Free-Living, Psychrotrophic Bacteria of the Genus Psychrobacter Are Descendants of Pathobionts

A seasonal study on the microbiomes of Diploid vs. Triploid eastern oysters and their denitrification potential

Oyster reefs are hotspots of denitrification mediated removal of dissolved nitrogen (N), however, information on their denitrifier microbiota is scarce. Furthermore, in oyster aquaculture, triploids are often preferred over diploids, yet again, microbiome differences between oyster ploidies are unknown. To address these knowledge gaps, farmed diploid and triploid oysters were collected over an annual growth cycle and analyzed using shotgun metagenomics and quantitative microbial elemental cycling (QMEC) techniques. Regardless of ploidy, Psychrobacter genus was abundant, with positive correlations found for genes of central metabolism, DNA metabolism, and carbohydrate metabolism. MAGs (metagenome-assembled genomes) yielded multiple Psychrobacter genomes harboring norB, narH, narI, and nirK denitrification genes, indicating their functional relevance within the eastern oysters. QMEC analysis indicated the predominance of carbon (C) and nitrogen (N) cycling genes, with no discernable patterns between ploidies. Among the N-cycling genes, the nosZII clade was overrepresented, suggesting its role in the eastern oyster's N removal processes.

Fecal and skin microbiota of two rescued Mediterranean monk seal pups during rehabilitation

IMPORTANCE

This study showed that during the rehabilitation of two rescued Mediterranean monk seal pups (Monachus monachus), the skin and fecal bacterial communities showed similar succession patterns between the two individuals. This finding means that co-housed pups share their microbiomes, and this needs to be considered in cases of infection outbreaks and their treatment. The housing conditions, along with the feeding scheme and care protocols, including the admission of antibiotics as prophylaxis, probiotics, and essential food supplements, resulted in bacterial communities with no apparent pathogenic bacteria. This is the first contribution to the microbiome of the protected seal species of M. monachus and contributes to the animal's conservation practices through its microbiome.

Comparison of the Intestinal Bacterial Communities between Captive and Semi-Free-Range Red-Crowned Cranes (Grus japonensis) before Reintroduction in Zhalong National Nature Reserve, China

The wild populations of red-crowned cranes (Grus japonensis) in west China are gradually decreasing, necessitating the optimization of reintroduction measures. This study used 16S rRNA high-throughput sequencing technology to compare the gut microbiota communities of cranes living in two modes (captive and semi-free-range) before their reintroduction in Zhalong National Nature Reserve, Heilongjiang Province, China. The results showed that Proteobacteria (74.39%) and Firmicutes (25.29%) were the dominant gut bacterial phyla inhabiting these cranes. Significant differences were found in the gut microbiota community composition between semi-free-range and captive cranes (p < 0.01). Psychrobacter, Sporosarcina, and Lactococcus were significantly enriched in captive cranes (p < 0.05), while Pseudomonadaceae_Pseudomonas, Pantoea, Lysobacter, and Enterobacteriaceae_Pseudomonas were more abundant in semi-free-range cranes (p < 0.05). The functions and community structure of gut microbiota were affected by feeding patterns (p < 0.05). The metabolic pathways of ethylbenzene degradation, PPAR signaling pathway, betalain biosynthesis, systemic lupus erythematosus, and shigellosis were up-regulated in semi-free-range cranes (p < 0.05).

Microbiota Characterization of the Cow Mammary Gland Microenvironment and Its Association with Somatic Cell Count

Subclinical mastitis is a common disease that threatens the welfare and health of dairy cows and causes huge economic losses. Somatic cell count (SCC) is the most suitable indirect index used to evaluate the degree of mastitis. To explore the relationship between SCC, diversity in the microbiome, and subclinical mastitis, we performed next-generation sequencing of the 16S rRNA gene of cow's milk with different SCC ranges. The data obtained showed that the microbiota was rich and coordinated with SCC below 2 × 105. SCC above 2 × 105 showed a decrease in the diversity of microbial genera. When SCC was below 2 × 105, the phylum Actinobacteriota accounted for the most. When SCC was between 2 × 105 and 5 × 105, Firmicutes accounted for the most, and when SCC exceeded 5 × 105, Firmicutes and Proteobacteria accounted for the most. Pathogenic genera such as Streptococcus spp. were absent, while SCC above 2 × 105 showed a decrease in the diversity of microbial genera. SCC was positively correlated with the percentage of Romboutsia, Turicibacter, and Paeniclostridium and negatively correlated with the percentage of Staphylococcus, Psychrobacter, Aerococcus, and Streptococcus. Romboutsia decreased 6.19 times after the SCC exceeded 2 × 105; the SCC increased exponentially from 2 × 105 to 5 × 105 and above 1 × 106 in Psychrobacter. Analysis of the microbiota of the different SCC ranges suggests that the development of mastitis may not only be a primary infection but may also be the result of dysbiosis in the mammary gland.

