Sources of propionic acid bacteria contamination in the milking parlor environment on Alpine Dairy Farms.

High quality raw milk is an important prerequisite for the production of long ripened raw milk cheeses. This implies not only the absence of pathogenic microorganisms in raw milk, but also low levels of spoilage bacteria, including dairy propionic acid bacteria (dPAB), that can cause blowing and sensory defects in cheese, resulting in severe economic losses for producers. Raw milk contamination with dPAB has been primarily associated with improperly cleaned milking systems, but they have been detected in feed, soil, feces and on the teat skin. The objective of this study was to identify potential sources of raw milk contamination with dPAB in the barn and milking parlor environments. We also wanted to know more about the prevalence of the dPAB species in these environments and the levels of contamination. For this purpose, 16 small scale Alpine dairy farms were visited in August 2022: samples were taken from the barn environment (e.g., swab samples, air, feed, bedding), the milking system (swab samples, residual cleaning water, cleaning sponges, milk filters) and milk samples were collected at various sampling points along the milking system. Samples were analyzed for dPAB contamination, and results showed contamination at multiple sampling locations. We observed potential adverse effects of improperly set cleaning parameters of the milking system, as well as of farm specific practices. In addition, we identified cleaning water residues as an important source of contamination. Based on these findings, we propose potential mitigation strategies to reduce the risk of raw milk contamination with cheese spoilage bacteria, thereby contributing to a more sustainable food production.

One-Year Monitoring of Prevalence and Diversity of Dairy Propionic Acid Bacteria in Raw Milk by Means of Culture-Dependent and Culture-Independent Methods.

Even low levels of dairy propionic acid bacteria (dPAB) can cause cheese defects, resulting in severe economic losses for the producers of selected raw milk cheeses. Therefore, routine quality control of raw cheese milk for dPAB contamination is essential if propionic acid fermentation is undesired. Although knowledge of dPAB contamination of raw milk is important to understand cheese spoilage, long-term dPAB screening data are outdated, and studies taking into account different farm management parameters and their potential influence on dPAB levels are scarce. This study aims to provide insight into the dPAB levels of raw milk over time, to identify farm management factors that potentially influence dPAB levels, and to compare a cultural yeast extract lactate agar (YELA) and lithium glycerol agar (LGA) and a culture-independent method (qPCR) for dPAB quantification with respect to their applicability in routine quality control for the dairy industry. For this purpose, bulk tank milk from 25 dairy farms was screened for dPAB contamination over a one-year period. We were able to identify significant differences in the dPAB contamination levels in raw milk depending on selected farm-specific factors and observed relationships between the different types of milking systems and dPAB contamination levels in raw milk. When dPAB were quantified by cultivation on YELA, strong overgrowth of commensal microbiota impeded counting. Therefore, we conclude that quantification on LGA or by qPCR is preferable. Both methods, colony counting on LGA as well as quantification of dPAB using qPCR, have advantages for the application in (routine) quality control of raw milk, one being low-tech and inexpensive, the other being fast and highly specific, but the detection of (low level) dPAB contamination in raw milk remains a challenge.

Aerobic spore-forming bacteria associated with ropy bread: Identification, characterization and spoilage potential assessment.

Aerobic spore-forming (ASF) bacteria have been reported to cause ropiness in bread. Sticky and stringy degradation, discoloration, and an odor reminiscent of rotting fruit are typical characteristics of ropy bread spoilage. In addition to economic losses, ropy bread spoilage may lead to health risks, as virulent strains of ASF bacteria are not uncommon. However, the lack of systematic approaches to quantify physicochemical spoilage characteristics makes it extremely difficult to assess rope formation in bread. To address this problem, the aim of this study was to identify, characterize and objectively assess the spoilage potential of ASF bacteria associated with ropy bread. Hence, a set of 82 ASF bacteria, including isolates from raw materials and bakery environments as well as strains from international culture collections, were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and their species identity confirmed by 16S rRNA and gyrA or panC gene sequencing. A standardized approach supported by objective colorimetric measurements was developed to assess the rope-inducing potential (RIP) of a strain by inoculating autoclaved bread slices with bacterial spores. In addition, the presence of potential virulence factors such as swarming motility or hemolysis was investigated. This study adds B. velezensis, B. inaquosorum and B. spizizenii to the species potentially implicated of causing ropy bread spoilage. Most importantly, this study introduces a standardized classification protocol for assessing the RIP of a bacterial strain. Colorimetric measurements are used to objectively quantify the degree of breadcrumb discoloration. Furthermore, our results indicate that strains capable of inducing rope spoilage in bread often exhibit swarming motility and virulence factors such as hemolysis, raising important food quality considerations.

