High-throughput Method for Novel Medium Development for Culture of Anaerobic Gut Bacteria

Gut microbiota play important roles in the health of their host and detailed investigation of these organisms requires in vitro culture. Culturing strictly anaerobic bacteria can be a challenge as the gut environment they inhabit is nutritionally complex. Use of complex media containing nutritionally rich but undefined gut fluid reduces the accuracy of physiological and metabolomic studies. Here we present a high-throughput protocol for comparing growth rates of fastidiously anaerobic bacteria on different media. These protocols can be used to develop a solid medium made up of commercially sourced ingredients, providing replicable growth conditions for previously uncultured anaerobic bacteria. As many fastidious bacteria grow poorly in a liquid broth, these protocols measure bacterial growth rate on solid media. These protocols speed up and simplify the growth rate measurement process by using a multiwell format and equations in place of physical McFarland standards to calculate approximate cell density. Bacterial strains belonging to the families Erysipelotrichaceae and Lachnospiraceae (phylum Firmicutes) isolated from the hindgut of Kyphosus sydneyanus were used to demonstrate the efficacy of these protocols. Bacterial growth rates were compared between a nutritionally rich medium with gut fluid versus a novel replicable medium with mannitol. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Preparation of solid YCFA growth medium Basic Protocol 2: Collection of fish gut samples and plating to single isolates Basic Protocol 3: Genetic identification of single isolates with colony PCR and 16S rRNA gene sequencing Basic Protocol 4: Measurement of bacterial growth rates on solid media.

Pseudomonas aeruginosa Bacterioferritin Is Assembled from FtnA and BfrB Subunits with the Relative Proportions Dependent on the Environmental Oxygen Availability

Ferritins are iron storage proteins assembled from 24 subunits into a spherical and hollow structure. The genomes of many bacteria harbor genes encoding two types of ferritin-like proteins, the bacterial ferritins (Ftn) and the bacterioferritins (Bfr), which bind heme. The genome of P. aeruginosa PAO1 (like the genomes of many bacteria) contains genes coding for two different types of ferritin-like molecules, ftnA (PA4235) and bfrB (PA3531). The reasons for requiring the presence of two distinct types of iron storage protein in bacterial cells have remained largely unexplained. Attempts to understand this issue in P. aeruginosa through the recombinant expression of the ftnA and bfrB genes in E. coli host cells, coupled to the biochemical and structural characterization of the recombinant 24-mer FtnA and 24-mer BfrB molecules, have shown that each of the recombinant molecules can form an Fe³⁺-mineral core. These observations led to the suggestion that 24-mer FtnA and 24-mer BfrB molecules coexist in P. aeruginosa cells where they share iron storage responsibilities. Herein, we demonstrate that P. aeruginosa utilizes a single heterooligomeric 24-mer Bfr assembled from FtnA and BfrB subunits. The relative content of the FtnA and BfrB subunits in Bfr depends on the O₂ availability during cell culture, such that Bfr isolated from aerobically cultured P. aeruginosa is assembled from a majority of BfrB subunits. In contrast, when the cells are cultured in O₂-limiting conditions, the proportion of FtnA subunits in the isolated Bfr increases significantly and can become the most abundant subunit. Despite the variability in the subunit composition of Bfr, the 24-mer assembly is consistently arranged from FtnA subunit dimers devoid of heme and BfrB subunit dimers each containing a heme molecule.

Bloodstream infection caused by Bacteroides caccae in a patient with renal hypertension: a case report

Bacteroides caccae is an anaerobic bacterium with a reportedly high isolation rate; however, it rarely causes bloodstream infections. Patients with hypertension are at increased risk of developing anaerobic bacterial infection. In this study, we report a case of bacteremia caused by B. caccae in a patient with renal hypertension and gastrointestinal hemorrhage. This study describes the clinical manifestations of bloodstream infection involving B. caccae to provide guidance for laboratory technicians and clinicians. A 42-year-old Chinese man was admitted for gastrointestinal hemorrhage and subsequently diagnosed with anaerobic blood infection. The pathogenic bacteria isolated from anaerobic blood culture bottles were identified as B. caccae by using an automatic bacterial identification instrument and mass spectrometry (MS). B. caccae is an intestinal opportunistic pathogen that can invade the intestinal mucosa and cause anaerobic bloodstream infection. Two or more sets of blood cultures and MS identification can greatly improve the positive detection rate of blood cultures of anaerobic bacteria. Furthermore, the increased drug resistance of anaerobic bacteria necessitates drug sensitivity tests for anaerobic bacteria in many hospitals. Thus, the early prevention and control of primary diseases with appropriate diagnoses and timely anti-infection therapies are necessary to reduce B. caccae bloodstream infection.