Comparative analysis of changes in diarrhea and gut microbiota in Beigang pigs

Increasing evidence indicated that the gut microbiota is a large and complex organic combination, which is closely related to the host health. Diarrhea is a disease with devastating effects on livestock that has been demonstrated to be associated with gut microbiota. Currently, studies on gut microbiota and diarrhea have involved multiple species, but changes in gut microbiota of Beigang pigs during diarrhea have not been characterized. Here, we described gut microbial changes of Beigang pigs during diarrhea. Results indicated that a total of 4423 OTUs were recognized in diarrheic and healthy Beigang pigs, and Firmicutes and Bacteroidota were the most dominant phyla regardless of health status. However, the major components of the gut microbiota changed between diarrheic and healthy Beigang pigs. Bacterial taxonomic analysis revealed that the relative abundances of 3 phyla (Synergistota, Actinobacteriota and Spirochaetota) and 30 genera increased significantly during diarrhea, whereas the relative abundances of 3 phyla (Patescibacteria, Bacteroidota and Fibrobacterota) and 41 genera decreased significantly. In conclusion, this study found significant changes in the gut microbiota of Beigang pigs during diarrhea. Meanwhile, this also lays the foundation for the prevention and treatment of diarrhea in Beigang pigs and the further discovery of more anti-diarrhea probiotics.

Body site microbiota of Magellanic and king penguins inhabiting the Strait of Magellan follow species-specific patterns

Animal hosts live in continuous interaction with bacterial partners, yet we still lack a clear understanding of the ecological drivers of animal-associated bacteria, particularly in seabirds. Here, we investigated the effect of body site in the structure and diversity of bacterial communities of two seabirds in the Strait of Magellan: the Magellanic penguin (Spheniscus magellanicus) and the king penguin (Aptenodytes patagonicus). We used 16S rRNA gene sequencing to profile bacterial communities associated with body sites (chest, back, foot) of both penguins and the nest soil of Magellanic penguin. Taxonomic composition showed that Moraxellaceae family (specifically Psychrobacter) had the highest relative abundance across body sites in both penguin species, whereas Micrococacceae had the highest relative abundance in nest soil. We were able to detect a bacterial core among 90% of all samples, which consisted of Clostridium sensu stricto and Micrococcacea taxa. Further, the king penguin had its own bacterial core across its body sites, where Psychrobacter and Corynebacterium were the most prevalent taxa. Microbial alpha diversity across penguin body sites was similar in most comparisons, yet we found subtle differences between foot and chest body sites of king penguins. Body site microbiota composition differed across king penguin body sites, whereas it remained similar across Magellanic penguin body sites. Interestingly, all Magellanic penguin body site microbiota composition differed from nest soil microbiota. Finally, bacterial abundance in penguin body sites fit well under a neutral community model, particularly in the king penguin, highlighting the role of stochastic process and ecological drift in microbiota assembly of penguin body sites. Our results represent the first report of body site bacterial communities in seabirds specialized in subaquatic foraging. Thus, we believe it represents useful baseline information that could serve for long-term comparisons that use marine host microbiota to survey ocean health.

Phylogenomics-based reclassifications in the genus Psychrobacter including emended descriptions of Psychrobacter pacificensis, Psychrobacter proteolyticus and Psychrobacter submarinus

