Characterization of bacterial populations in Danish raw milk cheeses made with different starter cultures by denaturating gradient gel electrophoresis and pyrosequencing

Acute nitrite exposure causes gut microbiota dysbacteriosis and proliferation of pathogenic Photobacterium in shrimp

Nitrite exposure has become a significant concern in the aquaculture industry, posing a severe threat to aquatic animals such as shrimp. While studies have reported the adverse effects of nitrite on shrimp growth, the part played by the gut microbiota in shrimp mortality resulting from nitrite exposure is poorly understood. Here, the effects of nitrite on shrimp gut bacterial community were investigated using 16S rRNA amplicon sequencing, bacterial isolation, genomic analysis, and infection experiments. Compared to the control_healthy group, changes in the bacterial composition of the nitrite_dead group were associated with reduced abundance of specific beneficial bacteria and increased abundance of certain pathogenic bacteria. Notably, members of the Photobacterium genus were found to be significantly enriched in the nitrite_dead group. Genomic analysis of a representative Photobacterium strain (LvS-8n3) revealed a variety of genes encoding bacterial toxins, including hemolysin, adhesin, and phospholipase. Furthermore, it was also found that LvS-8n3 exhibits strong pathogenicity, probably due to its high production of pathogenic factors and the ability to utilize nitrite for proliferation. Therefore, the proliferation of pathogenic Photobacterium species appears pivotal for driving shrimp mortality caused by nitrite exposure. These findings provide novel insights into the disease mechanism in shrimp under conditions of environmental change.

Dissolved organic matter accelerates microbial degradation of 17 alpha-ethinylestradiol in the presence of iron mineral

Dissolved organic matter (DOM) and iron minerals widely existing in the natural aquatic environment can mediate the migration and transformation of organic pollutants. However, the mechanism of interaction between DOM and iron minerals in the microbial degradation of pollutants deserves further investigation. In this study, the mechanism of 17 alpha-ethinylestradiol (EE2) biodegradation mediated by humic acid (HA) and three kinds of iron minerals (goethite, magnetite, and pyrite) was investigated. The results found that HA and iron minerals significantly accelerated the biodegradation process of EE2, and the highest degradation efficiency of EE2 (48%) was observed in the HA-mediated microbial system with pyrite under aerobic conditions. Furthermore, it had been demonstrated that hydroxyl radicals (HO•) was the main active substance responsible for the microbial degradation of EE2. HO• is primarily generated through the reaction between hydrogen peroxide secreted by microorganisms and Fe(II), with aerobic conditions being more conducive. The presence of iron minerals and HA could change the microbial communities in the EE2 biodegradation system. These findings provide new information for exploring the migration and transformation of pollutants by microorganisms in iron-rich environments.

The Microbial Diversity on the Surface of Smear-Ripened Cheeses and Its Impact on Cheese Quality and Safety

Smear-ripened cheeses are characterized by a viscous, red-orange surface smear on their rind. It is the complex surface microbiota on the cheese rind that is responsible for the characteristic appearance of this cheese type, but also for the wide range of flavors and textures of the many varieties of smear-ripened cheeses. The surface smear microbiota also represents an important line of defense against the colonization with undesirable microorganisms through various types of interaction, such as competitive exclusion or production of antimicrobial substances. Predominant members of the surface smear microbiota are salt-tolerant yeast and bacteria of the phyla Actinobacteria, Firmicutes, and Proteobacteria. In the past, classical culture-based approaches already shed light on the composition and succession of microorganisms and their individual contribution to the typicity of this cheese type. However, during the last decade, the introduction and application of novel molecular approaches with high-resolution power provided further in-depth analysis and, thus, a much more detailed view of the composition, structure, and diversity of the cheese smear microbiota. This led to abundant novel knowledge, such as the identification of so far unknown community members. Hence, this review is summarizing the current knowledge of the diversity of the surface smear microbiota and its contribution to the quality and safety of smear-ripened cheese. If the succession or composition of the surface-smear microbiota is disturbed, cheese smear defects might occur, which may promote food safety issues. Hence, the discussion of cheese smear defects in the context of an increased understanding of the intricate surface smear ecosystem in this review may not only help in troubleshooting and quality control but also paves the way for innovations that can lead to safer, more consistent, and higher-quality smear-ripened cheeses.

Diversity of the Microbiota of Traditional Izmir Tulum and Izmir Brined Tulum Cheeses and Selection of Potential Probiotics

High-throughput DNA sequencing (HTS) was used to study the microbial diversity of commercial traditional Izmir Tulum (IT) and Izmir Brined Tulum (IBT) cheeses from Izmir, Türkiye. Simultaneously, cultivation-dependent methods were used to isolate, identify and characterize bacterial strains displaying probiotic potential. At the phylum level, Firmicutes dominated the microbiota of both cheese types comprising >98% of the population. Thirty genera were observed, with Streptococcus being the most abundant genus and with Streptococcus thermophilus and S. infantarius subsp. infantarius being the most abundant species. Genera, including Bifidobacterium and Chryseobacterium, not previously associated with IT and IBT, were detected. IT cheeses displayed higher operational taxonomic units (OTUs; Richness) and diversity index (Simpson) than IBT cheeses; however, the difference between the diversity of the microbiota of IT and IBT cheese samples was not significant. Three Lacticaseibacillus paracasei strains isolated from IBT cheeses exhibited probiotic characteristics, which included capacity to survive under in vitro simulated gastrointestinal conditions, resistance to bile salts and potential to adhere to HT-29 human intestinal cells. These findings demonstrate that Tulum cheeses harbor bacterial genera not previously reported in this cheese and that some strains display probiotic characteristics.

Distribution of corrosive microbial communities in rust layers of steel immersed in seawater

In this paper, high-throughput sequencing technology was adopted to visualize the microbial communities on the surfaces of two types of carbon steel immersed in Sea Area Ⅰ. The results showed that different microbial communities were formed on different carbon steel surfaces, in which the genus with the highest abundance on the surface of Q235 was Escherichia-Shigella, while anaerobic Desulfovibrio on the surface of 921a was the most abundant, and the dominant genus varied with the depth of the rust layer. In addition, the distribution of sulfate-reducing bacteria (SRB) on the surface of Q235 submerged in Sea Area Ⅱ was compared with the sulfate-reducing bacteria's distribution in Sea Area Ⅰ, using the environmental factors correlation analysis. The results showed that the concentrations of Ca2+, Na+, K+, Mg2+, and Al3+ were positively correlated with the distribution of SRB, while the concentrations of Cu2+, Zn2+, SO4 2-, Cl-, NO3 -, and organic carbon were negatively correlated with it. Furthermore, there was a highly significant correlation between each geochemical factor and Desulfotomaculum (p < 0.01).

