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Human health and the human microbiome are inevitably intertwined, increasing their relevance in clinical research. However, the collection, transportation and storage of faecal samples may introduce bias due to methodological differences, especially since postal shipping is a common practise in large-scale clinical cohort studies. Using four different Omics layer, we determined the structural (16S rRNA sequencing, cytometric microbiota profiling) and functional integrity (SCFAs, global metabolome) of the microbiota in relation to different easy-to-handle conditions. These conditions were storage at −20 °C, −20 °C as glycerol stock, 4 °C and room temperature with and without oxygen exposure for a maximum of one week. Storage time affected the microbiota on all Omics levels. However, the magnitude was donor-dependent, highlighting the need for purpose-optimized sample collection in clinical multi-donor studies. The effects of oxygen exposure were negligible for all analyses. At ambient temperature, SCFA and compositional profiles were stable for 24 h and 48 h, respectively, while at 4 °C, SCFA profiles were maintained for 48 h. The global metabolome was highly susceptible, already changing at 24 h in non-frozen conditions. Thus, faecal microbiota was best preserved on all levels when transported as a native sample frozen within 24 h, leading to the least biased outcomes in the analysis. We conclude that the immediate freezing of native stool samples for transportation to the lab is best suited for planned multi-Omics analyses that include metabolomics to extend standard sequencing approaches. [ABSTRACT FROM AUTHOR]

Shiga toxin-producing Escherichia coli (STEC) is known as a crucial zoonotic food-borne pathogen. The main virulence factor of STEC is the production of Shiga toxins 1 and 2. A total of 400 poultry faecal samples were collected from different poultry farms in and around Tirupathi, Andhra Pradesh. The samples were cultured in selective and differential culture media, and the virulence genes of E. coli isolates were analyzed by PCR assay. Out of 400 poultry faecal samples, 170 isolates were isolated and confirmed as E. coli by different biochemical tests with an overall prevalence of 42.5%. Out of 170 E. coli isolates 154 (90.5%) were found positive by targeting uspA gene with an amplification of 884 bp. All the 154 PCR confirmed E. coli isolates subjected to multiplex PCR for the detection of virulent genes targeting eae A, stx 1 and stx 2 and obtained an amplification products, respectively at 384 bp, 180 bp and 254 bp. Out of 154 E. coli isolates, 54 (35.06%) isolates had eae A gene, 36 (23.37 %) had stx 1 gene, 41 (26.62 %) isolates had stx 2 gene, 16 (3.89 %) isolates had both eae A & stx 2, and 12 (7.79%) isolates had both stx 1 & stx 2. By avoiding contact with contaminated faeces and by maintaining proper hygienic measures at farm, contamination of poultry and poultry products may be avoided which in turn may safeguard the health of public. [ABSTRACT FROM AUTHOR]

The aim of the study was to investigate the prevalence and resistance of biofilm-forming Salmonella strains on poultry farms in Kazakhstan, Latvia, and Turkey. During the study, samples of faeces, tissues (liver and intestines) and water from drinkers were collected and analysed from January to December 2023. Salmonella strains were isolated and identified using standard microbiological methods. A total of 150 Salmonella strains were isolated and identified, of which 90 strains were obtained from faecal samples, 40 from tissue samples and 20 from water samples. The distribution of strains by country showed that in Kazakhstan, Latvia and Turkey, the largest number of strains were isolated from faecal samples. Of the 80 Salmonella Enteritidis strains, most showed the ability to form biofilms, as determined by the crystal violet method, with subtypes SE1 and SE2 showing the highest propensity for biofilm formation. Among the Salmonella Typhimurium strains, a significant biofilm formation ability was found in the ST1 subtype. Antibiotic resistance was determined using the disc diffusion method. The biofilm-forming strains showed higher antibiotic resistance compared to the non-biofilm-forming strains. Of the 150 strains isolated, 105 showed resistance to at least one of the antibiotics tested, with the highest level of resistance among Salmonella Typhimurium strains. Correlation analysis revealed a significant positive relationship between the level of biofilm formation and antibiotic resistance. The results demonstrate the need to introduce the development of new methods of control and prevention of infections on poultry farms, which would take into account the peculiarities of biofilm formation and antibiotic resistance of certain strains