The taxonomic status of 43 Psychrobacter species was examined based upon the genome sequences of their type strains. Three groups of type strains were found to be conspecific, Psychrobacter salsus Shivaji et al. (Syst Appl Microbiol 27:628-635, 2004. 10.1078/0723202042369956) and Psychrobacter submarinus Romanenko et al. (Int J Syst Evol Microbiol 52:1291-1297, 2002. 10.1099/00207713-52-4-1291); Psychrobacter oceani Matsuyama et al. (Int J Syst Evol Microbiol 65:1450-1455, 2015. 10.1099/ijs.0.000118) and Psychrobacter pacificensis Maruyama et al. (Int J Syst Evol Microbiol 50:835-846, 2000. 10.1099/00207713-50-2-835); and Psychrobacter proteolyticus Denner et al. (Syst Appl Microbiol 24:44-53, 2001. 10.1078/0723-2020-00006), Psychrobacter marincola Romanenko et al. (Int J Syst Evol Microbiol 52:1291-1297, 2002. 10.1099/00207713-52-4-1291) and Psychrobacter adeliensis Shivaji et al. (Syst Appl Microbiol 27:628-635, 2004. 10.1078/0723202042369956). For all three groups, the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values are > 97.69% and > 80.2%, respectively. This conclusion is supported by similarities in morphology, growth properties, and fatty acid compositions. Based on this evidence, we propose the reclassification of Psychrobacter salsus Shivaji et al. (Syst Appl Microbiol 27:628-635, 2004. 10.1078/0723202042369956) as a later heterotypic synonym of Psychrobacter submarinus Romanenko et al. (Int J Syst Evol Microbiol 52:1291-1297, 2002. 10.1099/00207713-52-4-1291); Psychrobacter oceani Matsuyama et al. (Int J Syst Evol Microbiol 65:1450-1455, 2015. 10.1099/ijs.0.000118) as a later heterotypic synonym of Psychrobacter pacificensis Maruyama et al. (Int J Syst Evol Microbiol 50:835-846, 2000. 10.1099/00207713-50-2-835), and Psychrobacter marincola Romanenko et al. (Int J Syst Evol Microbiol 52:1291-1297, 2002. 10.1099/00207713-52-4-1291) and Psychrobacter adeliensis Shivaji et al. (Syst Appl Microbiol 27:628-635, 2004. 10.1078/0723202042369956) as later heterotypic synonyms of Psychrobacter proteolyticus Denner et al. (Syst Appl Microbiol 24:44-53, 2001. 10.1078/0723-2020-00006).

Bacterial microbiota in different types of processed meat products: diversity, adaptation, and co-occurrence

As a double-edged sword, some bacterial microbes can improve the quality and shelf life of meat products, but others mainly responsible for deterioration of the safety and quality of meat products. This review aims to present a landscape of the bacterial microbiota in different types of processed meat products. After demonstrating a panoramic view of the bacterial genera in meat products, the diversity of bacterial microbiota was evaluated in two dimensions, namely different types of processed meat products and different meats. Then, the influence of environmental factors on bacterial communities was evaluated according to the storage temperature, packaging conditions, and sterilization methods. Furthermore, microbes are not independent. To explore interactions among those genera, co-occurrence patterns were examined. In these respects, this review highlighted the recent advances in fundamental principles that underlie the environmental adaption tricks and why some species tend to occur together frequently, such as metabolic cross-feeding, co-aggregate at microscale, and the intercellular signaling system. Further investigations are required to unveil the underlying molecular mechanisms that govern microbial community systems, ultimately contributing to developing new strategies to harness beneficial microorganisms and control harmful microorganisms.

Shotgun-metagenomics reveals a highly diverse and communal microbial network present in the drains of three beef-processing plants

Background

Multi-species biofilms pose a problem in various environments, especially food-processing environments. The diversity of microorganisms in these biofilms plays a critical role in their integrity and protection against external biotic and abiotic factors. Compared to single-species biofilms, mixed-species biofilms are more resistant to various stresses, including antimicrobials like sanitizers. Therefore, understanding the microbiome composition and diversity in biofilms and their metabolic potential is a priority when developing intervention techniques to combat foodborne pathogens in food processing environments.

Methods

This study aimed to describe and compare the microbiome profile of 75 drain biofilm samples obtained from five different locations (Hotscale, Hotbox, Cooler, Processing, & Grind room) of three beef-processing plants (Plant A, B & C) taken over two timepoints 2017-18 (T1) and 2021 (T2) by shotgun sequencing.

Results

Core microbiome analysis found Pseudomonas, Psychrobacter, and Acinetobacter to be the top three prevalent genera among the plants and locations. Alpha diversity analysis demonstrated a high diversity of microbiome present in all the plants and locations across the time points. Functional analysis showed the high metabolic potential of the microbial community with abundance of genes in metabolism, cell-adhesion, motility, and quorum sensing. Moreover, Quaternary Ammonium Compound (QAC) resistance genes were also observed, this is significant as QAC sanitizers are commonly used in many food processing facilities. Multi-functional genes such as transposases, polymerases, permeases, flagellar proteins, and Mobile Genetic Elements (MGEs) were found suggesting these are dynamic microbial communities that work together to protect themselves against environmental stresses through multiple defense mechanisms.