Specificity of the AMP-6000 Method for Enumerating Clostridium Endospores in Milk.

Enumeration of endospores of butyric acid-forming clostridia in cheese milk is an essential part of milk quality monitoring for cheese producers to avoid late blowing, severe spoilage caused by clostridia during ripening. However, due to the lack of an internationally standardized method, different methods are used and it is important to consider how the choice of method affects the results. This is particularly relevant when clostridial spore counts in milk are considered for quality payments. The aim of this study was to evaluate the specificity of the AMP-6000 method for the enumeration of endospores of cheese spoiling clostridia in milk. First, to assess the prevalence of Clostridium diversity and to determine potential non-target species, we identified isolates from positive reactions of the AMP-6000 method used to quantify clostridial endospores in raw milk and teat skin samples by MALDI-TOF MS. Based on these results, a strain library was designed to evaluate method inclusivity and exclusivity using pure cultures of target and non-target strains according to ISO 16140-2:2016. Most target Clostridium tyrobutyricum strains, as well as all tested C. butyricum and C. sporogenes strains were inclusive. However, C. beijerinckii may be underestimated as only some strains gave positive results. All non-target strains of bacilli and lysinibacilli, but not all paenibacilli, were confirmed to be exclusive. This study provides performance data to better understand the results of microbiological enumeration of butyric acid-forming clostridia in milk and serves as a basis for future methodological considerations and improvements.

Clostridium strain FAM25158, a unique endospore-forming bacterium related to Clostridium tyrobutyricum and isolated from Emmental cheese shows low tolerance to salt.

The genus Clostridium is a large and diverse group of species that can cause food spoilage, including late blowing defect (LBD) in cheese. In this study, we investigated the taxonomic status of strain FAM25158 isolated from Emmental cheese with LBD using a polyphasic taxonomic and comparative genomic approach. A 16S rRNA gene sequence phylogeny suggested affiliation to the Clostridium sensu stricto cluster, with Clostridium tyrobutyricum DSM 2637T being the closest related type strain (99.16% sequence similarity). Average Nucleotide Identity (ANI) analysis revealed that strain FAM25158 is at the species threshold with C. tyrobutyricum, with ANI values ranging from 94.70 to 95.26%, while the digital DNA-DNA hybridization values were below the recommended threshold, suggesting that FAM25158 is significantly different from C. tyrobutyricum at the genomic level. Moreover, comparative genomic analysis between FAM25158 and its four closest C. tyrobutyricum relatives revealed a diversity of metabolic pathways, with FAM25158 differing from other C. tyrobutyricum strains by the presence of genes such as scrA, srcB, and scrK, responsible for sucrose utilization, and the absence of many important functional genes associated with cold and osmolality adaptation, which was further supported by phenotypic analyses. Surprisingly, strain FAM25158 exhibited unique physiologic traits, such as an optimal growth temperature of 30°C, in contrast to its closest relatives, C. tyrobutyricum species with an optimal growth temperature of 37°C. Additionally, the growth of FAM25158 was inhibited at NaCl concentrations higher than 0.5%, a remarkable observation considering its origin from cheese. While the results of this study provide novel information on the genetic content of strain FAM25158, the relationship between its genetic content and the observed phenotype remains a topic requiring further investigation.

Importance of Pre-Milking Udder Hygiene to Reduce Transfer of Clostridial Spores from Teat Skin to Raw Milk.

Butyric acid producing clostridia (BAPC) cause the so-called late-blowing defect, a serious quality problem in semi-hard and hard cheeses. Late-blown cheeses are characterized by undesired slits and cracks, irregular eyes, and off-flavors due to excessive amounts of gas and organic acids produced by clostridia. Clostridial transfer to raw milk can occur during milking through dirty teats. Therefore, teat cleaning before milking is a key factor in preventing clostridial contamination of the milk. However, different cleaning methods are used, and little information is available on the efficacy of routine teat cleaning in reducing clostridial endospores. The main objectives of this study were to assess the extent of udder contamination with BAPC spores and to investigate the efficacy of routine teat cleaning on BAPC spore counts in milk. In a longitudinal study, eight dairy farms were visited during five sampling events. Clostridial spore counts were quantified from teat skin before and after routine teat cleaning, in pooled quarter milk samples from individual cows, and in bulk tank milk samples using a most probable number method. In addition, farm management data were collected periodically through a survey, and average cow cleanliness was assessed by a veterinarian. On average, teat cleaning resulted in a 0.6 log unit reduction in BAPC spores on teat skin, and a strong positive correlation was found between BAPC spore concentrations on teat skin after cleaning and in pooled quarter milk samples. Seasonal variations and the potential influence of differences in farm management were also noted. Interestingly, average cow cleanliness correlated strongly with BAPC spore levels in milk, suggesting the potential for a quick and rough estimation method of clostridial contamination that could be implemented by farmers.