Improved assessments of bulk milk microbiota composition via sample preparation and DNA extraction methods

Although bacterial detection by 16S rRNA gene amplicon DNA sequencing is a widely-applied technique, standardized methods for sample preparation and DNA extraction are needed to ensure accuracy, reproducibility, and scalability for automation. To develop these methods for bovine bulk milk, we assembled and tested a bacterial cell mock community (BCMC) containing bacterial species commonly found in milk. The following protocol variations were examined:: BCMC enumeration (colony enumeration or microscopy), sample volume (200 μl to 30 ml), sample storage condition (frozen in PBS or 25% glycerol or exposure to freeze-thaw cycles), cell lysis method (bead-beating, vortex, enzymatic), and DNA extraction procedure (MagMAX Total, MagMAX CORE, and MagMAX Ultra 2.0, with and without either Proteinase K or RNase A). Cell enumeration by microscopy was more accurate for quantification of the BCMC contents. We found that least 10 mL (≥ 10⁴ cells in high quality milk) is needed for reproducible bacterial detection by 16S rRNA gene amplicon DNA sequencing, whereas variations in storage conditions caused minor differences in the BCMC. For DNA extraction and purification, a mild lysis step (bead-beating for 10 s at 4 m/s or vortexing at 1800 rpm for 10 s) paired with the MagMAX Total kit and Proteinase K digestion provided the most accurate representation of the BCMC. Cell lysis procedures conferred the greatest changes to milk microbiota composition and these effects were confirmed to provide similar results for commercial milk samples. Overall, our systematic approach with the BCMC is broadly applicable to other milk, food, and environmental samples therefore recommended for improving accuracy of culture-independent, DNA sequence-based analyses of microbial composition in different habitats.

Lactic Acid Bacteria in Raw-Milk Cheeses: From Starter Cultures to Probiotic Functions

Traditional cheeses produced from raw milk exhibit a complex microbiota, characterized by a sequence of different microorganisms from milk coagulation and throughout maturation. Lactic acid bacteria (LAB) play an essential role in traditional cheese making, either as starter cultures that cause the rapid acidification of milk or as secondary microbiota that play an important role during cheese ripening. The enzymes produced by such dynamic LAB communities in raw milk are crucial, since they support proteolysis and lipolysis as chief drivers of flavor and texture of cheese. Recently, several LAB species have been characterized and used as probiotics that successfully promote human health. This review highlights the latest trends encompassing LAB acting in traditional raw milk cheeses (from cow, sheep, and goat milk), and their potential as probiotics and producers of bioactive compounds with health-promoting effects.

Analysis of Microbiota Persistence in Quebec's Terroir Cheese Using a Metabarcoding Approach

Environmental short amplicon sequencing, or metabarcoding, is commonly used to characterize the bacterial and fungal microbiota of cheese. Comparisons between different metabarcoding studies are complicated by the use of different gene markers. Here, we systematically compare different metabarcoding molecular targets using V3–V4 and V6–V8 regions of the bacterial 16S rDNA and fungal ITS1 and ITS2 regions. Taxonomic profiles varied depending on the molecular markers used. Based on data quality and detection capacity of the markers toward microorganisms usually associated with the dairy environment, the ribosomal regions V3–V4 and ITS2 were selected and further used to evaluate variability in the microbial ecosystem of terroir cheeses from the province of Quebec in Canada. Both fungal and bacterial ecosystem profiles were described for 32 different ready-to-eat bloomy-, washed- and natural-rind specialty cheese varieties. Among them, 15 were studied over two different production years. Using the Bray–Curtis dissimilarity index as an indicator of microbial shifts, we found that most variations could be explained by either a voluntary change in starter or ripening culture composition, or by changes in the cheesemaking technology. Overall, our results suggest the persistence of the microbiota between the two years studied—these data aid understanding of cheese microbiota composition and persistence during cheese ripening.

Microbiota and volatilome of dry-cured pork loins manufactured with paprika and reduced concentration of nitrite and nitrate

Dry-cured pork loin is a very popular meat product in Mediterranean countries. Pork-loin is manufactured rubbing curing salts, nitrite and nitrate, and spices on the surface of the loin which is then dry-cured or smoked for several months. Although nitrite-derived compounds are crucial for the microbiological safety and development of a distinct flavour, there have been recent concerns about the adverse health effects of nitrite-derived compounds driving to the reduction of curing agents in meat products. In this study, we have evaluated the differences in microbiota and aroma of dry-cured pork loins manufactured with or without paprika and reduced ingoing amounts of nitrate and nitrite. Staphylococcus dominated the microbiota of pork loins without paprika, regardless of the nitrite and nitrate reduction. On the contrary, the reduction of nitrite and nitrate in loins with paprika had an important effect on the microbiota. In these loins a codominance of Staphylococcus and Bacillus together by Enterobacteriaceae occurred. Moreover, paprika addition and reduction of nitrite and nitrate seemed to promote proliferation of lactic acid bacteria. Occurrence of these genera was correlated with the generation of free amino acids and their derived volatile compounds setting clear differences in the aroma profile of dry-cured loins.