Conclusion

This study provides a framework for understanding the collective microbial network spanning a beef processing system. The results can be used to develop intervention strategies to best control these highly communicative microbial networks.

Biocidal effects of a wipe-down procedure using common veterinary cleansers on microbial burden within working canine exterior coats

Introduction

Recent work demonstrating reduction of aerosolized contamination via a wipe-down procedure using common veterinary antiseptics offers promise regarding health concerns associated with cross-contamination from working canines to humans. While mechanical reduction can be achieved via a wipe-down procedure, the biocidal impact on flora within the exterior coat is unknown.

Methodology

This study assessed the biocidal impact of antiseptics on the exterior bacterial community of the canine. Lint-free towels were saturated with 2% chlorhexidine gluconate scrub, or 7.5% povidone-iodine scrub diluted at a 1:4 ratio. Treatments were rotated across the dorsal aspect of kennel housed Foxhounds (n = 30). Sterile swabs were collected in triplicate prior to, and following wipe down, stored in Amies solution at 4°C, plated onto nutrient agar and reduction in colony forming units (CFU) was measured across both treatments. Statistical analysis utilizing PROC GLM examined effects of treatment (p ≤ 0.05). Molecular analysis of the 16S rRNA gene was completed for 3 hounds.

Results

Reduction in CFU was measured (p < 0.001) for both antiseptics. Qualitative molecular data indicated that both antiseptics had a biocidal effect on the dominant microbial community on the exterior coat with gram-positive, spore-forming taxa predominating post-treatment.

Conclusion

Effective wipe-down strategies using common veterinary cleansers should be further investigated and incorporated to safeguard working canine health and prevent cross-contamination of human personnel.

Filling in the gaps in biowaste biorefineries: The use of the solid residue after enzymatic hydrolysis for the production of biopesticides through solid-state fermentation

Alternative production processes using waste are necessary to preserve non-renewable resources and prevent scarcity of materials for future generations. Biowaste, the organic fraction of municipal solid waste, is abundant and easily available. It can be fractionated into building blocks for which fermentative processes can be designed. By using solid-state fermentation, this paper proposes a method of valorizing biowaste's residual solid fraction after enzymatic hydrolysis. In a 22 L bioreactor, two digestates from anaerobic digestion processes were evaluated as cosubstrates to modify the acidic pH of the solid residue after enzymatic hydrolysis and promote the growth of the bacterial biopesticide producer Bacillus thuringiensis. Regardless of the cosubstrate used, the final microbial populations were similar indicating microbial specialization. The final product contained 4 × 10⁸ spores per gram of dry matter and also crystal proteins of Bacillus thuringiensis var israelensis, which have insecticidal activity against pests. This method allows for the sustainable use of all materials liberated during the enzymatic hydrolysis of biowaste, including residual solids.

Current levels of microplastic pollution impact wild seabird gut microbiomes

Microplastics contaminate environments worldwide and are ingested by numerous species, whose health is affected in multiple ways. A key dimension of health that may be affected is the gut microbiome, but these effects are relatively unexplored. Here, we investigated if microplastics are associated with changes in proventricular and cloacal microbiomes in two seabird species that chronically ingest microplastics: northern fulmars and Cory's shearwaters. The amount of microplastics in the gut was significantly correlated with gut microbial diversity and composition: microplastics were associated with decreases in commensal microbiota and increases in (zoonotic) pathogens and antibiotic-resistant and plastic-degrading microbes. These results illustrate that environmentally relevant microplastic concentrations and mixtures are associated with changes in gut microbiomes in wild seabirds.