Development of a DNA Metabarcoding Method for the Identification of Insects in Food.

Insects have the potential to become an efficient and reliable food source for humans in the future and could contribute to solving problems with the current food chain. Analytical methods to verify the authenticity of foods are essential for consumer acceptance. We present a DNA metabarcoding method that enables the identification and differentiation of insects in food. The method, developed on Illumina platforms, is targeting a 200 bp mitochondrial 16S rDNA fragment, which we found to be suitable for distinguishing more than 1000 insect species. We designed a novel universal primer pair for a singleplex PCR assay. Individual DNA extracts from reference samples, DNA extracts from model foods and food products commercially available were investigated. In all of the samples investigated, the insect species were correctly identified. The developed DNA metabarcoding method has a high potential to identify and differentiate insect DNA in the context of food authentication in routine analysis.

Comparing the Efficacy of MALDI-TOF MS and Sequencing-Based Identification Techniques (Sanger and NGS) to Monitor the Microbial Community of Irrigation Water.

In order to intensify and guarantee the agricultural productivity and thereby to be able to feed the world's rapidly growing population, irrigation has become very important. In parallel, the limited water resources lead to an increase in usage of poorly characterized sources of water, which is directly linked to a higher prevalence of foodborne diseases. Therefore, analyzing the microorganisms or even the complete microbiome of irrigation water used for food production can prevent the growing numbers of such cases. In this study, we compared the efficacy of MALDI-TOF Mass spectrometry (MALDI TOF MS) identification to 16S rRNA gene Sanger sequencing of waterborne microorganisms. Furthermore, we analyzed the whole microbial community of irrigation water using high-throughput 16S rRNA gene amplicon sequencing. The identification results of MALDI-TOF MS and 16S rRNA gene Sanger sequencing were almost identical at species level (66.7%; 64.3%). Based on the applied cultivation techniques, Acinetobacter spp., Enterobacter spp., Pseudomonas spp., and Brevundimonas spp. were the most abundant cultivable genera. In addition, the uncultivable part of the microbiome was dominated by Proteobacteria followed by Actinobacteria, Bacteroidota, Patescibacteria, and Verrucomicrobiota. Our findings indicate that MALDI-TOF MS offers a fast, reliable identification method and can act as an alternative to 16S rRNA gene Sanger sequencing of isolates. Moreover, the results suggest that MALDI-TOF MS paired with 16S rRNA gene amplicon sequencing have the potential to support the routine monitoring of the microbiological quality of irrigation water.

Ropiness in Bread-A Re-Emerging Spoilage Phenomenon.

As bread is a very important staple food, its spoilage threatens global food security. Ropy bread spoilage manifests in sticky and stringy degradation of the crumb, slime formation, discoloration, and an odor reminiscent of rotting fruit. Increasing consumer demand for preservative-free products and global warming may increase the occurrence of ropy spoilage. Bacillus amyloliquefaciens, B. subtilis, B. licheniformis, the B. cereus group, B. pumilus, B. sonorensis, Cytobacillus firmus, Niallia circulans, Paenibacillus polymyxa, and Priestia megaterium were reported to cause ropiness in bread. Process hygiene does not prevent ropy spoilage, as contamination of flour with these Bacillus species is unavoidable due to their occurrence as a part of the endophytic commensal microbiota of wheat and the formation of heat-stable endospores that are not inactivated during processing, baking, or storage. To date, the underlying mechanisms behind ropy bread spoilage remain unclear, high-throughput screening tools to identify rope-forming bacteria are missing, and only a limited number of strategies to reduce rope spoilage were described. This review provides a current overview on (i) routes of entry of Bacillus endospores into bread, (ii) bacterial species implicated in rope spoilage, (iii) factors influencing rope development, and (iv) methods used to assess bacterial rope-forming potential. Finally, we pinpoint key gaps in knowledge and related challenges, as well as future research questions.