Microbial Interactions within the Cheese Ecosystem and Their Application to Improve Quality and Safety

The cheese microbiota comprises a consortium of prokaryotic, eukaryotic and viral populations, among which lactic acid bacteria (LAB) are majority components with a prominent role during manufacturing and ripening. The assortment, numbers and proportions of LAB and other microbial biotypes making up the microbiota of cheese are affected by a range of biotic and abiotic factors. Cooperative and competitive interactions between distinct members of the microbiota may occur, with rheological, organoleptic and safety implications for ripened cheese. However, the mechanistic details of these interactions, and their functional consequences, are largely unknown. Acquiring such knowledge is important if we are to predict when fermentations will be successful and understand the causes of technological failures. The experimental use of "synthetic" microbial communities might help throw light on the dynamics of different cheese microbiota components and the interplay between them. Although synthetic communities cannot reproduce entirely the natural microbial diversity in cheese, they could help reveal basic principles governing the interactions between microbial types and perhaps allow multi-species microbial communities to be developed as functional starters. By occupying the whole ecosystem taxonomically and functionally, microbiota-based cultures might be expected to be more resilient and efficient than conventional starters in the development of unique sensorial properties.

Grazing Affects Bacterial and Fungal Diversities and Communities in the Rhizosphere and Endosphere Compartments of Leymus chinensis through Regulating Nutrient and Ion Distribution

Plant-associated endophytic microorganisms are essential to developing successful strategies for sustainable agriculture. Grazing is an effective practice of grassland utilization through regulating multitrophic relationships in natural grasslands. This study was conducted for exploring the effects of grazing on the diversities and communities of bacteria and fungi presented in rhizosphere soils, roots, stems, and leaves of Leymus chinensis (L. chinensis), based on high-throughput sequencing. Grazing increased bacterial diversity but reduced fungal diversity in plant leaves. Further analysis confirmed that the abundance of Chloroflexi, Gemmatimonadota, Nitrospirota, Sordariales, and Pezizales in plant leaves was increased by grazing. The Bray-Curtis similarities of microbial communities in the endosphere were higher under grazing plots than non-grazing plots. Moreover, the bacterial communities were significantly correlated with ions, while the nutrient and negative ions exhibited strong influence on fungal communities. We concluded that grazing-induced changes of microbial diversities and communities in different compartments of a dominant perennial grass (L. chinensis) could be attributed to the nutrient and ion distribution in host plant. The current study highlights the importance of livestock in mediating diversities and communities of endophytic microbes, and will be useful for better understanding the complexity of multitrophic interactions in a grassland ecosystem.

Metataxonomic and metagenomic approaches for the study of undefined strain starters for cheese manufacture

Undefined strain starters are used for the production of many traditional and artisanal cheeses. Composition of undefined starters depends on several factors, and the diversity in strains and species significantly affects cheese quality and features. Culture-dependent approaches have long been used for the microbial profiling and functionalities of undefined cultures but underestimate their diversity due to culturability biases. Recently, culture-independent methods, based on high-throughput sequencing (HTS), have been preferred, with a significant boost in resolution power and sensitivity level. Amplicon targeted (AT) metagenomics, based on 16S rRNA sequencing, returned a larger microbiota diversity at genus and, sometimes, at species levels for artisanal starters of several PDO cheeses, but was inappropriate for populations with high strain diversity, and other gene targets were tested in AT approaches. Shotgun metagenomics (total DNA) and metatranscriptomics (total RNA), although are more powerful in depicting diversity and functionality of undefined cultures, have been rarely applied because of some limitations (e.g., high costs and laboriousness, need for bioinformatics skills). The advantages of HTS technologies are undoubted, but some hurdles need to be still overcame (e.g., resolution power, discrepancy between active and inactive cells, robust analytic pipelines, cost and time reduction for integrated approaches) so that HTS become routinary and convenient for defining complexity, microbial interactions (including host-phage relationships) and evolution in cheeses of undefined starters.

Genomic and in vitro properties of the dairy Streptococcus thermophilus SMQ-301 strain against selected pathogens

Cumulative studies have suggested that probiotic bacterial strains could be an effective alternative in inhibiting conditions caused by foodborne and vaginal pathogens. The use of genomic techniques is becoming highly useful in understanding the potential of these beneficial microorganisms. This study presents some genomic and in vitro properties of the Streptococcus thermophilus SMQ-301 strain against foodborne and vaginal pathogens (Staphylococcus aureus, Escherichia coli, and Gardnerella vaginalis) to validate its use in dairy food formulations. Genomic analyses include bacteriocin production, stress response systems, antioxidant capability, and RAST-based functional annotation. In vitro investigations focused on the antimicrobial effects of the S. thermophilus SMQ-301 cell-free solution (CFS) against the selected pathogens after enzymatic actions and pH treatments, assessment of cytotoxic effects using murine RAW264.7 cells, and assessment of organic acid production levels using supplementary carbon sources. The results show that the S. thermophilus SMQ-301 genome possesses essential pathways for stress management, antioxidant activities, and bacteriocin production. For the first time, the bacteriocin-producing peptides of S. thermophilus SMQ-301 are reported, which gives an insight into its inhibitory potential. In vitro, the CFS of S. thermophilus SMQ-301 had significant (P < 0.05) antimicrobial effects on the selected pathogens, with S. aureus ATCC25923 being the most resistant. All antimicrobial activities of the CFS against the selected pathogens were eliminated at pH 6.5 and 7.0. S. thermophilus SMQ-301 CFS yielded the highest lactic (25.58 ± 0.24 mg mL-1) and acetic (5.53 ± 0.12 mg mL-1) acid production levels, with 1% fructooligosaccharide (P < 0.05). The S. thermophilus SMQ-301 strain also lowered murine RAW264.7 cell activities from 101.77% (control) to 80.16% (T5 - RAW264.7 cells + 1 × 109 CFU mL-1 cells) (P < 0.05). This study showed that although the S. thermophilus SMQ-301 strain had excellent genomic characteristics, the in vitro effects varied markedly against all three pathogens. In all, the S. thermophilus SMQ-301 strain has promising applications as a potential probiotic in the food and allied industries.