Longitudinal, Multi-Platform Metagenomics Yields a High-Quality Genomic Catalog and Guides an In Vitro Model for Cheese Communities

Microbiomes are intricately intertwined with human health, geochemical cycles, and food production. While many microbiomes of interest are highly complex and experimentally intractable, cheese rind microbiomes have proven to be powerful model systems for the study of microbial interactions. To provide a more comprehensive view of the genomic potential and temporal dynamics of cheese rind communities, we combined longitudinal, multi-platform metagenomics of three ripening washed-rind cheeses with whole-genome sequencing of community isolates. Sequencing-based approaches revealed a highly reproducible microbial succession in each cheese and the coexistence of closely related Psychrobacter species and enabled the prediction of plasmid and phage diversity and their host associations. In combination with culture-based approaches, we established a genomic catalog and a paired 16-member in vitro washed-rind cheese system. The combination of multi-platform metagenomic time-series data and an in vitro model provides a rich resource for further investigation of cheese rind microbiomes both computationally and experimentally. IMPORTANCE Metagenome sequencing can provide great insights into microbiome composition and function and help researchers develop testable hypotheses. Model microbiomes, such as those composed of cheese rind bacteria and fungi, allow the testing of these hypotheses in a controlled manner. Here, we first generated an extensive longitudinal metagenomic data set. This data set reveals successional dynamics, yields a phyla-spanning bacterial genomic catalog, associates mobile genetic elements with their hosts, and provides insights into functional enrichment of Psychrobacter in the cheese environment. Next, we show that members of the washed-rind cheese microbiome lend themselves to in vitro community reconstruction. This paired metagenomic data and in vitro system can thus be used as a platform for generating and testing hypotheses related to the dynamics within, and the functions associated with, cheese rind microbiomes.

The variation of intestinal autochthonous bacteria in cultured tiger pufferfish Takifugu rubripes

Intestinal autochthonous bacteria play important roles in the maintenance of the physiological homeostasis of animals, especially contributing to the host immune system. In the present study, the variation of autochthonous bacterial community in the intestinal tract of 2-7 months-old tiger pufferfish Takifugu rubripes and bacterial communities in the seawater of recirculating aquaculture system (RAS) and the following offshore sea cage aquaculture system (OSCS) were analyzed during the aquaculture period from May to October 2021. Proteobacteria was found to be the most dominant phyla in both intestinal and seawater bacterial communities, which accounted for 68.82% and 65.65% of the total bacterial abundance, respectively. Arcobacter was the most core bacterial taxon in the intestinal bacterial community, with the most dominant abundance (42.89%) at the genus level and dominant positions in co-occurrence relationships with other bacterial taxa (node-betweenness value of 150). Enterococcaceae was specifically enriched in the intestinal bacterial community of pufferfishes from RAS, while Vibrionaceae was enriched in the intestinal bacterial community from OSCS. The F-values of beta diversity analysis between intestinal and seawater bacterial communities generally increased from May (6.69) to October (32.32), indicating the increasing differences between the intestinal and seawater bacterial communities along with the aquaculture process. Four bacterial taxa of Weissella sp., Akkermansia muciniphila, Dietzia sp. and Psychrobacter pacificensis had significant correlations with immune response parameters, and they were suggested to be the indicators for immune status and pathological process of pufferfish. The knowledge about the specific core bacteria, potentially pathogenic bacteria and the change of bacterial community in the intestinal tract of cultured pufferfish is of great scientific significance and will contribute to the understanding of intestinal bacterial homeostasis and biosecurity practice in pufferfish aquaculture.

Microbiome Population Dynamics of Cold-Smoked Sockeye Salmon during Refrigerated Storage and after Culture Enrichment

ABSTRACT

Cold-smoked salmon is a ready-to-eat seafood product of high commercial importance. The processing and storage steps facilitate the introduction, growth, and persistence of foodborne pathogens and spoilage bacteria. The growth of commensal bacteria during storage and once the product is opened also influence the quality and safety of cold-smoked salmon. Here we investigated the microbial community through targeted 16S rRNA gene and shotgun metagenomic sequencing as means to better understand the interactions among bacteria in cold-smoked salmon. Cold-smoked salmon samples were tested over 30 days of aerobic storage at 4°C and cultured at each time point in a buffered Listeria enrichment broth (BLEB) commonly used to detect Listeria in foods. The microbiomes were composed of Firmicutes and Proteobacteria, namely, Carnobacterium, Brochothrix, Pseudomonas, Serratia, and Psychrobacter. Pseudomonas species were the most diverse species, with 181 taxa identified. In addition, we identified potential homologs to 10 classes of bacteriocins in microbiomes of cold-smoked salmon stored at 4°C and corresponding BLEB culture enrichments. The findings presented here contribute to our understanding of microbiome population dynamics in cold-smoked salmon, including changes in bacterial taxa during aerobic cold storage and after culture enrichment. This may facilitate improvements to pathogen detection and quality preservation of this food.

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