Irradiated Non-replicative Lactic Acid Bacteria Preserve Metabolic Activity While Exhibiting Diverse Immune Modulation.

In the recent years, safety concerns regarding the administration of probiotics led to an increased interest in developing inactivated probiotics, also called "paraprobiotics". Gamma irradiation represents a promising tool that can be used to produce safe paraprobiotics by inhibiting replication while preserving the structure, the metabolic activity, and the immunogenicity of bacteria. In this study, we evaluated the ability of four strains of lactic acid bacteria (LAB: Lacticaseibacillus casei, Lactobacillus acidophilus, Lactiplantibacillus plantarum, and Lacticaseibacillus paracasei) in preserving the metabolic activity and the immune modulation of swine porcine peripheral blood mononuclear cells, after gamma irradiation or heat inactivation. Our results show that all four strains retained the metabolic activity following gamma irradiation but not after heat inactivation. In terms of immune-modulatory capacity, irradiated L. acidophilus and Lc. paracasei were able to maintain an overall gene expression pattern similar to their live state, as heat inactivation did with Lc. casei. Moreover, we show that the two inactivation methods applied to the same strain can induce an opposed expression of key genes involved in pro-inflammatory response (e.g., IFNα and interleukin-6 for Lc. casei), whereas gamma irradiation of L. acidophilus and Lc. paracasei was able to induce a downregulation of the anti-inflammatory TGFß. Taken together, our data show that immune modulation can be impacted not only by different inactivation methods but also by the strain of LAB selected. This study highlights that gamma irradiation harbors the potential to produce safe non-replicative metabolically active LAB and identifies immunomodulatory capacities that may be applied as vaccine adjuvants.

Comparative Genomics Provides Insights Into Genetic Diversity of Clostridium tyrobutyricum and Potential Implications for Late Blowing Defects in Cheese.

Clostridium tyrobutyricum has been recognized as the main cause of late blowing defects (LBD) in cheese leading to considerable economic losses for the dairy industry. Although differences in spoilage ability among strains of this species have been acknowledged, potential links to the genetic diversity and functional traits remain unknown. In the present study, we aimed to investigate and characterize genomic variation, pan-genomic diversity and key traits of C. tyrobutyricum by comparing the genomes of 28 strains. A comparative genomics analysis revealed an "open" pangenome comprising 9,748 genes and a core genome of 1,179 genes shared by all test strains. Among those core genes, the majority of genes encode proteins related to translation, ribosomal structure and biogenesis, energy production and conversion, and amino acid metabolism. A large part of the accessory genome is composed of sets of unique, strain-specific genes ranging from about 5 to more than 980 genes. Furthermore, functional analysis revealed several strain-specific genes related to replication, recombination and repair, cell wall, membrane and envelope biogenesis, and defense mechanisms that might facilitate survival under stressful environmental conditions. Phylogenomic analysis divided strains into two clades: clade I contained human, mud, and silage isolates, whereas clade II comprised cheese and milk isolates. Notably, these two groups of isolates showed differences in certain hypothetical proteins, transcriptional regulators and ABC transporters involved in resistance to oxidative stress. To the best of our knowledge, this is the first study to provide comparative genomics of C. tyrobutyricum strains related to LBD. Importantly, the findings presented in this study highlight the broad genetic diversity of C. tyrobutyricum, which might help us understand the diversity in spoilage potential of C. tyrobutyricum in cheese and provide some clues for further exploring the gene modules responsible for the spoilage ability of this species.

Storage media and RNA extraction approaches substantially influence the recovery and integrity of livestock fecal microbial RNA.

