Microbial Characterization Research Articles

A combined molecular approach utilizing microbial DNA and microRNAs in a qPCR multiplex for the classification of five forensically relevant body fluids.

Body fluid identification is an essential step in the forensic biology workflow that can assist DNA analysts in determining where to collect DNA evidence. Current presumptive tests lack the specificity that molecular techniques can achieve; therefore, molecular methods, including microRNA (miRNA) and microbial signature characterization, have been extensively researched in the forensic community. Limitations of each method suggest combining molecular markers to increase the discrimination efficiency of multiple body fluids from a single assay. While microbial signatures have been successful in identifying fluids with high bacterial abundances, microRNAs have shown promise in fluids with low microbial abundance (blood and semen). This project synergized the benefits of microRNAs and microbial DNA to identify multiple body fluids using DNA extracts. A reverse transcription (RT)-qPCR duplex targeting miR-891a and let-7g was validated, and miR-891a differential expression was significantly different between blood and semen. The miRNA duplex was incorporated into a previously reported qPCR multiplex targeting 16S rRNA genes of Lactobacillus crispatus, Bacteroides uniformis, and Streptococcus salivarius to presumptively identify vaginal/menstrual secretions, feces, and saliva, respectively. The combined classification regression tree model resulted in the presumptive classification of five body fluids with 94.6% overall accuracy, now including blood and semen identification. These results provide proof of concept that microRNAs and microbial DNA can classify multiple body fluids simultaneously at the quantification step of the current forensic DNA workflow.

Indoor environmental conditions of selected shopping malls in Nigeria: A comparative study of microclimatic conditions, noise levels, and microbial burdens

The activities of people and equipment used within shopping malls are major factors that contribute to air pollution and increased sound levels, thereby affecting indoor environmental quality and the well-being of mall operators. This study assessed indoor environmental quality through microbial characterization and measurement of environmental conditions present in selected shopping malls. Investigations were conducted at three shopping malls in Ibadan selected through convenience sampling technique. Environmental parameters such as noise level, relative humidity, temperature, PM2.5 levels, total volatile organic compound (TVOC) levels, microbial characterization, and quantity were determined. Microclimatic parameters (temperature and relative humidity) were measured using a 4-in-1 Precision Gold N09AQ multi-tester. Culturable airborne microbes were collected using the settle plate technique. PM2.5 and TVOC levels were measured using a Thermo Scientific MIE pDR-1500 PM monitor and sf200-TVOC meter respectively. Two bacteria species and five fungi species were isolated across the malls. The noise levels ranged from 61.27 to 81.20 dB. The mean temperatures (highest mean of 33.44 ± 1.42 °C), PM2.5 (highest mean of 114.06 ± 25.64 μg/m3), and TVOC (highest mean of 55.21 ± 8.28 ppm) concentrations were higher than the permissible limits stipulated by the WHO guidelines and NESREA standard limits across all the selected malls. A positive correlation was found to exist between particulate matter and TVOC (r = 0.174, p = 0.004). The total bacteria count was generally high with the highest mean of 1965.33 ± 368.56 CFU/m3, while the total fungi count was generally low with the highest mean of 579.82 ± 51.55 CFU/m3. Bacillus spp. and Candida spp. were found to the consistent from all sample points across the three malls. The bacteria isolated are Gram-positive bacteria associated with human skin which suggests a high rate of indoor pollution from humans. In conclusion, this research has demonstrated the necessity to monitor noise levels and indoor air quality in malls. Also, there is need for government policies to improve indoor air quality which must be enforced and regulated, especially within shopping malls.

Efficacy of Nitrogen and Phosphorus Removal and Microbial Characterization of Combined A2O-MBBR Constructed Wetlands

A combined anaerobic–anoxic–oxic moving bed biofilm reactor (A2O-MBBR) constructed wetlands process was used to treat low carbon-to-nitrogen (C/N) simulated sewage. The results showed that the removal rates of chemical oxygen demand (COD), ammonia nitrogen (NH4+-N), total nitrogen (TN), and total phosphorus (TP) by this process were 94.06%, 94.40%, 67.11%, and 84.57%, respectively, and the concentrations of COD, NH4+-N, TN, and TP in the effluent were lower than the Class I-A standard of GB18918-2002. In the anoxic zone, NH4+-N had an inhibitory effect on phosphorus uptake via phosphorus-accumulating organisms (PAOs). The highest community diversity was observed in the anoxic zone sludge at 24 d. During the water-quality-shock loads stage, microbial community diversity decreased in a combined A2O-MBBR constructed wetlands reactor. At the phylum level, bacteria within the mature activated sludge were dominated by Proteobacteria, while Planctomycetes bacteria were the dominant species in the constructed wetlands. At the genus level, Tolumonas spp. were the dominant species in the 12 d and 24 d constructed wetlands and the anaerobic zone, with relative abundance percentages ranging from 20.24 to 33.91%. In the water-quality-shock loads stage, they were replaced by denitrifying bacteria such as Herbaspirillum spp. Unclassified_Burkholderiales was the dominant species in the constructed wetlands, with a relative abundance of 33.09%.

