Microbiology Research

12 pages, 2050 KiB

Open AccessArticle

Characterization of Alistipes montrealensis sp. nov., Isolated from Human Feces of a Patient with Metastatic Melanoma Treated with Immune Checkpoint Inhibitors

by Bertrand Routy, Corentin Richard, Myriam Benlaïfaoui, Simon Grandjean Lapierre, Nicholas Armstrong, Afnan Al-Saleh, Mélodie Boko, Maxime Jacq, Ian R. Watson, Catalin Mihalcioiu, Arielle Elkrief, Maryam Tidjani Alou, Meriem Messaoudene and Khoudia Diop

Microbiol. Res. 2022, 13(1), 140-151; https://doi.org/10.3390/microbiolres13010012 - 26 Feb 2022

Cited by 2 | Viewed by 4838

Abstract

Fecal microbiome culturomics of a cancer patient treated with immune checkpoint inhibitors led to the identification of a Gram-negative, rod-shaped, obligate anaerobic, non-motile, non-spore-forming bacterium, designated strain kh20^T, which was phylogenetically assigned to the genus Alistipes. Strain kh20^T demonstrated [...] Read more.

Fecal microbiome culturomics of a cancer patient treated with immune checkpoint inhibitors led to the identification of a Gram-negative, rod-shaped, obligate anaerobic, non-motile, non-spore-forming bacterium, designated strain kh20^T, which was phylogenetically assigned to the genus Alistipes. Strain kh20^T demonstrated a 98.61% 16S rRNA sequence similarity with A.shahii WAL 8301^T. The bacteria cells generated catalase but no oxidase. Iso-C_15:0 (26.6%), anteiso-C_15:0 (19.9%), and iso-C_17:0 (17.2%) were the major cellular fatty acids identified in its composition. The G+C content of its genome was 57.2%. Strain kh20^T showed significantly low values for DNA-DNA Hybridation (DDH ≤ 33.70%) and Average Nucleotide Identity (ANI ≤ 86.35%) compared with other Alistipes species. Based on these findings, we concluded that strain kh20^T represented a novel bacterium, and we proposed the name Alistipes montrealensis sp. nov. (CECT 30384 and CSUR Q6005). Full article

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3 pages, 154 KiB

Open AccessEditorial

Publisher’s Note: We Changed Page Numbers to Article Numbers for Articles Published in Microbiology Research Volumes 1–Volume 11, Issue 1

by Microbiology Research Editorial Office

Microbiol. Res. 2022, 13(1), 137-139; https://doi.org/10.3390/microbiolres13010011 - 23 Feb 2022

Viewed by 1735

Abstract

Microbiology Research [...] Full article

9 pages, 272 KiB

Open AccessArticle

Inoculation, Growth and Bactericidal Effects of Three Kombucha Cultures

by Jill Ann Jarrell, Namrata Walia, Diana Nemergut, Amar Agadi and Joan W. Bennett

Microbiol. Res. 2022, 13(1), 128-136; https://doi.org/10.3390/microbiolres13010010 - 18 Feb 2022

Cited by 5 | Viewed by 4602

Abstract

Kombucha, a domesticated consortium of several microorganisms grown on sugared tea, has been valued as a nutritive health aid for over a millennium. In this study, three cultures of kombucha were obtained from diverse sources. Different inoculation methods were compared, and the wet [...] Read more.

Kombucha, a domesticated consortium of several microorganisms grown on sugared tea, has been valued as a nutritive health aid for over a millennium. In this study, three cultures of kombucha were obtained from diverse sources. Different inoculation methods were compared, and the wet and dry weights of the nascent pellicles were measured when cultured on several carbon sources. In addition, the anti-bacterial properties of the fermented kombucha teas were tested against Escherichia coli and Staphylococcus epidermis. Inoculation with macerated pellicles gave the fastest kombucha growth. The best carbon sources for growth of the nascent kombucha pellicles were sucrose, glucose, and fructose. On maltose, galactose, and lactose, not only did the kombucha pellicles grow poorly but 25% were also contaminated by common airborne molds. Good growth of the kombucha cultures was correlated with low pH of the fermented tea. Antibacterial effects of concentrated fermented teas and vinegar were similar to those of 1 mmol ampicillin against Escherichia coli or 0.01 mmol penicillin against Staphylococcus epidermis. When the pH of concentrated kombucha teas was neutralized, their bactericidal effects were no better than unfermented controls. Full article