Solar composting greenhouse for organic waste treatment in fed-batch mode: Physicochemical and microbiological dynamics

Composting is a sustainable means of managing organic waste, and solar composters offer a viable solution in rural areas lacking connection to municipal power supplies. This study tracked the physicochemical and microbiological changes that occur in a solar composting greenhouse during the treatment of food and green cellulosic waste in fed-batch mode, which remain poorly understood. Solar composting greenhouse performed well on waste reduction and nutrient retention, resulting in a 45.0-58.8% decrease in feedstock volume over 12-day composting cycles, a 41% removal in dry matter after three batches of composting, and 29.5%, 252.9% and 96.6% increase in the nitrogen, phosphorus and potassium content respectively after 42 days of composting. Batch feeding and composting jointly influenced microbiological succession by altering the physicochemical properties of compost. The contents of nitrogen and phosphorus, pH, and electrical conductivity significantly accounts for variations in culturable microbial populations. The succession of dominant bacterial genera such as Lactobacillus, Pseudoxanthomonas, Bacillus, and Pseudomonas were closely related to pH, cellulose, NH₄⁺-N, carbon content, and temperature. In addition, Pichia kudriavzevii, Thermomyces lanuginosus, and Scopulariopsis brevicaulis successively became the dominant fungal species during composting. Preliminary compost quality assessments showed that solar composting greenhouse has a high potentiality to transform organic waste into organic fertilizer. Additionally, corresponding purposeful suggestions were proposed for future optimization in this system, mainly from a microbiological aspect.

Effects of aerosol pollution on PM2.5-associated bacteria in typical inland and coastal cities of northern China during the winter heating season

Frequent heavy aerosol pollution occurs during the winter heating season in northern China. Here, we characterized the airborne bacterial community structure and concentration, during typical pollution episodes that occurred during the winter heating season of 2017-2018 in Jinan and Weihai. During this heating season, five and four heavy pollution episodes were observed in Jinan and Weihai, respectively. Compared with December and January, pollution episodes in March were significantly affected by sand dust events. Higher Bacillales were identified in the March samples from Jinan, indicating that sand dust influences bacterial communities. During similar pollution episodes, air pollution in the coastal city of Weihai was lower than the inland city of Jinan. The predominant bacteria included Staphylococcus, Cyanobacteria, Lactobacillus, Deinococcus, Enbydrobacter, Ralstonia, Bacillus, Comamonas, and Sphingomonas. These predominant bacteria are mainly from Proteobacteria, Firmicutes, Cyanobacteria, Actinobacteria, and Bacteroidetes phyla. Bacterial concentration showed significant variation with increased airborne pollutants. The highest concentration appeared during moderate pollution (up to 10⁶ cells/m³), whereas bacterial concentration decreased during heavy and severe pollution (10⁵ cells/m³), which may be related to toxic effects of high pollutant concentrations during heavy or severe pollution. Community structure variation indicated that Cyanobacterial genera were dominant in clean or slight pollution. With increased PM_2.5, Staphylococcus increased and became the most abundant bacteria in moderate pollution (up to 40%). During heavy or severe pollution, bacteria that are adaptable to harsh or extreme environments predominate, such as Deinococcus and Bacillus. In the assessment of health risks from air pollution, the bioaerosols risks must consider. Additionally, although most microbial genera are similar between the two cities, there are important differences associated with pollution level. During air pollution regulation in different regions with varied geographical and climatic conditions, bioaerosol pollution difference is an unignored factor.

Suitability of the Nisin Z-producer Lactococcus lactis subsp. lactis CBM 21 to be Used as an Adjunct Culture for Squacquerone Cheese Production

This research investigated the technological and safety effects of the nisin Z producer Lactococcus lactis subsp. lactis CBM 21, tested as an adjunct culture for the making of Squacquerone cheese in a pilot-scale plant. The biocontrol agent remained at a high level throughout the cheese refrigerated storage, without having a negative influence on the viability of the conventional Streptococcus thermophilus starter. The inclusion of CBM 21 in Squacquerone cheesemaking proved to be more effective compared to the traditional one, to reduce total coliforms and Pseudomonas spp. Moreover, the novel/innovative adjunct culture tested did not negatively modify the proteolytic patterns of Squacquerone cheese, but it gave rise to products with specific volatile and texture profiles. The cheese produced with CBM 21 was more appreciated by the panelists with respect to the traditional one.

Ecological networks reveal contrasting patterns of bacterial and fungal communities in glacier-fed streams in Central Asia

Bacterial and fungal communities in biofilms are important components in driving biogeochemical processes in stream ecosystems. Previous studies have well documented the patterns of bacterial alpha diversity in stream biofilms in glacier-fed streams, where, however, beta diversity of the microbial communities has received much less attention especially considering both bacterial and fungal communities. A focus on beta diversity can provide insights into the mechanisms driving community changes associated to large environmental fluctuations and disturbances, such as in glacier-fed streams. Moreover, modularity of co-occurrence networks can reveal more ecological and evolutionary properties of microbial communities beyond taxonomic groups. Here, integrating beta diversity and co-occurrence approach, we explored the network topology and modularity of the bacterial and fungal communities with consideration of environmental variation in glacier-fed streams in Central Asia. Combining results from hydrological modeling and normalized difference of vegetation index, this study highlighted that hydrological variables and vegetation status are major variables determining the environmental heterogeneity of glacier-fed streams. Bacterial communities formed a more complex and connected network, while the fungal communities formed a more clustered network. Moreover, the strong interrelations among the taxonomic dissimilarities of bacterial community (BC) and modules suggest they had common processes in driving diversity and taxonomic compositions across the heterogeneous environment. In contrast, fungal community (FC) and modules generally showed distinct driving processes to each other. Moreover, bacterial and fungal communities also had different driving processes. Furthermore, the variation of BC and modules were strongly correlated with hydrological properties and vegetation status but not with nutrients, while FC and modules (except one module) were not associated with environmental variation. Our results suggest that bacterial and fungal communities had distinct mechanisms in structuring microbial networks, and environmental variation had strong influences on bacterial communities but not on fungal communities. The fungal communities have unique assembly mechanisms and physiological properties which might lead to their insensitive responses to environmental variations compared to bacterial communities. Overall, beyond alpha diversity in previous studies, these results add our knowledge that bacterial and fungal communities have contrasting assembly mechanisms and respond differently to environmental variation in glacier-fed streams.