High-temperature fermentation of corn stover for biodiesel production using Candida tropicalis with enhanced lipid accumulation: A new strategy for breeding thermotolerant biodiesel-production strains

Efficient biodiesel production from biomass is essential for the green-oriented energy transition. The current incongruity between fermentation temperature and microbial thermotolerance is one of the key factors restricting biodiesel production, and it is difficult to solve this problem relying only on conventional microbial characterization and breeding methods. We propose a strategy to solve the corn stover cellulose utilization problem by developing thermotolerant biodiesel-production yeast strains. Candida tropicalis was initially improved by adaptive laboratory evolution and then mutated by atmospheric and room-temperature plasma mutagenesis to obtain a thermotolerant strain capable of growing at temperatures up to 45 °C. Two rounds of fluorescence-activated cell sorting were used to select high lipid content cells, which resulted in a 16.8% increase in lipid accumulation capacity compared to the original cells. The simultaneous saccharification fermentation of the generated strain with pretreated corn stover at 44 °C yielded a lipid generation efficiency of 86.2 ± 2 mg/g. This study provides a new method and an alternative strain for the selection and breeding of high-thermotolerance and high biodiesel-production yeasts and offers a feasible strategy for lignocellulosic fermentation for biodiesel production at elevated temperatures using the new industrial strain.

Enhanced biological wastewater treatment supplemented with anaerobic fermentation liquid of primary sludge

The wastewater treatment performance in an inverted A2/O reactor supplemented with fermentation liquid of primary sludge was explored comparing to commercial carbon sources sodium acetate and glucose. Similar COD removal rate was observed with the effluent COD stably reaching the discharge standard for those 3 carbon sources. However, the fermentation liquid distributed more carbon source in the anaerobic zone. Fermentation liquid and sodium acetate tests achieved better nitrogen removal rate than glucose test. The fermentation liquid test showed the best biological phosphorus removal performance with the effluent phosphorus barely reaching the discharge standard. The microbial community characterization revealed that the fermentation liquid test was dominated by phylum Proteobacter in all the anoxic, anaerobic and aerobic zones. Denitrifying phosphorus accumulating organisms (PAOs) (i.e., genera Dechloromonas and unclassified_f__Rhodocyclaceae) were selectively enriched with high abundances (over 20%), which resulted in improved phosphorus removal efficiency. Moreover, the predicted abundances of enzymes involved in nitrogen and phosphorus removal were also enhanced by the fermentation liquid.

Terroir in View of Bibliometrics

This study aimed to perform a bibliometric analysis of terroir and explore its conceptual horizons. Advancements in terroir research until 2022 were investigated using the Scopus database, R, and VOSviewer. Out of the 907 results, the most prevalent document types were articles (771) and reviews (70). The annual growth rate of published manuscripts in this field was 7.8%. The research on terroir encompassed a wide range of disciplines, with significant contributions from Agricultural and Biological Sciences, Social Sciences, Environmental Science, Biochemistry, Genetics, and Molecular Biology. Through keyword analysis, the study identified the most frequently occurring terms in titles, abstracts, and keywords fields, including ‘terroir’, ‘wine’, ‘soil’, ‘wines’, ‘grape’, ‘analysis’, ‘vineyard’, ‘composition’, and ‘climate’. A trend topic analysis revealed that research in terroir primarily focused on the geo-ecology and physiology of grapes. Furthermore, considerable attention was given to methods and techniques related to the physicochemical, sensory, and microbial characterization of terroir and various aspects of the wine industry. Initially, the research in this domain was focused on terroir, authenticity, grapevine, soils, soil moisture, and wine quality. However, over time, the research agenda expanded to include topics such as food analysis, viticulture, wine, taste, sustainability, and climate change. New research areas emerged, including phenolic compounds, anthocyanin, phenols, sensory analysis, and precision agriculture—all of which became integral components of the scientific studies on terroir. Overall, this study provided valuable insights into the historical trends and current developments in terroir research, contributing to our understanding of the frontiers in this field.

