sequencing the V3/V4 regions of the 16S rRNA gene (bacteria) and the ITS region (fungi), revealed an increase in bacterial diversity, with a predominance of Enterococcus and Acetobacter, while fungal diversity decreased, with a predominance of Kazachstania. The physicochemical parameters remained stable. The concentration of volatile compounds, analyzed using a gas chromatograph coupled to a mass spectrometer, decreased, except for an increase in 2-heptanol. The aromatic profile was enriched with alcohols and ketones, possibly influenced by Enterococcus and Acetobacter. These findings show that kefir maintained microbiological stability and adequate sensory characteristics throughout the period analyzed. The study provides subsidies for the standardization of artisanal kefir and compliance with Brazilian quality standards, as well as guiding future research into durability, quality, and consumer perception.