Prospecting Plant Growth-Promoting Bacteria Isolated from the Rhizosphere of Sugarcane Under Drought Stress

In the rhizosphere, the soil bacteria and the plants are closely related, with the plant-associated microbiota playing an important role in promoting plant growth under both normal and stress conditions. In this study, the cultivable bacteria in the sugarcane rhizosphere under different levels of drought stress were characterized and screened for plant growth activities. The results suggested that the microbial community associated with the sugarcane rhizosphere was strongly affected by drought, but some important genera of bacteria such as Arthrobacter, Pseudomonas, Microbacterium, and Bacillus remained present during the entire experiment, indicating the adaptability of these organisms and their importance in the rhizosphere community. Many isolates exhibited positive results for one or more plant growth activity, and they were also capable of growing under simulated drought stress, suggesting that the microorganisms isolated from the sugarcane rhizosphere could be explored for uses such as biofertilizers or biocontrol agents in agriculture.

Targeting gut microbiota as a possible therapy for mastitis

Mastitis, a disease that affects both dairy herds and humans, is recognized as the most common source of losses in the dairy industry. Antibiotics have been used for years as the primary treatment for mastitis. However, abuse of antibiotics has led to the emergence of resistant strains and the presence of drug residues and has increased the difficulty of curing this disease. In addition, antibiotics kill most of the microbes that are present in the digestive tract, leading to imbalances in the gut microbiome and destruction of the ecosystem that is normally present in the gut. Gut microbiota play an important role in the host's health and could be considered the "second brain" of the body. In recent years, the gut microbiota and their metabolites, including lipopolysaccharide (LPS) and short-chain fatty acids (SCFAs), have been shown to participate in the development of mastitis. LPS is the main component of the cell walls of gram-negative bacteria. Overproduction of rumen-derived LPS injures the rumen epithelium, resulting in the entry of LPS into the blood and damaged liver function; once in the blood, it circulates into the mammary gland, increasing blood-barrier permeability and leading to mammary gland inflammation. SCFAs, which are produced by gut microbiota as fermentation products, have a protective effect on mammary gland inflammatory responses and help maintain the function of the blood-milk barrier. Recently, increasing attention has been focused on the use of probiotics as a promising alternative for the treatment of mastitis. This review summarizes the effects of the gut microbiome and its metabolites on mastitis as well as the current of probiotics in mastitis. This work may provide a valuable theoretical foundation for the development of fresh ideas for the prevention and treatment of mastitis.

Size distribution of bioaerosols from biomass burning emissions: Characteristics of bacterial and fungal communities in submicron (PM1.0) and fine (PM2.5) particles

The North China Plain is the agricultural heartland in China. High PM_2.5 levels and elevated chemical pollutants have been observed during crop harvest seasons due to open biomass burning. Biomass burning in the wheat-harvest season may significantly deteriorate the regional air quality. The harmful ingredients in smoke particles also have severe implications for toxicity and health effects. Previous studies have illustrated the potential role of bioaerosols as ice-nuclei and cloud condensation nuclei and highlighted their influence on biochemical cycles and human health effects. In a monthly field observation campaign of biomass burning conducted at the summit of Mount Tai in July 2015, we reported the composition, potential role, size distribution of microorganisms in particulate matters PM_1.0, PM_2.5, and estimated their contribution to particles. The wide-range particle spectrometer suggested that the predominant particles were distributed in submicron particles (PM_1.0), which resulted in a similar community structure for bacteria and fungi in PM_1.0 and PM_2.5. Among bacteria, the predominant Pseudomonas accounted for 18.06% and 21.29% in PM_1.0 and PM_2.5, respectively. Alternaria covered up to 69.01% and 72.76% of the fungal community in PM_1.0 and PM_2.5, respectively. A disparity between bacterial communities was identified by the abundance of rare species, such as Bacilli being higher in PM_1.0 (2.4%) than in PM_2.5 (1.8%), and Defluviicoccus being higher in PM_2.5 (2.5%) than in PM_1.0 (0.5%), which may be related to cell size and cell growth patterns. Quantitative PCR revealed that microbial cell numbers in PM_2.5 were higher than in PM_1.0, and that the bacterial cell number was about an order of magnitude greater than the fungal cell number. However, the mass concentration and contribution of fungi to particulate matter was much higher than that of bacteria, suggesting the underestimated role of fungi in atmospheric aerosols. Airborne microorganisms in alpine areas remained less characterized. The findings presented here illustrated the potentially important impacts on air quality and bioaerosol pollution by biomass burning, which provides an essential reference for understanding the transmission and health effects of bioaerosols.

Analysis of marine microbial communities colonizing various metallic materials and rust layers

High-throughput sequencing was used to visualize microbial biocoenoses on different metallic surfaces and rust layers of highly corroded steels after immersion in coastal marine water for 30 months at Sanya, China. Distinct microbial community compositions were observed on these metallic surfaces. The dominant genus was the copper-tolerant, acid-producing Lactobacillus on copper alloys, the common aerobic surface colonizers Bacillus and Ruegeria on aluminum alloys, and aerobic biofilm-forming Pseudomonas on carbon steel. Most of these are copiotrophic microbes compared to planktonic microbes, which are oligotrophic. Additionally, sulfate-reducing prokaryotes (SRP) were detected in the rust layer, but the dominant genera changed from the outer layer to the inner part. The dominant genera detected in the outer, middle and inner rusts layers were Desulfotomaculum, Desulfonatronum (obligate anaerobe) and Desulfovibiro (electroactive), respectively. Further, the coexistence of methanogens with SRP suggests interspecies interactions.

Characteristics of atmospheric bacterial and fungal communities in PM2.5 following biomass burning disturbance in a rural area of North China Plain

Biomass burning (BB) in North China Plain has been urgent issue in recent years due to the severe environmental impaction. Bacteria and fungi are ubiquitous in particulate matter. Their taxonomic composition, concentration, ecophysiological functions have potentially important implications in atmospheric biochemical cycle and human health. However, current knowledge about airborne microbes during biomass burning period is scant. Here we investigated bacterial and fungal community composition, abundance and potential function in Yucheng, the center of the North China Plain during summer harvest season in 2014. Monthly field observation suggested serious pollution with high concentration of PM_2.5 and water-soluble ions during biomass burning period. Elevated total bacterial and fungal concentration determined by real-time quantitative PCR was observed for samples during burning events. The predominant bacterial taxa were gram-negative, e.g. Acinetobacter, Cyanobacterium, Janthinobacterium, Massilia, Pseudomonas, accounted for 70.9% of total bacteria. The filamentous fungi Alternaria, Aspergillus, Cladosporium and Penicillium were predominant fungal genera. Metastats analysis showed significant disparity in terms of carbohydrate, amino acids metabolism, human and plant disease predicted by PICRUSt analysis between BB and non-BB events. Microbial community structure were mainly influenced by organic carbon and water-soluble ions (magnesium and potassium) suggested by redundancy analysis (RDA) and co-occurrence analysis. Our data yielded insights into microbial community dynamics following biomass burning disturbance. This study may provide potentially important reference for environmental, agricultural and health management.