The aim of the study was to investigate the prevalence and resistance of biofilm-forming Salmonella strains on poultry farms in Kazakhstan, Latvia, and Turkey. During the study, samples of faeces, tissues (liver and intestines) and water from drinkers were collected and analysed from January to December 2023. Salmonella strains were isolated and identified using standard microbiological methods. A total of 150 Salmonella strains were isolated and identified, of which 90 strains were obtained from faecal samples, 40 from tissue samples and 20 from water samples. The distribution of strains by country showed that in Kazakhstan, Latvia and Turkey, the largest number of strains were isolated from faecal samples. Of the 80 Salmonella Enteritidis strains, most showed the ability to form biofilms, as determined by the crystal violet method, with subtypes SE1 and SE2 showing the highest propensity for biofilm formation. Among the Salmonella Typhimurium strains, a significant biofilm formation ability was found in the ST1 subtype. Antibiotic resistance was determined using the disc diffusion method. The biofilm-forming strains showed higher antibiotic resistance compared to the non-biofilm-forming strains. Of the 150 strains isolated, 105 showed resistance to at least one of the antibiotics tested, with the highest level of resistance among Salmonella Typhimurium strains. Correlation analysis revealed a significant positive relationship between the level of biofilm formation and antibiotic resistance. The results demonstrate the need to introduce the development of new methods of control and prevention of infections on poultry farms, which would take into account the peculiarities of biofilm formation and antibiotic resistance of certain strains. [ABSTRACT FROM AUTHOR]

Human health and the human microbiome are inevitably intertwined, increasing their relevance in clinical research. However, the collection, transportation and storage of faecal samples may introduce bias due to methodological differences, especially since postal shipping is a common practise in large-scale clinical cohort studies. Using four different Omics layer, we determined the structural (16S rRNA sequencing, cytometric microbiota profiling) and functional integrity (SCFAs, global metabolome) of the microbiota in relation to different easy-to-handle conditions. These conditions were storage at −20 °C, −20 °C as glycerol stock, 4 °C and room temperature with and without oxygen exposure for a maximum of one week. Storage time affected the microbiota on all Omics levels. However, the magnitude was donor-dependent, highlighting the need for purpose-optimized sample collection in clinical multi-donor studies. The effects of oxygen exposure were negligible for all analyses. At ambient temperature, SCFA and compositional profiles were stable for 24 h and 48 h, respectively, while at 4 °C, SCFA profiles were maintained for 48 h. The global metabolome was highly susceptible, already changing at 24 h in non-frozen conditions. Thus, faecal microbiota was best preserved on all levels when transported as a native sample frozen within 24 h, leading to the least biased outcomes in the analysis. We conclude that the immediate freezing of native stool samples for transportation to the lab is best suited for planned multi-Omics analyses that include metabolomics to extend standard sequencing approaches.

AbstractWithin the UK, the western European hedgehog (Erinaceus europaeus) has suffered a long-term population decline to the point of being considered vulnerable to extinction in Great Britain. Here we test whether the pollen content of hedgehog faeces reflects their dominantly insect diet, rather than atmospheric contamination. Palynological results show that entomophilous pollen is the most common in hedgehog faeces. This implies that the pollen signature of hedgehog faeces reflects the habitat within which they were feeding. This could therefore be used to track hedgehogs through botanically heterogeneous landscapes such as urban and sub-urban gardens. An exploratory study was also performed to assess the presence of microplastics within faecal samples. Microplastics were present in all but two samples. [ABSTRACT FROM AUTHOR]