(This article belongs to the Collection Microbiology and Technology of Fermented Foods)

14 pages, 2538 KiB

Open AccessArticle

Interactive Inhibition of Aflatoxigenic Aspergillus flavus and Ochratoxigenic Aspergillus carbonarius by Aspergillus oryzae under Fluctuating Temperatures

by Retty Putri Utami Dwipa, Thanapoom Maneeboon, Chananya Chuaysrinule and Warapa Mahakarnchanakul

Microbiol. Res. 2022, 13(1), 114-127; https://doi.org/10.3390/microbiolres13010009 - 15 Feb 2022

Cited by 6 | Viewed by 2965

Abstract

This study aimed to evaluate the effectiveness of A. oryzae in inhibiting aflatoxin B₁ (AFB₁) and ochratoxin A (OTA) production by A. flavus and A. carbonarius, respectively, under shifting temperatures. A. oryzae was tested on different agar, namely coconut cream [...] Read more.

This study aimed to evaluate the effectiveness of A. oryzae in inhibiting aflatoxin B₁ (AFB₁) and ochratoxin A (OTA) production by A. flavus and A. carbonarius, respectively, under shifting temperatures. A. oryzae was tested on different agar, namely coconut cream agar (CCA) and chili-based agar to figure out the variation in the effectiveness of A. oryzae on the most appropriate medium for A. flavus and A. carbonarius to produce mycotoxin and under natural condition where they are predominantly found. On CCA, the temperatures applied were 20, 30, 35, 40, 20/30, 20/35, and 20/40 °C, while on chili-based agar, the temperatures imposed were 20, 40, and 20/40 °C, at varied water activity of 0.92 and 0.97a_w. The findings indicated that A. oryzae was much more effective in inhibiting the growth of A. flavus rather than A. carbonarius, yet it was able to inhibit higher OTA concentration than AFB₁ at fluctuating temperatures on CCA as the most appropriate medium for A. flavus and A. carbonarius. A. oryzae effectively inhibited AFB₁ and OTA at static temperature of 20 °C and water activity of 0.97a_w on chili-based agar. Under fluctuating temperatures (20/40 °C), A. oryzae was also able to control mycotoxin, particularly OTA at high water activity (0.97a_w). Full article

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12 pages, 1427 KiB

Open AccessArticle

First Report of Streptococcus ruminantium in Wildlife: Phenotypic Differences with a Spanish Domestic Ruminant Isolate

by Carlos Neila-Ibáñez, Ester Pintado, Roser Velarde, Xavier Fernández Aguilar, Enric Vidal, Virginia Aragon and M. Lourdes Abarca

Microbiol. Res. 2022, 13(1), 102-113; https://doi.org/10.3390/microbiolres13010008 - 8 Feb 2022

Cited by 2 | Viewed by 3053

Abstract

Streptococcus ruminantium is a recent reclassification of the former Streptococcus suis serovar 33. Although knowledge about S. suis is extensive, information on S. ruminantium host range and pathogenic potential is still scarce. This bacterium has been isolated from lesions in domestic ruminants, but [...] Read more.

Streptococcus ruminantium is a recent reclassification of the former Streptococcus suis serovar 33. Although knowledge about S. suis is extensive, information on S. ruminantium host range and pathogenic potential is still scarce. This bacterium has been isolated from lesions in domestic ruminants, but there are no reports in wild animals. Here, we provide information on lesions associated with S. ruminantium in Pyrenean chamois (Rupicapra pyrenaica) and domestic sheep from NE Spain, as well as phenotypic biopatterns and antimicrobial resistance (AMR) of the isolates. Overall, lesions caused by S. ruminantium were similar to those caused by S. suis, excluding polyserositis. Heterogeneity of the phenotypic profiles was observed within the S. ruminantium strains by VITEK-2, resulting in only two tests common to all S. ruminantium isolates and different from S. suis: Alpha-Galactosidase and Methyl-B-D-Glucopyranoside, both positive for S. suis and negative for S. ruminantium strains. Isolates from Pyrenean chamois were susceptible to all antimicrobials tested, except danofloxacin, whereas the domestic sheep isolate was resistant to tetracycline. In conclusion, S. ruminantium can cause infection and be associated with pathology in both wild and domestic ruminants. Due to its phenotypic diversity, a specific PCR is optimal for identification in routine diagnosis. Full article