Microbial diversity characterizations, associated pathogenesis and antimicrobial resistance profiling of Najafgarh drain

The Najafgarh drain plays a significant role in the pollution of the Yamuna River, accounting for 40% of the total pollution. Therefore, it is crucial to investigate and analyze the microbial diversity, metabolic functional capacity, and antibiotic resistance genes (ARGs) present in the Najafgarh drain. Additionally, studying the water quality and its relationship with the proliferation of microorganisms in the drain is of utmost importance. Results obtained confirmed the deteriorated water quality as physico-chemical parameters such as biochemical oxygen demand (BOD), chemical oxygen demand (COD), dissolved oxygen (DO), and total suspended solids (TSS) in the range of 125–140, 400–460, 0–0.2, 25–140.4 mg/l respectively violated the standard permissible national and global standards. In addition, the next generation sequencing (NGS) analysis confirm the presence of genus such as Thauera, Arcobacter, Pseudomonas, Geobacter, Dechloromonas, Tolumonas, Sulfurospirullum, Desulfovibrio, Aeromonas, Bacteroides, Prevotella, Cloacibacterium, Bifidobacterium, Clostridium etc. along with 864 ARGs in the wastewater obtained from the Najafgarh drain. Findings confirm that the pathogenic species reported from this dataset possess severe detrimental impact on faunal and human health. Further, Pearson's r correlation analysis indicated that environmental variables, mainly total dissolved solids (TDS) and chemical oxygen demand (COD), play a pivotal role in driving microbial community structure of this heavily polluted drain. Thus, the poor water quality, presence of a microbial nexus, pathogenic markers, and ARGs throughout this drain confirmed that it would be one potential contributor to the dissemination of disease-causing agents (pathogens) to the household and drinking water supplies in the near future.

Assessment of microbial flora, characterization and public health implications of two species of smoked fish sold in ‘Otuocha’ Market in Anambra State

Microbiological assessment of fresh and smoked Synodontis schall and Oreochromis niloticus fish species was conducted. Three replicates of fresh and smoked fish samples were aseptically obtained from fishermen and open market in Otuocha area of Anambra State, Nigeria. The culture from organs of fresh fish and smoked samples were inoculated on Nutrient agar (NA.), Salmonella Shigella Agar (SSA), MacConkey Agar (MCA) and Potato Dextrose Agar respectively for heterotrophic bacteria and fungi counts. Colonial and microscopic characterizations of the isolates from the cultured media were examined. There no growth of coliform and Salmonella sp from tissue of the fresh fish and the smoked fish samples. Total plate counts of bacteria and fungi from gills, intestine and skin were found above 1 x 106 cfu/g safety limit recommended for foods. Bacteria count ranged from 1.27 x 107 cfu/g to 2.95 x 107 cfu/g and 1.0 x 106 cfu/g to 2.88 x 108 cfu/g for fungi. Six genera of bacteria namely Salmonella sp, Escherichia coli, Staphylococcus sp, Enterococcus sp, Bacillus sp and Pseudomonas sp were suspected from fish samples. Four fungi genera: Saccharomyces sp, Penicillium sp, Rhizopus sp and Mucor sp were indicated in this work. This assessment has revealed the level of gross contamination of fresh fish and safety of smoked fish samples from foodborne microorganisms.

Earth to Mars: A Protocol for Characterizing Permafrost in the Context of Climate Change as an Analog for Extraplanetary Exploration.

Abstract Permafrost is important from an exobiology and climate change perspective. It serves as an analog for extraplanetary exploration, and it threatens to emit globally significant amounts of greenhouse gases as it thaws due to climate change. Viable microbes survive in Earth's permafrost, slowly metabolizing and transforming organic matter through geologic time. Ancient permafrost microbial communities represent a crucial resource for gaining novel insights into survival strategies adopted by extremotolerant organisms in extraplanetary analogs. We present a proof-of-concept study on ∼22 Kya permafrost to determine the potential for coupling Raman and fluorescence biosignature detection technology from the NASA Mars Perseverance rover with microbial community characterization in frozen soils, which could be expanded to other Earth and off-Earth locations. Besides the well-known utility for biosignature detection and identification, our results indicate that spectral mapping of permafrost could be used to rapidly characterize organic carbon characteristics. Coupled with microbial community analyses, this method has the potential to enhance our understanding of carbon degradation and emissions in thawing permafrost. Further, spectroscopy can be accomplished in situ to mitigate sample transport challenges and in assessing and prioritizing frozen soils for further investigation. This method has broad-range applicability to understanding microbial communities and their associations with biosignatures and soil carbon and mineralogic characteristics relevant to climate science and astrobiology.