Background: There is growing interest in understanding gut microbiome dynamics, to increase the sustainability of livestock production systems and to better understand the dynamics that regulate antibiotic resistance genes (i.e., the resistome). High-throughput sequencing of RNA transcripts (RNA-seq) from microbial communities (metatranscriptome) allows an unprecedented opportunity to analyze the functional and taxonomical dynamics of the expressed microbiome and emerges as a highly informative approach. However, the isolation and preservation of high-quality RNA from livestock fecal samples remains highly challenging. This study aimed to determine the impact of the various sample storage and RNA extraction strategies on the recovery and integrity of microbial RNA extracted from selected livestock (chicken and pig) fecal samples. Methods: Fecal samples from pigs and chicken were collected from conventional slaughterhouses. Two different storage buffers were used at two different storage temperatures. The extraction of total RNA was done using four different commercially available kits and RNA integrity/quality and concentration were measured using a Bioanalyzer 2100 system with RNA 6000 Nano kit (Agilent, Santa Clara, CA, USA). In addition, RT-qPCR was used to assess bacterial RNA quality and the level of host RNA contamination. Results: The quantity and quality of RNA differed by sample type (i.e., either pig or chicken) and most significantly by the extraction kit, with differences in the extraction method resulting in the least variability in pig feces samples and the most variability in chicken feces. Considering a tradeoff between the RNA yield and the RNA integrity and at the same time minimizing the amount of host RNA in the sample, a combination of storing the fecal samples in RNALater at either 4 °C (for 24 h) or -80 °C (up to 2 weeks) with extraction with PM kit (RNEasy Power Microbiome Kit) had the best performance for both chicken and pig samples. Conclusion: Our findings provided a further emphasis on using a consistent methodology for sample storage, duration as well as a compatible RNA extraction approach. This is crucial as the impact of these technical steps can be potentially large compared with the real biological variability to be explained in microbiome and resistome studies.

Effect of Two Soybean Varieties Treated with Different Heat Intensities on Ileal and Caecal Microbiota in Broiler Chickens.

Soybean products are of high importance for the protein supply of poultry. Heat treatment of soybeans is essential to ensure optimal digestibility because of intrinsic antinutritive factors typical for this feed category. However, excessive treatment promotes the Maillard reaction and reduces protein digestibility. Furthermore, Europe's efforts are to decrease dependence on imports of soybean products and enlarge local production. This process will include an increase in the variability of soybean batches, posing great challenges to adequate processing conditions. Intrinsic soybean properties plus heat treatment intensity might be able to modulate the gut microbiota, which is of crucial importance for an animal's health and performance. To assess the influence of heat treatment and soybean variety on gut microbiota, 2 soybean cakes from 2 varieties were processed at 110 °C or 120 °C and subsequently fed to 336 one-day-old broiler chickens. After 36 days, the animals were slaughtered, and the digesta of the ileum and caecum was collected. Next, 16S rRNA amplicon sequencing of the extracted DNA revealed a high discrepancy between gut sections, but there were no differences between male and female birds. Significant differences attributed to the different soybean varieties and heat intensity were detected for certain bacterial taxa. However, no effect on specific families or genera appeared. In conclusion, the results indicated the potential of processing conditions and soybean variety as microbiota-modulating factors.

Metatranscriptomic Analysis of the Chicken Gut Resistome Response to In-Feed Antibiotics and Natural Feed Additives.

The emergence of resistance against common antibiotics in the gut microbiota is a major issue for both human and livestock health. This highlights the need for understanding the impact of such application on the reservoir of antibiotic resistance genes in poultry gut and devising means to circumvent the potential resistome expansion. Phytogenic feed additives (PFAs) are potential natural alternative to antibiotic to improve animal health and performance, supposedly via positively affecting the gut microbial ecosystem, but there is little systematic information available. In this time-course study, we applied a shotgun meta-transcriptomics approach to investigate the impact of a PFA product as well as the commonly used antibiotic, zinc bacitracin either at AGP concentration or therapeutic concentration on the gut microbiome and resistome of broiler chickens raised for 35 days. Over the course of the trial, PFA treatments increased the abundance of Firmicutes such as Lactobacillus and resulted in a lower abundance of Escherichia, while the latter group increased significantly in the feces of chickens that received either AGP or AB doses of bacitracin. Tetracycline resistance and aminoglycoside resistance were the predominant antibiotic resistance gene (ARG) classes found, regardless of the treatment. PFA application resulted in a decrease in abundance of ARGs compared to those in the control group and other antibiotic treatment groups. In summary, the findings from this study demonstrate the potential of phytogenic feed additives could be an alternative to antibiotics in poultry farming, with the added benefit of counteracting antimicrobial resistance development.

The gut bacterial microbiome of Nile tilapia (Oreochromis niloticus) from lakes across an altitudinal gradient.