Endophytic bacterial communities of Jingbai Pear trees in north China analyzed with Illumina sequencing of 16S rDNA

Plant endophytes play a crucial role in plant growth, health and ecological function. Jingbai pear (the best quality cultivar of Pyrus ussuriensi Maxim. ex Rupr.) has important ecological and economic value in north China. Conversation of its genetics has great meanings to pear genus (Pyrus L.). However, the bacterial community associated with the cultivar remains unknown. In this study, the structure of endophytic bacterial communities associated with different tissues and soil of Jingbai Pear trees was analyzed with Illumina Miseq sequencing of bacterial 16S rDNA. This is the first report on bacterial microbiome associated with Jingbai pear. Our results demonstrated that different tissues harbored a unique bacterial assemblage. Interestingly, Cyanobacteria was the most abundant phylum, followed by Proteobacteria and Actinobacteria. Samples from three different sites (soils) had significant differences in microbial communities structure. Redundancy analysis (RDA) showed that the bacterial community structure correlated significantly with soil properties-temperature, pH, nitrogen and carbon contents. The conclusion could facilitate to understand the interaction and ecological function of endophytic bacteria with host Jingbai pear trees, so as to benefit the pear variety genetic resource conservation and protection.

Characterization of Bacterial Communities in Mexican Artisanal Raw Milk "Bola de Ocosingo" Cheese by High-Throughput Sequencing

The dynamics of bacteria community of "Bola de Ocosingo" cheese, a Mexican artisanal raw milk cheese was investigated by high-throughput sequencing (454 pyrosequencing). Dairy samples (raw milk, curd, cheese at 50 and 110 days of ripening) were collected at dry (March-June) and rainy season (August-November) from three producers located in Chiapas, Mexico. In general, raw milk contained high bacterial diversity which was reduced throughout cheese manufacture. However, in two productions an important increase during cheese ripening was observed probably due to cross-contamination. Species such as Streptococcus thermophilus, Lactococcus lactis, Lactobacillus helveticus, L. delbrueckii and L. plantarum from which potential probiotic strains may be obtained, predominated during processing, varying its prevalence from one producer to another. Furthermore, low proportions of Escherichia coli/Shigella flexnerii were detected in almost all processes, however, could not be recovered by traditional methodology, indicating presence of non-cultivable cells. This work provides insights into bacteria communities of Bola de Ocosingo cheese for starter culture development, many of which are reported to provide health related benefits, and the usefulness of high-throughput sequencing to evidence cross-contamination during processing.

The role of the surface smear microbiome in the development of defective smear on surface-ripened red-smear cheese

The complex smear microbiota colonizing the surface of red-smear cheese fundamentally impacts the ripening process, appearance and shelf life of cheese. To decipher the prokaryotic composition of the cheese smear microbiome, the surface of a semi-hard surface ripened cheese was studied post-ripening by culture-based and culture-independent molecular approaches. The aim was to detect potential bacterial alterations in the composition of the cheese smear microbiota resulting from cheese storage in vacuum film-prepackaging, which is often accompanied by the development of a surface smear defect. Next-generation sequencing of amplified 16S rRNA gene fragments revealed an unexpected high diversity of a total of 132 different genera from the domains Bacteria and Archaea on the cheese surface. Beside typical smear organisms, our study revealed the presence of several microorganisms so far not associated with cheese, but related to milk, farm and cheese dairy environments. A 16S ribosomal RNA based analysis from total RNA identified the major metabolically active populations in the cheese surface smear as Actinobacteria of the genera Corynebacterium, Brevibacterium, Brachybacterium and Agrococcus. Comparison of data on a higher phylogenetic level revealed distinct differences in the composition of the cheese smear microbiome from the different samples. While the proportions of Proteobacteria and Bacteroidetes were increased in the smear of prepacked samples and in particular in defective smear, staphylococci showed an opposite trend and turned out to be strongly decreased in defective smear. In conclusion, next-generation sequencing of amplified 16S rRNA genes and 16S rRNA from total RNA extracts provided a much deeper insight into the bacterial composition of the cheese smear microbiota. The observed shifts in the microbial composition of samples from defect surface smear suggest that certain members of the Proteobacteria contribute to the observed negative organoleptic properties of the surface smear of cheese after prepacking in plastic foil.

Insights Into the Bovine Milk Microbiota in Dairy Farms With Different Incidence Rates of Subclinical Mastitis

Bovine mastitis continues to be a complex disease associated with significant economic loss in dairy industries worldwide. The incidence rate of subclinical mastitis (IRSCM) can show substantial variation among different farms; however, the milk microbiota, which have a direct influence on bovine mammary gland health, have never been associated with the IRSCM. Here, we aimed to use high-throughput DNA sequencing to describe the milk microbiota from two dairy farms with different IRSCMs and to identify the predominant mastitis pathogens along with commensal or potential beneficial bacteria. Our study showed that Klebsiella, Escherichia-Shigella, and Streptococcus were the mastitis-causing pathogens in farm A (with a lower IRSCM), while Streptococcus and Corynebacterium were the mastitis-causing pathogens in farm B (with a higher IRSCM). The relative abundance of all pathogens in farm B (22.12%) was higher than that in farm A (9.82%). However, the genus Bacillus was more prevalent in farm A. These results may be helpful for explaining the lower IRSCM in farm A. Additionally, the gut-associated genera Prevotella, Ruminococcus, Bacteroides, Rikenella, and Alistipes were prevalent in all milk samples, suggesting gut bacteria can be one of the predominant microbial contamination in milk. Moreover, Listeria monocytogenes (a foodborne pathogen) was found to be prevalent in farm A, even though it had a lower IRSCM. Overall, our study showed complex diversity between the milk microbiota in dairy farms with different IRSCMs. This suggests that variation in IRSCMs may not only be determined by the heterogeneity and prevalence of mastitis-causing pathogens but also be associated with potential beneficial bacteria. In the future, milk microbiota should be considered in bovine mammary gland health management. This would be helpful for both the establishment of a targeted mastitis control system and the control of the safety and quality of dairy products.

