The Historical Development of Cultivation Techniques for Methanogens and Other Strict Anaerobes and Their Application in Modern Microbiology

Hanišáková, Nikola; Vítězová, Monika; Rittmann, Simon K.-M. R.

doi:10.3390/microorganisms10020412

Cited by 14 publications

(8 citation statements)

References 148 publications

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“…In contrast to 16S rRNA analysis, only eight obligate anaerobes were cultured from HS samples and Porphyromonas in specific could not be cultured at all (table 2). Although obligate anaerobes were identified in previous culture-based studies 37–41,55 , this was rather limited in our study, indicating a potential underestimation of anaerobic bacteria, associated with sub-optimal culturing conditions for anaerobes 56 .…”

Section: Discussioncontrasting

confidence: 77%

Understanding the bacterial imbalance in Hidradenitis Suppurativa patients: Insights into microbial community shifts and colonization by opportunistic pathogens

Bens,

Vanhoutvin,

Kerremans

et al. 2023

Preprint

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Patients suffering from hidradenitis suppurativa (HS) develop painful skin lesions, significantly decreasing their quality of life. This chronic disease is triggered by plugged hair follicles resulting in an aberrant immune response, skin microbiome imbalance and secondary bacterial colonization. As a result, a diversity of treatment options are currently applied, including antibiotics, biologicals like adalimumab and surgery, which often provide only short-term relief. Alternative strategies, like phage therapy, have been proposed but identification of the target bacterium is key. Therefore, a spatial and longitudinal analysis was performed on skin swabs of lesions from 39 HS patients and 18 healthy controls, leading to a total collection of 108 lesional samples and 35 control samples at different time points and locations throughout the body. Samples were subjected to 16S rRNA community analysis, as well as bacterial isolation using aerobic and anaerobic culturing in combination with MALDI-TOF. Our data demonstrate that the bacterial community present in lesions of patients with HS is out of balance compared to healthy individuals, in which the niche ofStaphylococcusandCorynebacteriumis taken over byEscherichia-Shigella. Overall, three bacterial community profiles of HS lesions and one of healthy individuals could be distinguished. Although the overall bacterial composition was not associated with the disease severity defined by the Hurley classification system, lesions often become colonized with opportunistic pathogens includingStaphylococcus aureusandPseudomonas aeruginosaat increasing disease severities. Furthermore, patients with a concurrent IBD diagnosis did not reveal a significantly different bacterial skin community.

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Section: Discussioncontrasting

confidence: 77%

Understanding the bacterial imbalance in Hidradenitis Suppurativa patients: Insights into microbial community shifts and colonization by opportunistic pathogens

Bens,

Vanhoutvin,

Kerremans

et al. 2023

Preprint

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show abstract

“…Traditional methods that limit competition for finite resources (i.e., by nutrient privatization) typically rely on spatial separation and include dilution-to-extinction or plating for colony forming units [ 9 , 10 ]. However, these techniques depend on cell abundances, are low-throughput, and are not conducive to recovering microbes that grow poorly at air-liquid interfaces, especially anaerobes [ 11 , 12 ]. Droplet microfluidics approaches have emerged as a powerful high-throughput technique to cultivate novel microorganisms in isolated bioreactors each with precise distributions of reagents necessary for growth [ 10 , 13 – 16 ], facilitating screens for antibiotic resistances [ 13 , 17 , 18 ], and measurements of cellular activity [ 19 – 21 ].…”

Section: Introductionmentioning

confidence: 99%

Double emulsions as a high-throughput enrichment and isolation platform for slower-growing microbes

McCully

Yao

Brower

et al. 2023

ISME Communications

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Our understanding of in situ microbial physiology is primarily based on physiological characterization of fast-growing and readily-isolatable microbes. Microbial enrichments to obtain novel isolates with slower growth rates or physiologies adapted to low nutrient environments are plagued by intrinsic biases for fastest-growing species when using standard laboratory isolation protocols. New cultivation tools to minimize these biases and enrich for less well-studied taxa are needed. In this study, we developed a high-throughput bacterial enrichment platform based on single cell encapsulation and growth within double emulsions (GrowMiDE). We showed that GrowMiDE can cultivate many different microorganisms and enrich for underrepresented taxa that are never observed in traditional batch enrichments. For example, preventing dominance of the enrichment by fast-growing microbes due to nutrient privatization within the double emulsion droplets allowed cultivation of slower-growing Negativicutes and Methanobacteria from stool samples in rich media enrichment cultures. In competition experiments between growth rate and growth yield specialist strains, GrowMiDE enrichments prevented competition for shared nutrient pools and enriched for slower-growing but more efficient strains. Finally, we demonstrated the compatibility of GrowMiDE with commercial fluorescence-activated cell sorting (FACS) to obtain isolates from GrowMiDE enrichments. Together, GrowMiDE + DE-FACS is a promising new high-throughput enrichment platform that can be easily applied to diverse microbial enrichments or screens.

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“…The total number of samples was 50 samples. Incubation of microorganisms was carried out on selective media according to species [17]. Cultivation of microscopic fungi was carried out in Petri dishes on Capek-Dox medium [18].…”

Section: Methods For Determining Microbial Contamination In a Poultry...mentioning

confidence: 99%

Improving the technique of protecting concrete floors in poultry houses

Fotina,

Petrov,

Havryliuk

et al. 2023

EEJET

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The object of the study was concrete floors in a poultry house with different types of litter. The paper addressed the problem of reducing microorganism contamination of concrete floors in poultry houses to prevent biological corrosion. Corrosion of the surface of the concrete floor in the form of the formation of calcium oxalate monohydrate crystals was established by scanning electron microscopy; microscopic fungi: A. pullulans, F. sporotrichioides, and A. niger were detected. The TPD MS method established that concrete samples obtained in a room with straw lose moisture by 51.52 % more, with granules – by 342.42 % (р≤0.05), with shavings by 6.06 %, compared to control. CO from concrete samples is released less with sawdust litter by 86.40 %, with straw – by 83.49 %, with shavings – by 76.69 %, with granules – by 69.90 % (р≤0.05). The CO2 content in concrete samples from the room with sawdust was lower by 86.88 % (р≤0.05), with straw – by 55.73 %, with shavings – by 38.52 %, with granules – by 23.77 %, compared to control without litter. Microbiological studies have established that 48 hours after disinfection, the total number of colonies of microorganisms on a concrete floor with a sawdust litter likely decreased by an average of 90.19 %, straw – by 91.62 %, shavings – by 79.76 %, granules – by 82.88 % (р≤0.05), in the control – by 83.73 %. It can be argued that the disinfectant destroys microorganisms on the concrete surface regardless of the type of substrate. The peculiarity of the experiment was the use of scanning electron microscopy and TPD MS methods to study structural changes in concrete. The research is distinguished by the use of a powdered disinfectant to reduce microbial damage to a concrete floor with different types of litter. The results of the experiment could be used in the aggressive environment of poultry houses to reduce the impact on concrete structures

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The Historical Development of Cultivation Techniques for Methanogens and Other Strict Anaerobes and Their Application in Modern Microbiology

Cited by 14 publications

References 148 publications

Understanding the bacterial imbalance in Hidradenitis Suppurativa patients: Insights into microbial community shifts and colonization by opportunistic pathogens

Understanding the bacterial imbalance in Hidradenitis Suppurativa patients: Insights into microbial community shifts and colonization by opportunistic pathogens

Double emulsions as a high-throughput enrichment and isolation platform for slower-growing microbes

Improving the technique of protecting concrete floors in poultry houses

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