Multicentre study of the burden of multidrug-resistant bacteria in the aetiology of infected diabetic foot ulcers

Background

Infected diabetic foot ulcer (IDFU) is a public health issue and the leading cause of non-traumatic limb amputation. Very few published data on IDFU exist in most West African countries.

Objective

The study investigated the aetiology and antibacterial drug resistance burden of IDFU in tertiary hospitals in Osun state, Nigeria, between July 2016 and April 2017.

Methods

Isolates were cultured from tissue biopsies or aspirates collected from patients with IDFU. Bacterial identification, antibiotic susceptibility testing and phenotypic detection of extended-spectrum beta-lactamase and carbapenemase production were done by established protocols. Specific resistance genes were detected by polymerase chain reaction.

Results

There were 218 microorganisms isolated from 93 IDFUs, comprising 129 (59.2%) Gram-negative bacilli (GNB), 59 (27.1%) Gram-positive cocci and 29 (13.3%) anaerobic bacteria. The top five facultative anaerobic bacteria isolated were: Staphylococcus aureus (34; 15.6%), Escherichia coli (23; 10.6%), Pseudomonas aeruginosa (20; 9.2%), Klebsiella pneumoniae (19; 8.7%) and Citrobacter spp. (19; 8.7%). The most common anaerobes were Bacteroides spp. (7; 3.2%) and Peptostreptococcus anaerobius (6; 2.8%). Seventy-four IDFUs (80%) were infected by multidrug-resistant bacteria, predominantly methicillin-resistant S. aureus and GNB producing extended-spectrum β-lactamases, mainly of the CTX-M variety. Only 4 (3.1%) GNB produced carbapenemases encoded predominantly by bla _VIM. Factors associated with presence of multidrug-resistant bacteria were peripheral neuropathy (adjusted odds ratio [AOR] = 4.05, p = 0.04) and duration of foot infection of more than 1 month (AOR = 7.63, p = 0.02).

Conclusion

Multidrug-resistant facultative anaerobic bacteria are overrepresented as agents of IDFU. A relatively low proportion of the aetiological agents were anaerobic bacteria.

Resveratrol Improves Liver Steatosis and Insulin Resistance in Non-alcoholic Fatty Liver Disease in Association With the Gut Microbiota

Resveratrol (RSV) is a potential alternative therapy for non-alcoholic fatty liver disease (NAFLD) that has been evaluated in many clinical trials, but the mechanisms of RSV action have not been fully elucidated. Recent studies suggested that the gut microbiota is an important RSV target; therefore, we speculated that the gut microbiota might mediate the beneficial effects of RSV in NAFLD. To verify this hypothesis, we established a high-fat diet (HFD)-induced NAFLD mouse model, which was subjected to RSV gavage to evaluate the therapeutic effects. We observed that RSV reduced liver steatosis and insulin resistance in NAFLD. RSV significantly changed the diversity and composition of the gut microbiota according to 16S rRNA sequencing. Gut microbiota gene function prediction showed that the enrichment of pathways related to lipid and glucose metabolism decreased after RSV treatment. Furthermore, correlation analysis indicated that the improvements in NAFLD metabolic indicators were closely related to the altered gut microbiota. We further fermented RSV with the gut microbiota in vitro to verify that RSV directly affected the gut microbiota. Our data suggested that the gut microbiota might be an important target through which RSV exerts its anti-NAFLD effect.

Effects of Anaerobic Culturing on Pathogenicity and Virulence-Related Gene Expression in Pneumococcal Pneumonia

BACKGROUND

The pathogenicity of Streptococcus pneumoniae under anaerobic conditions remains largely unknown. We examined the pathogenicity of S. pneumoniae cultured under anaerobic conditions in a murine model of pneumococcal pneumonia.

METHODS

Mice were infected with S. pneumoniae grown under anaerobic or aerobic conditions. The pathogenic effects in vivo in the lower airway tract were then compared. The effect of anaerobic culture on lytA/ply transcript levels in vitro and in vivo were analyzed by quantitative real-time polymerase chain reaction.