Physiological response, microbial diversity characterization, and endophytic bacteria isolation of duckweed under cadmium stress

Duckweed is a cadmium (Cd) hyperaccumulator. However, its enrichment characteristics and physiological responses to Cd have not been systematically studied. The physiological responses, enrichment characteristics, diversity of endophytic bacterial communities, and isolation of Cd-resistant endophytes in duckweed (Lemna minor 0014) were studied for different durations and Cd concentrations. The results indicated that peroxidase (POD) and catalase (CAT) activities decreased while superoxide dismutase activity first increased and then decreased with increasing Cd stress duration. POD activities, CAT activities, and O2− increased as Cd concentrations increased. Malondialdehyde content and Cd accumulation in duckweed increased with increasing concentrations and time. This endophytic diversity study identified 488 operational taxonomic units, with the dominant groups being Proteobacteria, Firmicutes, and Actinobacteria. Paenibacillus sp. Y11, a strain tolerant to high concentrations of Cd and capable of significantly promoting duckweed growth, was isolated from the plant. Our study revealed the effects of heavy metals on aquatic plants, providing a theoretical basis for the application of duckweed in water pollution.

Physio-chemical and microbial characterization of organic and biodynamic manures collected from different farms in India

The organic and biodynamic manures based on animal, plant and house hold waste which have both direct and indirect benefits to soil and crop growth. This paper reports the characterization of organic and biodynamic manures collected from three farms in India. A total of 14 manures were collectedand processed for determination of physico-chemical properties such as pH, EC, total nitrogen, total phosphorus, total potassium, calcium, magnesium, sodium, iron, zinc, manganese, copper, organic carbon and humic acids and microbial enumerations by following the standard methods.The present work on the physico- chemical analysis of different organic and biodynamic manures corroborated with all the results that the biodynamic preparations are rich in micronutrients and BD compost, CPP vermicompost and FarmYard Manure was high in major nutrients (N and K).Based on physico-chemical properties the nutritional index of biodynamic manures was derived. Agriculture or domestic waste can be effectively converted into nutrient enriched manures for soil fertility.

Microbial Community Characterization and Molecular Resistance Monitoring in Geriatric Intensive Care Units in China Using mNGS.

Surface pathogens in the ICU pose a global public health threat, especially to elderly patients who are immunocompromised. To detect these pathogens, unbiased methods such as metagenomic next-generation sequencing (mNGS) are increasingly utilized for environmental microbiological surveillance. In a six-month study from January to July 2022, we investigated microbial communities in Chinese geriatric ICUs by regularly monitoring multiple surfaces at three-month intervals. Using mNGS sequencing, we analyzed microorganisms present at eight specific locations within the ICU. Additionally, we compared pathogen profiles and drug resistance genes between patient cultures and environmental samples collected during the same period. The microbial composition remained relatively stable over time, but significant differences in alpha diversities were observed among various surfaces such as floors, hands, pumps, trolleys, and ventilator inlets/outlets. Surfaces with high contact frequency for healthcare workers, including workstations, ventilator panels, trolleys, pumps, and beds, harbored pathogenic microorganisms such as Acinetobacter baumannii, Cutibacterium acnes, Staphylococcus haemolyticus, Pseudomonas aeruginosa, and Enterococcus faecium. Acinetobacter baumannii, particularly the carbapenem-resistant strain (CRAB), was the most frequently identified pathogen in geriatric ICU patients regardless of testing method used. The mNGS approach enabled detection of viruses, fungi, and parasites that are challenging to culture. Additionally, an abundance of drug resistance genes was found in almost all environmental samples. The microbial composition and abundance in the ICU remained relatively constant over time. The floor exhibited the highest microbial diversity and abundance in the ICU environment. Drug-resistant genes in the ICU environment may migrate between patients. Overall, mNGS is an emerging and powerful tool for microbiological monitoring of the hospital environment.

Physico-Chemical and Microbial Characterisation of Water from the Abengourou dam in Eastern Côte d’Ivoire

Physico-Chemical and Microbial Characterisation of Water from the Abengourou dam in Eastern Côte d’Ivoire

Soil bacteria and fungi communities are shaped by elevation influences in Colombian forest and páramo natural ecosystems.