BACKGROUND: Microorganisms inhabiting the gut play a significant role in supporting fundamental physiological processes of the host, which contributes to their survival in varied environments. Several studies have shown that altitude affects the composition and diversity of intestinal microbial communities in terrestrial animals. However, little is known about the impact of altitude on the gut microbiota of aquatic animals. The current study examined the variations in the gut microbiota of Nile tilapia (Oreochromis niloticus) from four lakes along an altitudinal gradient in Ethiopia by using 16S rDNA Illumina MiSeq high-throughput sequencing. RESULTS: The results indicated that low-altitude samples typically displayed greater alpha diversity. The results of principal coordinate analysis (PCoA) showed significant differences across samples from different lakes. Firmicutes was the most abundant phylum in the Lake Awassa and Lake Chamo samples whereas Fusobacteriota was the dominant phylum in samples from Lake Hashengie and Lake Tana. The ratio of Firmicutes to Bacteroidota in the high-altitude sample (Lake Hashengie, altitude 2440 m) was much higher than the ratio of Firmicutes to Bacteroidota in the low altitude population (Lake Chamo, altitude 1235 m). We found that the relative abundances of Actinobacteriota, Chloroflexi, Cyanobacteria, and Firmicutes were negatively correlated with altitude, while Fusobacteriota showed a positive association with altitude. Despite variability in the abundance of the gut microbiota across the lakes, some shared bacterial communities were detected. CONCLUSIONS: In summary, this study showed the indirect influence of altitude on gut microbiota. Altitude has the potential to modulate the gut microbiota composition and diversity of Nile tilapia. Future work will be needed to elucidate the functional significance of gut microbiota variations based on the geographical environment. SIGNIFICANCE AND IMPACT OF THE STUDY: Our study determined the composition and diversity of the gut microbiota in Nile tilapia collected from lakes across an altitude gradient. Our findings greatly extend the baseline knowledge of fish gut microbiota in Ethiopian lakes that plays an important role in this species sustainable aquaculture activities and conservation.

Interaction of Soybean Varieties and Heat Treatments and Its Effect on Growth Performance and Nutrient Digestibility in Broiler Chickens.

As production of European soybeans is expected to grow, optimal processing conditions need to be ensured for small and heterogeneous batches of soybeans. The effect of different soybean varieties, as well as heat treatments, on the growth performance and nutrient digestibility in broiler chickens was investigated. Two varieties, regarded as heat stable and heat labile after preliminary experiments, were partially de-oiled and thermally processed at 110 °C for 20 min and 120 °C for 20 min. The resulting soybean cakes were integrated into a mash diet and subjected to a 36-day long feeding experiment. A total of 336 one-day-old broiler chickens were divided into 24 pens, resulting in 6 replicates per treatment. With application of the 110 °C treatment, analysis of soybean cakes showed that the commonly required reduction in trypsin inhibitor activity (TIA) was only reached with one soybean variety. The higher processing temperature of 120 °C ensured sufficient TIA reductions in both soybean varieties. Elevated TIA concentrations resulted in decreased growth performances (p < 0.05) of the chickens, whereas no negative effect from overheating on growth performance appeared. Total-tract nitrogen retention (p < 0.05) and pre-caecal digestibility of several amino acids (p < 0.10) decreased with higher processing temperatures but had no negative effects on growth performance. In conclusion, the results indicate that processing conditions adjusted to the different varieties are essential to ensure optimal product quality.

Propionic acid bacteria in the food industry: An update on essential traits and detection methods.

Propionic acid bacteria (PAB) is an umbrella term for a group of bacteria with the ability to produce propionic acid. In the past, due to this common feature and other phenotypic similarities, genetically heterogeneous bacteria were considered as a single genus, Propionibacterium. Members of this genus ranged from "dairy propionibacteria," which are widely known for their role in eye and flavor formation in cheese production, to "cutaneous propionibacteria," which are primarily associated with human skin. In 2016, the introduction of two new genera based on genotypic data facilitated a clear separation of cutaneous (Cutibacterium spp.) from dairy PAB (Propionibacterium spp., Acidipropionibacterium spp.). In light of these taxonomic changes, but with particular emphasis on dairy PAB, this review describes the current state of knowledge about metabolic pathways and other characteristics such as antibiotic resistance and virulence factors. In addition, the relevance of dairy PAB for the food industry and cheese production in particular is highlighted. Furthermore, methods for cultivation, detection, and enumeration are reviewed, incorporating the current taxonomy as well as the potential for routine applications.

The bifidobacterial distribution in the microbiome of captive primates reflects parvorder and feed specialization of the host.