RESULTS

Mice inoculated with anaerobically cultured S. pneumoniae exhibited significantly lower survival rates and higher bacterial loads in the lungs and blood as compared to those infected with aerobically cultured S. pneumoniae. Aerobically cultured S. pneumoniae in the early log phase of growth was also able to induce severe pneumonia at levels equivalent to those of anaerobic S. pneumoniae. However, ply/gyrB transcript levels were significantly increased in the lungs of mice infected with anaerobically grown S. pneumoniae. In vitro, S. pneumoniae grown under anaerobic culture conditions demonstrated greater proliferation than S. pneumoniae grown under aerobic culture conditions, and bacterial concentrations were maintained for 24 hours without detectable upregulation of lytA messenger RNA.

CONCLUSIONS

S. pneumoniae grown under anaerobic conditions had the potential to induce severe invasive bacteremic pneumococcal pneumonia in a manner different from that of S. pneumoniae grown under aerobic conditions.

Systematic Culturomics Shows that Half of Chicken Caecal Microbiota Members can be Grown in Vitro Except for Two Lineages of Clostridiales and a Single Lineage of Bacteroidetes

Epidemiological data show that the composition of gut microbiota influences host health, disease status, and even behaviour. However, to confirm these epidemiological observations in controlled experiments, pure cultures of gut anaerobes must be obtained. Since the culture of gut anaerobes is not a simple task due to the large number of bacterial species colonising the intestinal tract, in this study we inoculated 174 different culture media with caecal content from adult hens, and compared the microbiota composition in the original caecal samples and in bacterial masses growing in vitro by 16S rRNA sequencing. In total, 42% of gut microbiota members could be grown in vitro and since there were some species which were not cultured but for which the culture conditions are known, it is likely that more than half of chicken gut microbiota can be grown in vitro. However, there were two lineages of Clostridiales and a single lineage of Bacteroidetes which were common in chicken caecal microbiota but resistant to culture. Of the most selective culture conditions, nutrient broths supplemented with mono- or di-saccharides, including those present in fruits, positively selected for Lactobacillaceae. The addition of bile salts selected for Veillonellaceae and YCFA (yeast casitone fatty acid agar) enriched for Desulfovibrionaceae. In addition, Erysipelotrichaceae were positively selected by colistin, trimethoprim, streptomycin and nalidixic acid. Culture conditions tested in this study can be used for the selective enrichment of desired bacterial species but also point towards the specific functions of individual gut microbiota members.

Hydrostatic Pressure Helps to Cultivate an Original Anaerobic Bacterium From the Atlantis Massif Subseafloor (IODP Expedition 357): Petrocella atlantisensis gen. nov. sp. nov

Rock-hosted subseafloor habitats are very challenging for life, and current knowledge about microorganisms inhabiting such lithic environments is still limited. This study explored the cultivable microbial diversity in anaerobic enrichment cultures from cores recovered during the International Ocean Discovery Program (IODP) Expedition 357 from the Atlantis Massif (Mid-Atlantic Ridge, 30°N). 16S rRNA gene survey of enrichment cultures grown at 10–25°C and pH 8.5 showed that Firmicutes and Proteobacteria were generally dominant. However, cultivable microbial diversity significantly differed depending on incubation at atmospheric pressure (0.1 MPa), or hydrostatic pressures (HP) mimicking the in situ pressure conditions (8.2 or 14.0 MPa). An original, strictly anaerobic bacterium designated 70B-A^T was isolated from core M0070C-3R1 (1150 meter below sea level; 3.5 m below seafloor) only from cultures performed at 14.0 MPa. This strain named Petrocella atlantisensis is a novel species of a new genus within the newly described family Vallitaleaceae (order Clostridiales, phylum Firmicutes). It is a mesophilic, moderately halotolerant and piezophilic chemoorganotroph, able to grow by fermentation of carbohydrates and proteinaceous compounds. Its 3.5 Mb genome contains numerous genes for ABC transporters of sugars and amino acids, and pathways for fermentation of mono- and di-saccharides and amino acids were identified. Genes encoding multimeric [FeFe] hydrogenases and a Rnf complex form the basis to explain hydrogen and energy production in strain 70B-A^T. This study outlines the importance of using hydrostatic pressure in culture experiments for isolation and characterization of autochthonous piezophilic microorganisms from subseafloor rocks.