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12 pages, 1107 KiB

Open AccessArticle

Antibacterial Effect and Mode of Action of Secondary Metabolites from Fungal Endophyte Associated with Aloe ferox Mill

by Tsolanku Sidney Maliehe, Melusi Mbambo, Mduduzi Innocent Nqotheni, Ngema Siyanda Senzo and Jabulani Siyabonga Emmanuel Shandu

Microbiol. Res. 2022, 13(1), 90-101; https://doi.org/10.3390/microbiolres13010007 - 3 Feb 2022

Cited by 13 | Viewed by 4381

Abstract

The constant increase in drug resistance, occurrence of incurable diseases and high medical costs, have necessitated bio-prospecting of fungi as alternative sources of therapeutic compounds. This study aimed at assessing the antibacterial effect and mode of action of secondary metabolites from fungal endophyte [...] Read more.

The constant increase in drug resistance, occurrence of incurable diseases and high medical costs, have necessitated bio-prospecting of fungi as alternative sources of therapeutic compounds. This study aimed at assessing the antibacterial effect and mode of action of secondary metabolites from fungal endophyte associated with Aloe ferox Mill. Endophytic fungus was isolated from the gel of A. ferox and identified by internal transcribed spacer (ITS) rRNA gene sequence analysis. The targets of antibacterial activity were assessed based on minimum inhibitory concentration (MIC) and the effect of the extract on respiratory chain dehydrogenase (RCD) and membrane integrity. Fourier transform-infrared spectrophotometer (FTIR) was employed to ascertain functional groups. The fungus with the most promising antibiotic-production was identified as Aspergillus welwitschiae MK450668.1. Its extract exhibited antibacterial activity with the MIC values of 0.5 and 1 mg/mL against Staphylococcus aureus (ATCC 25925) and Escherichia coli (ATCC 25922). It demonstrated the inhibitory effect on the RCD activity and destruction of membrane integrity on the test bacteria. FTIR spectrum revealed hydroxyl, amine and alkene groups. A. welwitschiae MK450668.1 serves as a potential source of effective compounds to combat the challenge of drug resistance. Full article

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3 pages, 199 KiB

Open AccessEditorial

Acknowledgment to Reviewers of Microbiology Research in 2021

by Microbiology Research Editorial Office

Microbiol. Res. 2022, 13(1), 87-89; https://doi.org/10.3390/microbiolres13010006 - 29 Jan 2022

Viewed by 2078

Abstract

Rigorous peer-reviews are the basis of high-quality academic publishing [...] Full article

23 pages, 15421 KiB

Open AccessArticle

Effect of In Situ Bioremediation of Soil Contaminated with DDT and DDE by Stenotrophomonas sp. Strain DXZ9 and Ryegrass on Soil Microorganism

by Hui Xie, Ruiyuan Liu, Yuxin Xu, Xin Liu, Fengxia Sun, Yuhan Ma and Yuying Wang

Microbiol. Res. 2022, 13(1), 64-86; https://doi.org/10.3390/microbiolres13010005 - 28 Jan 2022

Cited by 6 | Viewed by 3646

Abstract

In the present study, the changes in the microbial populations, enzyme activity and bacterial community structure in contaminated soils were investigated during the bioremediation of using Stenotrophomonas sp. strain DXZ9 and ryegrass. The results showed that the removal rates were 81% for DDT [...] Read more.

In the present study, the changes in the microbial populations, enzyme activity and bacterial community structure in contaminated soils were investigated during the bioremediation of using Stenotrophomonas sp. strain DXZ9 and ryegrass. The results showed that the removal rates were 81% for DDT and 55% for DDE (69% for DDTs) with ryegrass-microbe. Microbial activity was remarkably improved, and the number of bacteria increased sharply from 7.32 × 10⁶ to 2.56 × 10⁸ cells/g in the 10 days due to successful colonization of the strains and effects of the ryegrass rhizosphere. There was significant difference in fungi number with ryegrass when comparing the 30th and 90th days with the 210th day: The actinomycete number in the soil with ryegrass was higher than without ryegrass, and it indicated that the number of microorganisms significantly increased under the action of ryegrass. The activities of polyphenol oxidase, dehydrogenase and catalase were significantly activated by the combination of ryegrass and microbe, and urease activity was less affected: It has influence on the diversity of bacterial community structure in the soil, but its influence gradually decreased by denaturing gradient gel electrophoresis with an extension in time. The activities represented promising tools for decontaminating and restoring the ecosystem in sustainable ways, and proposing new approaches and technological bottlenecks to promote DDT biodegradation is very significant. Full article