Dynamics of the bacterial community in a channel catfish nursery pond with a cage-pond integration system

The changes in the bacterial community composition in a channel catfish nursery pond with a cage-pond integration system were investigated by sequencing of the 16S rRNA gene through Illumina MiSeq sequencing platforms. A total of 1 362 877 sequences and 1440 operational taxonomic units were obtained. Further analysis showed that the dominant phyla in the cage and pond groups were similar, including Actinobacteria, Cyanobacteria, Proteobacteria, and Bacteroidetes, although a significant difference was detected between them by ANOSIM (P < 0.05). Temporal changes and site variation were significantly related to the variation of the bacterial community. A comprehensive analysis of the diversity and evenness of the bacterial 16S rRNA gene, redundancy analysis (RDA), and partial Mantel test showed that the bacterial community composition in a cage-pond integration system was shaped more by temporal variation than by site variation. RDA also indicated that water temperature, total dissolved solids, and Secchi depth had the largest impact on bacterial populations.

Dynamics and diversity of microbial community succession during fermentation of Suan yu, a Chinese traditional fermented fish, determined by high throughput sequencing

The main goal of this study was to investigate the dynamics, diversity and succession of microbial community present during the preparation of Suan yu (fermented fish), with and without starter cultures by high-throughput sequencing of 16S rRNA and ITS1 genes. Firmicutes and Ascomycota were the predominant phyla of bacteria and fungi, respectively, in all samples. At the genus level, Lactobacillus, Macrococcus and Staphylococcus were the predominating bacteria throughout the fermentation process, regardless of the inclusion of starter cultures. Saccharomyces was the predominating fungal genus in the early-fermentation stage of samples that inoculated starter cultures (MS), while the final product was dominated by Candida and Wickerhamomyces. Compared with naturally-fermented samples (NS; no starter cultures), Lactococcus, Leuconostoc, Enterococcus, Vibrio, Fusicolla and Torulaspora were inhibited and Aureobasidium emerged in samples inoculated with starter cultures (P < .05). Unweighted pair-group and principal component analyses of bacterial and fungal compositions revealed that microbiota structures differed between NS and MS samples. Redundancy analysis indicated that water content and pH might be important factors influencing the dominant bacterial and fungal community. Results indicated that microbial community were dynamic during fermentation process and the inoculation of mixed starter culture inhibited the growth of many organisms associated with food spoilage and contributed to the improvement of the quality of Suan yu products.

Sequencing of the Cheese Microbiome and Its Relevance to Industry

The microbiota of cheese plays a key role in determining its organoleptic and other physico-chemical properties. It is essential to understand the various contributions, positive or negative, of these microbial components in order to promote the growth of desirable taxa and, thus, characteristics. The recent application of high throughput DNA sequencing (HTS) facilitates an even more accurate identification of these microbes, and their functional properties, and has the potential to reveal those microbes, and associated pathways, responsible for favorable or unfavorable characteristics. This technology also facilitates a detailed analysis of the composition and functional potential of the microbiota of milk, curd, whey, mixed starters, processing environments, and how these contribute to the final cheese microbiota, and associated characteristics. Ultimately, this information can be harnessed by producers to optimize the quality, safety, and commercial value of their products. In this review we highlight a number of key studies in which HTS was employed to study the cheese microbiota, and pay particular attention to those of greatest relevance to industry.

16S rRNA Gene Primer Validation for Bacterial Diversity Analysis of Vegetable Products

High-throughput sequencing of the 16S rRNA gene enhances understanding of microbial diversity from complex environmental samples. The 16S rRNA gene is currently the most important target in bacterial evolution and ecology studies, particularly for determination of phylogenetic relationships among taxa, exploration of bacterial diversity in a given environment, and quantification of the relative abundance of taxa at various levels. However, some parts of the conserved region of the bacterial 16S rRNA gene are similar to the conserved regions of plant chloroplasts and eukaryotic mitochondria. Therefore, if DNA contains a large amount of nontarget DNA, this nontarget DNA can be coamplified and consequently produce useless sequence reads. We experimentally assessed the primer pair 335f/769r and the widely used bacterial primer pair SD (S-D-Bact-0341-b-S-17/S-D-Bact-0785-a-A-21). The primer pair 335f/769r was examined for its ability to amplify bacterial DNA in plant and animal feed samples by using the single-strand confirmation polymorphism method. In our present study, these primer pairs were validated for microbial community structure analysis with complex food matrices by using next-generation sequencing. The sequencing results revealed that the primer pair 335f/769r successfully resulted in fewer chloroplast and mitochondrial sequence reads than generated by the universal primer pair SD and therefore is comparatively suitable for metagenomic analyses of complex food matrices, particularly those that are rich in plant DNA. Additionally, some taxonomic groups were missed entirely when only the SD primer pair was used.

Diversity within Italian Cheesemaking Brine-Associated Bacterial Communities Evidenced by Massive Parallel 16S rRNA Gene Tag Sequencing

This study explored the bacterial diversity of brines used for cheesemaking in Italy, as well as their physicochemical characteristics. In this context, 19 brines used to salt soft, semi-hard, and hard Italian cheeses were collected in 14 commercial cheese plants and analyzed using a culture-independent amplicon sequencing approach in order to describe their bacterial microbiota. Large NaCl concentration variations were observed among the selected brines, with hard cheese brines exhibiting the highest values. Acidity values showed a great variability too, probably in relation to the brine use prior to sampling. Despite their high salt content, brine microbial loads ranged from 2.11 to 6.51 log CFU/mL for the total mesophilic count. Microbial community profiling assessed by 16S rRNA gene sequencing showed that these ecosystems were dominated by Firmicutes and Proteobacteria, followed by Actinobacteria and Bacteroidetes. Cheese type and brine salinity seem to be the main parameters accountable for brine microbial diversity. On the contrary, brine pH, acidity and protein concentration, correlated to cheese brine age, did not have any selective effect on the microbiota composition. Nine major genera were present in all analyzed brines, indicating that they might compose the core microbiome of cheese brines. Staphylococcus aureus was occasionally detected in brines using selective culture media. Interestingly, bacterial genera associated with a functional and technological use were frequently detected. Indeed Bifidobacteriaceae, which might be valuable probiotic candidates, and specific microbial genera such as Tetragenococcus, Corynebacterium and non-pathogenic Staphylococcus, which can contribute to sensorial properties of ripened cheeses, were widespread within brines.