Reduced Time to Positive Cutibacterium acnes Culture Utilizing a Novel Incubation Technique: A Retrospective Cohort Study

Introduction

Cutibacterium acnes (C. acnes) is a common pathogen in postoperative shoulder infections. The purpose of this study was to evaluate the time to positive cultures for C. acnes and compare our experience before and after implementation of a regulated anaerobic chamber system. We hypothesized that this would reduce the time to identify positive cultures.

Methods

This was a retrospective review of 34 patients with cultures obtained from the shoulder that were positive for C. acnes. The time until positive result was evaluated before and after implementation of a regulated anaerobic incubation chamber.

Results

Following implementation of the regulated anaerobic incubation chamber, the time until C. acnes culture growth significantly decreased from 6.5 days (range 3–10 days) to 4.9 days (range 2.75–10 days) (mean difference: 1.6 days, 95% confidence interval: 1.06–2.66 days; P = .002). True infections had a significantly shorter time to positive culture compared to contaminants (5.5 vs 6.8 days, respectively, P = .003). Increased number of positive culture specimens correlated with a shorter time to positivity (Spearman rank = −0.58, P = .007).

Conclusion

Improved anaerobic culture protocols and techniques may lead to greater accuracy and earlier diagnosis and initiation of treatment of postoperative shoulder infections.

Bacteriological Profile of Aerobic and Anaerobic Isolates of Trophic Ulcer in Leprosy: A Study from Eastern India

Introduction

Trophic ulcer is a dreaded complication of leprosy. Secondary infection compounds the damage to the already neglected ulcer.

Aims

To find out the bacterial pathogens in the isolates from trophic ulcers of leprosy and to find the drug sensitivity of the aerobic isolates so as to start a suitable antibiotic therapy.

Methodology

An institution-based, cross-sectional study done over a period of 2 years. Swab was taken from the deeper part of the ulcer. It was put on a suitable culture media. Bacteriological profile was determined and antibiogram was done subsequently.

Results

Sixty patients with trophic ulcer secondary to leprosy were screened, among which all were screened for aerobic isolates and 38 were screened for anaerobic isolates. Among the aerobic isolates, 88% of patients were culture-positive. The most common organism was Staphylococcus aureus (37.7%), followed by Pseudomonas aeruginosa (22.64%), Proteus mirabilis (15.09%), Escherischia coli (13.2%), Klebsiella (9.43%). Maximum overall sensitivity was seen with amikacin (93.1%) and linezolid (89.65%). Maximum overall resistance was noted with cotrimoxazole (58.62%) and coamoxiclav (51.72%). Among the 38 patients cultured for anaerobic isolates, 17 were culture-positive for anaerobic organisms. Isolates showing Peptococcus were 6 (15.7%), purely Peptostreptococcus were 4 (10.5%), purely bacteroides were 3 (7.8%), and mixed growths were 4 (10.5%).

Conclusion

Secondary bacterial infection is quite common in leprosy trophic ulcers. The most common organism was Staphylococcus aureus. Isolates were mostly sensitive to amikacin and linezolid and resistant to cotrimoxazole and coamoxiclav. Anaerobic isolates were not uncommon, with Peptococcus being the most common among them.

Do Positive Anaerobic Culture Results Affect Physicians' Clinical Management Decisions?

Background

Aerobic and anaerobic cultures from body fluids, abscesses, and wounds are ordered routinely. Prior studies have shown that the results of anaerobic blood cultures do not frequently lead to changes in patient management.

Methods

We performed a retrospective chart review to determine whether positive results of anaerobic tissue and fluid cultures (excluding blood) affect physicians’ treatment approaches. Of 3234 anaerobic cultures, 174 unique patient admissions had positive cultures and met inclusion criteria.

Results

Only 18% (n = 31) of patient charts with positive cultures had documented physician acknowledgment (90.3% of acknowledgments by infectious diseases physicians), with 9% (n = 15) leading to change in antibiotic regimens based on results. Seventy percent of all patients received initial empiric antibiotics active against anaerobes. Of the remaining 30% (inappropriate, unknown, or no empiric coverage), 1 regimen change was documented after culture results were known.

Conclusions

Given the lack of management change based on results of anaerobic wound cultures, the value of routine anaerobic culturing is of questionable utility.