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15 pages, 995 KiB

Open AccessArticle

Molecular Diagnosis, Antimicrobial Resistance Profiles and Disease Patterns of Gram-Positive Pathogens Recovered from Clinical Infections in Major Ha’il Hospitals

by Kamaleldin B. Said, Ahmed Alsolami, Amany M. Khalifa, Nuha A. Khalil, Soha Moursi, Ehab Rakha, Abuzar Osman, Musleh Rashidi, Taha E. Taha, Abdelhafiz I. Bashir, Safia Moussa, Ahmed Al Jadani, Hatem Nagi, Mohammad Kuddus, Obaid M. Alrashedi, Amar S. Alharbi, Abdulrahman Alfaraj, Roba Mustafa and on behalf of the Ha’il COM Research Unit Group

Microbiol. Res. 2022, 13(1), 49-63; https://doi.org/10.3390/microbiolres13010004 - 25 Jan 2022

Viewed by 3968

Abstract

Nosocomial resistance in staphylococci and enterococci is challenging. The aim of this work was to conduct a multipoint study using molecular detections, antimicrobial resistances profiles, patient demographics and disease patterns for objective assessments of Staphilococcus aureus and other Gram-positive pathogens recovered from clinical [...] Read more.

Nosocomial resistance in staphylococci and enterococci is challenging. The aim of this work was to conduct a multipoint study using molecular detections, antimicrobial resistances profiles, patient demographics and disease patterns for objective assessments of Staphilococcus aureus and other Gram-positive pathogens recovered from clinical infections in the Ha’il region. We have surveyed 188 non-duplicate Gram-positives against 22 antimicrobials for molecular-differentiation, resistance, patient demographics, and disease patterns from January–April 2021. According to definitions for acquired resistance, Staphylococcus aureus was the most frequent with multidrug resistant (65.4%), where MRSA was 60% (n = 72 out of 121). In age-identified patients, 43% were seniors ≥50 years, 38% 21–49 years, and 19% 0–20 years. In gender-identified patients, 63% were males, and 37% were females. While 25% of specimens were from the ICU, the majority (60%) of specimens were from surgical infection in other wards. Staphylococcus epidermidis was the second (15.4%) species of infection identified with 81% from bloodstream infections at the ICU and other wards. The majority of S. epidermidis patients (69%) were seniors ≥50 years, while other age groups 0–20 and 21–49 each had 14% isolates. Although S. epidermidis was multidrug-resistant, it was susceptible to many drugs. Enterococcus faecalis (13%) ranked third with two major infections; bloodstream (64%) and urinary-tract infections (36%) in mainly seniors (86%). Its isolates were fully resistant to oxacillin, penicillin, cefoxitin, and cefotaxime but nearly 100% susceptible to seven others. Other Gram-positive bacteria (6%) were susceptible to many antibiotics. The use of combinations of objective criteria is a well thought out approach in infection control. While the low-frequency of Gram-positives is an impressive achievement, future large-scale investigations should include all private hospitals, clinics and other cities over a longer sampling time to gain more insights. Although geriatric susceptibility can be justified by age and comorbidities, the staphylococcal infections in young adults and children is a global concern and warrants more vertical studies. Full article

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11 pages, 1654 KiB

Open AccessArticle

Human and Companion Animal Proteus mirabilis Sharing

by Cátia Marques, Adriana Belas, Juliana Menezes, Joana Moreira da Silva, Patrícia Cavaco-Silva, Graça Trigueiro, Luís T. Gama and Constança Pomba

Microbiol. Res. 2022, 13(1), 38-48; https://doi.org/10.3390/microbiolres13010003 - 29 Dec 2021

Cited by 6 | Viewed by 9069

Abstract

Proteus mirabilis is an important pathogen that is associated with urinary tract infections. This study aims to determine the colonization and sharing of P. mirabilis between healthy companion animals and humans that are living together and to evaluate the clonal relatedness of the [...] Read more.