Coupling electrochemical and biological methods for 17α-ethinylestradiol removal from water by different microorganisms

17α-ethynylestradiol (EE2) has become a growing concern due to its wide detection and high estrogenic potency. However, biodegradation of EE2 with individual microorganisms demonstrated poor degradation efficiency ranging from 10.3% to 45.8% in 120h. Now, a system combining electrochemical with biological degradation was tested for its ability to remove EE2 from aqueous solution. EE2 removal is promoted at high dissolved oxygen concentrations and low pH when electrochemical methods alone are employed. Coupling electrochemical methods with anaerobic bacteria can improve the EE2 removal after 90min to as much as 81.9% with a reaction rate constant of 0.0195min^-1. An electric current of 100mA at pH5.5 inhibits the growth of most microbial species, but Shewanella and Aeromonas survive well. They can enhance the efficiency of direct electron transfer efficiency between the bacteria and the electrodes, promoting EE2 degradation. This study provided a theoretical basis for the future applicability of bioelectrochemical technology to remove steroids from waste water.

Response of the bacterial community in an on-farm biopurification system, to which diverse pesticides are introduced over an agricultural season

A biopurification system (BPS) is used on-farm to clean pesticide-contaminated wastewater. Due to high pesticide loads, a BPS represents a hot spot for the proliferation and selection as well as the genetic adaptation of discrete pesticide degrading microorganisms. However, while considerable knowledge exists on the biodegradation of specific pesticides in BPSs, the bacterial community composition of these systems has hardly been explored. In this work, the Shannon diversity, the richness and the composition of the bacterial community within an operational BPS receiving wastewater contaminated with various pesticides was, for the first time, elucidated over the course of an agricultural season, using DGGE profiling and pyrosequencing of 16S rRNA gene fragments amplified from total community DNA. During the agricultural season, an increase in the concentration of pesticides in the BPS was observed along with the detection of significant community changes including a decrease in microbial diversity. Additionally, a significant increase in the relative abundance of Proteobacteria, mainly the Gammaproteobacteria, was found, and OTUs (operational taxonomic units) affiliated to Pseudomonas responded positively during the course of the season. Furthermore, a banding-pattern analysis of 16S rRNA gene-based DGGE fingerprinting, targeting the Alpha- and Betaproteobacteria as well as the Actinobacteria, indicated that the Betaproteobacteria might play an important role. Interestingly, a decrease of Firmicutes and Bacteroidetes was observed, indicating their selective disadvantage in a BPS, to which pesticides have been introduced.

Hydrogen sulfide (H2S) emission control by aerobic sulfate reduction in landfill

H₂S emissions from landfill sites resulting from sulfate reduction has become a serious human health and ecological safety issue. This study investigated H₂S emission behavior and sulfate metabolism occurring in simulated landfills under different operating conditions. Under aerobic conditions, great attenuation of the original sulfate content (from around 6000 mg kg⁻¹ dropped to below 800 mg kg⁻¹) with corresponding accumulation of sulfides and elemental sulfur were observed, indicating that sulfate reduction processes were intense under such conditions. Analysis of the bacterial community in these landfills showed great abundance (1.10%) and diversity of sulfur reducing types, confirming their active involvement in this process. In particular, the total abundance of sulfate-reducing bacteria increased nearly 30 times under aerobic conditions, leading to the transformation of sulfate to sulfide and other reduced sulfur species. Although exposure to air promoted the accumulation of sulfide, it did not lead to an increase in H₂S release in these landfills.

Metagenomics analysis of microbial communities associated with a traditional rice wine starter culture (Xaj-pitha) of Assam, India

This is the first report on the microbial diversity of xaj-pitha, a rice wine fermentation starter culture through a metagenomics approach involving Illumine-based whole genome shotgun (WGS) sequencing method. Metagenomic DNA was extracted from rice wine starter culture concocted by Ahom community of Assam and analyzed using a MiSeq^® System. A total of 2,78,231 contigs, with an average read length of 640.13 bp, were obtained. Data obtained from the use of several taxonomic profiling tools were compared with previously reported microbial diversity studies through the culture-dependent and culture-independent method. The microbial community revealed the existence of amylase producers, such as Rhizopus delemar, Mucor circinelloides, and Aspergillus sp. Ethanol producers viz., Meyerozyma guilliermondii, Wickerhamomyces ciferrii, Saccharomyces cerevisiae, Candida glabrata, Debaryomyces hansenii, Ogataea parapolymorpha, and Dekkera bruxellensis, were found associated with the starter culture along with a diverse range of opportunistic contaminants. The bacterial microflora was dominated by lactic acid bacteria (LAB). The most frequent occurring LAB was Lactobacillus plantarum, Lactobacillus brevis, Leuconostoc lactis, Weissella cibaria, Lactococcus lactis, Weissella para mesenteroides, Leuconostoc pseudomesenteroides, etc. Our study provided a comprehensive picture of microbial diversity associated with rice wine fermentation starter and indicated the superiority of metagenomic sequencing over previously used techniques.

Metagenomics insights into food fermentations

This review describes the recent advances in the study of food microbial ecology, with a focus on food fermentations. High‐throughput sequencing (HTS) technologies have been widely applied to the study of food microbial consortia and the different applications of HTS technologies were exploited in order to monitor microbial dynamics in food fermentative processes. Phylobiomics was the most explored application in the past decade. Metagenomics and metatranscriptomics, although still underexploited, promise to uncover the functionality of complex microbial consortia. The new knowledge acquired will help to understand how to make a profitable use of microbial genetic resources and modulate key activities of beneficial microbes in order to ensure process efficiency, product quality and safety.