The influence of elevation on natural terrestrial ecosystems determines the arrangements of microbial communities in soils to be associated with biotic and abiotic factors. To evaluate changes of fungi and bacteria at the community level along an elevational gradient (between 1000 and 3800 m.a.s.l.), physicochemical measurements of soils, taxonomic identifications of plants, and metabarcoding sequences of the 16S rRNA gene for bacteria and the ITS1 region for fungi were obtained. The bacterial taxonomic composition showed that Acidobacteriota increased in abundance with elevation, while Actinobacteriota and Verrucomicrobiota decreased. Furthermore, Firmicutes and Proteobacteria maintained maximum levels of abundance at intermediate elevations (1200 and 2400 m.a.s.l.). In fungi, Ascomycota was more abundant at higher elevations, Basidiomycota tended to dominate at lower elevations, and Mortierellomycota had a greater presence at intermediate sites. These results correlated with the edaphic parameters of decreasing pH and increasing organic carbon and available nitrogen with elevation. In addition, the Shannon index found a greater diversity in bacteria than fungi, but both showed a unimodal pattern with maximum values in the Andean Forest at 2400 m.a.s.l. Through the microbial characterization of the ecosystems, the elevational gradient, soil properties, and vegetation were found to exert significant effects on microbial communities and alpha diversity indices. We conclude that the most abundant soil microorganisms at the sampling points differed in abundance and diversity according to the variations in factors influencing ecological communities.

Coupling effect of DOM and microbe on arsenic speciation and bioavailability in tailings soil after the addition of different biologically stabilized sludges

Dissolved organic matter (DOM) and microbes co-mediate the transformation of heavy metals in soil. However, few previous studies have investigated the effects of interaction between DOM and microbes on the transformation and bioavailability of heavy metals in tailings soil at the molecular level after the addition of organic wastes. This study used co-occurrence network analysis based on Fourier-transform ion cyclone resonance mass spectrometry and high-throughput sequencing to investigate the molecular mechanisms of different bio-stabilized sludge addition on arsenic fraction transformation and bioavailability in tailings soil. It was found that sludge amendments decreased the arsenic bioavailable fraction from 3.62% to 1.74% and 1.68% and promoted humification of DOM in soil. The extra inorganic salt ions introduced with sludge desorb the adsorbed As(V) into soil solution. Specifically, bio-stabilized sludge increased the contents of labile compounds that provided nutrients for microbial metabolism and shaped the microbial community composition into a more copiotrophic state, which increased the abundance of As(V)-reducing bacteria and then converted the As(V) into As(III) and precipitated as As2S3. This work innovatively explores the transformation mechanisms of As fractions through the perspectives of microbial community and DOM molecular characterization, providing an important basis for the remediation of As-contaminated soil using biosolids.

Evaluating nanopore sequencing for microbial community characterization in catfish pond water

AbstractIn the United States, catfish are primarily farmed in earthen ponds, resulting in an aquatic environment influenced both by management practices and natural ecological processes. Profiling pond water microbiota can be useful for understanding what conditions may lead to microbial communities associated with production issues and could inform management practices. The aim of this study was to identify appropriate methods for bacterial community profiling of catfish pond water with nanopore sequencing of the 16S rRNA gene. To this end, two forward primers, two reverse primers, and three different polymerase chain reaction (PCR) cycle numbers were tested on a mock community consisting of aquaculture‐relevant bacteria. The optimized protocol was applied to water samples obtained from three experimental catfish ponds sampled in May, June, August, and September 2020. Applying these methods to pond samples allowed for the identification of 1488 genera, primarily within four dominating phyla: Actinobacteriota, Bacteroidota, Cyanobacteria, and Firmicutes. High variation was observed between individual ponds and sampling timepoints; only 18 of the 1488 genera were found in relative abundances ≥1% in all ponds from at least one sampling point. Despite this variation, consistent results could be observed. Samples obtained from the month of September had the highest number of observed genera, and samples from June had the lowest. Overall, these data demonstrated individual ponds represent distinct microcosms composed of unique bacterial communities, although this pond effect was secondary to the influence of sampling month on pond community composition.