Bifidobacteria, which commonly inhabit the primate gut, are beneficial contributors to host wellbeing. Anatomical differences and natural habitat allow an arrangement of primates into two main parvorders; New World monkeys (NWM) and Old World monkeys (OWM). The number of newly described bifidobacterial species is clearly elevated in NWM. This corresponds to our finding that bifidobacteria were the dominant group of cultivated gut anaerobes in NWM, while their numbers halved in OWM and were often replaced by Clostridiaceae with sarcina morphology. We examined an extended MALDI-TOF MS database as a potential identification tool for rapid screening of bifidobacterial distribution in captive primates. Bifidobacterial isolates of NWM were assigned mainly to species of primate origin, while OWM possessed typically multi-host bifidobacteria. Moreover, bifidobacterial counts reflected the feed specialization of captive primates decreasing from frugivore-insectivores, gummivore-insectivores, frugivore-folivores to frugivore-omnivores. Amplicon sequencing analysis supported this trend with regards to the inverse ratio of Actinobacteria and Firmicutes. In addition, a significantly higher diversity of the bacterial population in OWM was found. The evolution specialization of primates seems to be responsible for Bifidobacterium abundance and species occurrence. Balanced microbiota of captive primates could be supported by optimized prebiotic and probiotic stimulation based on the primate host.

The Impact of Sampling Season and Catching Site (Wild and Aquaculture) on Gut Microbiota Composition and Diversity of Nile Tilapia (Oreochromis niloticus).

The gut microbiota of fishes is known to play an essential role in diverse aspects of host biology. The gut microbiota of fish is affected by various environmental parameters, including temperature changes, salinity and diet. Studies of effect of environment on gut microbiota enables to have a further understanding of what comprises a healthy microbiota under different environmental conditions. However, there is insufficient understanding regarding the effects of sampling season and catching site (wild and aquaculture) on the gut microbiota of Nile tilapia. This study characterised gut microbial composition and diversity from samples collected from Lake Tana and the Bahir Dar aquaculture facility centre using 16S rDNA Illumina MiSeq platform sequencing. Firmicutes and Fusobacteria were the most dominant phyla in the Lake Tana samples, while Proteobacteria was the most dominant in the aquaculture samples. The results of differential abundance testing clearly indicated significant differences for Firmicutes, Fusobacteria, Bacteroidetes and Cyanobacteria across sampling months. However, Proteobacteria, Chloroflexi, Fusobacteria and Cyanobacteria were significantly enriched in the comparison of samples from the Lake Tana and aquaculture centre. Significant differences were observed in microbial diversity across sampling months and between wild and captive Nile tilapia. The alpha diversity clearly showed that samples from the aquaculture centre (captive) had a higher diversity than the wild Nile tilapia samples from Lake Tana. The core gut microbiota of all samples of Nile tilapia used in our study comprised Firmicutes, Proteobacteria and Fusobacteria. This study clearly showed the impact of sampling season and catching site (wild and aquaculture) on the diversity and composition of bacterial communities associated with the gut of Nile tilapia. Overall, this is the first study on the effects of sampling season and catching site on the gut microbiota of Nile tilapia in Ethiopia. Future work is recommended to precisely explain the causes of these changes using large representative samples of Nile tilapia from different lakes and aquaculture farms.

Biofilm-Forming Ability of Microbacterium lacticum and Staphylococcus capitis Considering Physicochemical and Topographical Surface Properties.

Biofilm characteristics of Microbacterium lacticum D84 (M. lacticum) and Staphylococcus capitis subsp. capitis (S. capitis) on polytetrafluoroethylene and AISI-304 stainless steel at early- (24, 48 h) and late-stage (144, 192 h) biofilm formation were investigated. M. lacticum biofilm structure was more developed compared to S. capitis, representing vastly mature biofilms with a strongly developed amorphous matrix, possibly extracellular polymeric substances (EPSs), at late-stage biofilm formation. S. capitis showed faster growth behavior but still resulted in a relatively flat biofilm structure. Strong correlations were found between several roughness parameters and S. capitis surface coverage (r ≥ 0.98), and between total surface free energy (γs) and S. capitis surface coverage (r = 0.89), while M. lacticum remained mostly unaffected. The pronounced ubiquitous biofilm characteristics make M. lacticum D84 a suitable model for biofilm research. Studying biofilm formation of these bacteria may help one understand bacterial adhesion on interfaces and hence reduce biofilm formation in the food industry.