Batch-fed composting of food waste: Microbial diversity characterization and removal of antibiotic resistance genes

The aim of this work was to study the impact of batch-fed strategies on bacterial communities and ARGs in compost. The findings demonstrate that batch-feeding helped maintain high temperatures in the compost pile for an extended period (above 50 °C for 18 days), which in turn facilitated water dissipation. High-throughput sequencing showed that Firmicutes played a significant role in batch-fed composting (BFC). They had a high relative abundance at the beginning (98.64%) and end (45.71%) of compost. Additionally, BFC showed promising results in removing ARGs, with reductions of 3.04–1.09 log copies/g for Aminoglycoside and 2.26–2.44 log copies/g for β_Lactamase. This study provides a comprehensive survey of BFC and demonstrates its potential for eliminating resistance contamination in compost.

Pilot-scale investigation of conductive carbon cloth amendment for enhancing high-solids anaerobic digestion and mitigating antibiotic resistance

This study examined the effectiveness of introducing conductive carbon cloth into a pilot-scale high-solids anaerobic digestion (HSAD) system. Adding carbon cloth increased methane production by 22 % and improved the maximum methane production rate by 39 %. Microbial community characterization indicated a possible direct interspecies electron transfer–based syntrophic association among microbes. Using carbon cloth also enhanced microbial richness, diversity, and evenness. Carbon cloth effectively reduced the total abundance of antibiotic resistance genes (ARGs) by 44.6 %, mainly by inhibiting horizontal gene transfer, as shown by the significant decrease in the relative abundance of integron genes (particularly intl1). The multivariate analysis further demonstrated strong correlations of intl1 with most of the targeted ARGs. These findings suggest that carbon cloth amendment can promote efficient methane production and attenuate the spread of ARGs in HSAD systems.

Use of Selected Lactic Acid Bacteria and Carob Flour for the Production of a High-Fibre and "Clean Label" Plant-Based Yogurt-like Product.

Carob, an underutilized crop with several ecological and economic advantages, was traditionally used as animal feed and excluded from the human diet. Yet, nowadays, its beneficial effects on health are making it an interesting candidate as a food ingredient. In this study, a carob-based yogurt-like product was designed and fermented with six lactic acid bacteria strains, whose performances after fermentation and during shelf life were assessed through microbial and biochemical characterization. The strains showed different aptitudes to ferment the rice-carob matrix. Particularly, Lactiplantibacillus plantarum T6B10 was among the strains with the lowest latency phase and highest acidification at the end of fermentation. T6B10 also showed discrete proteolysis during storage, so free amino acids were up to 3-fold higher compared to the beverages fermented with the other strains. Overall, fermentation resulted in the inhibition of spoilage microorganisms, while an increase in yeasts was found in the chemically acidified control. The yogurt-like product was characterized by high-fiber and low-fat content; moreover, compared to the control, fermentation decreased the predicted glycemic index (-9%) and improved the sensory acceptability. Thus, this work demonstrated that the combination of carob flour and fermentation with selected lactic acid bacteria strains represents a sustainable and effective option to obtain safe and nutritious yogurt-like products.

Characterization of Bacterial Diversity in Aguamiel and Two Types of Pulque from the Zacatlán Region, México

Pulque is a traditional Mexican fermented beverage associated with numerous health benefits. Over time, there has been considerable interest in studying the bacterial diversity of pulque, and microbial characterization has been carried out using traditional microbiological and molecular methods. Therefore, the objective of this research was to characterize the microbiota of artisanal pulque obtained from the Zacatlán region in Puebla, México, by the means of Illumina sequencing, and to compare it with the microbial diversity of aguamiel (sap before fermentation), commercial pulque (supplemented with additives to increase its yield), and its seed (batch of pulque previously fermented). An analysis of the Shannon index showed medium diversity for both aguamiel and pulque samples (score > 2), while the Chao 1 index exhibited a non-significant difference between them. On the other hand, a principal components analysis confirmed the role of the seed as an essential inoculum to define the microbial diversity of pulque, emphasizing the importance of its preservation as a quality standard during the elaboration process. In addition, results showed that the dominant phyla in artisanal and commercial pulque were Firmicutes and Bacteroidetes. As the fermentation process progressed, it was possible to observe an increase in the population of lactic acid bacteria (LAB) in both types of pulque compared to those detected in aguamiel. Of these, the species Lactobacillus, Leuconostoc, and Lactococcus represented almost 95% of the total LAB. Finally, even though the safety of pulque has been in question due to its non-aseptic manufacturing process, the present study confirmed that less than 1% of its microbiota corresponds to the genera with a pathogenic potential such as γ-proteobacteria (Enterobacter and Hafnia), which decreases as the fermentation process advances.