Proteus mirabilis is an important pathogen that is associated with urinary tract infections. This study aims to determine the colonization and sharing of P. mirabilis between healthy companion animals and humans that are living together and to evaluate the clonal relatedness of the fecal and clinical stains. Eighteen households (24 humans, 18 dogs, 8 cats) with at least one human–animal pair were studied. Fecal samples were plated onto MacConkey and Hektoen agar and P. mirabilis PFGE analysis (NotI; Dice/UPGMA; 1.5% tolerance) was conducted for the households with multiple positive participants. Antimicrobial-resistance was tested according to CLSI. The fecal P. mirabilis pulse-types were compared with uropathogenic clinical strains (n = 183). Forty-nine P. mirabilis were isolated from eight households. The percentage of colonization in the dogs (44.4%, n = 8/18) was significantly higher (p = 0.0329) than in the humans (12.5%, n = 3/24). Three households had multiple colonized participants. One human–dog pair shared related P. mirabilis strains, which clustered with a clinical strain of animal origin (82.5%). One fecal P. mirabilis strain, from a dog, clustered with two human community-acquired clinical strains (80.9%, 88.9%). To our knowledge, this is the first report of dogs and humans living in close contact and sharing related P. mirabilis strains. The high frequency of colonization in the dogs underlines their possible role as P. mirabilis reservoirs for humans and other dogs. Full article

(This article belongs to the Special Issue Track Health at the Human-Animal-Ecosystem Interface: “One Health” Approach)

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24 pages, 1772 KiB

Open AccessReview

The History and Applications of Phage Therapy in Pseudomonas aeruginosa

by Carina Silva, Sara Sá, Carla Guedes, Carla Oliveira, Cláudio Lima, Marco Oliveira, João Mendes, Gonçalo Novais, Pilar Baylina and Ruben Fernandes

Microbiol. Res. 2022, 13(1), 14-37; https://doi.org/10.3390/microbiolres13010002 - 28 Dec 2021

Cited by 11 | Viewed by 6598

Abstract

The Pseudomonas aeruginosa is one of the bacteria that cause serious infections due to resistance to many antibiotics can be fatal in severe cases. Antimicrobial resistance is a global public health concern. To solve this problem, interest in phage therapy has revived; some [...] Read more.

The Pseudomonas aeruginosa is one of the bacteria that cause serious infections due to resistance to many antibiotics can be fatal in severe cases. Antimicrobial resistance is a global public health concern. To solve this problem, interest in phage therapy has revived; some studies are being developed to try to prove the effectiveness of this therapy. Thus, in this opinion article, several historical aspects are addressed as well some applications of phage therapy against P. aeruginosa. Full article

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13 pages, 532 KiB

Open AccessReview

Influence of Maternal Microbiome and Inflammatory Response in Preterm Birth: Recent Aspects of the Prevention of Preterm Birth

by Hee Young Cho, Sung Shin Shim, Hee Jin Park and Dong Hyun Cha

Microbiol. Res. 2022, 13(1), 1-13; https://doi.org/10.3390/microbiolres13010001 - 22 Dec 2021

Cited by 3 | Viewed by 4606

Abstract

Preterm birth (PTB) is a global health issue and one of the most challenging problems affecting 12.9 million births worldwide. PTB is a multi-etiological disease and remains incompletely understood. The major cause of PTB is infection or inflammation and disruption of the vaginal [...] Read more.

Preterm birth (PTB) is a global health issue and one of the most challenging problems affecting 12.9 million births worldwide. PTB is a multi-etiological disease and remains incompletely understood. The major cause of PTB is infection or inflammation and disruption of the vaginal microbiome, which affects the maternal immunologic response leading to PTB. The vaginal microbiome composition changes by a shift in the community are typically dominated by Lactobacillus during pregnancy. There are complex interactions between the maternal microbiome in pregnancy and the development of PTB, therefore, researchers have struggled to connect the maternal microbiome with the dysregulation of the maternal immune response in cases of PTB. The host microbiome affects alterations of the microorganisms with external stimuli such as disease, nutrition, immunity, and behavior. In this review, we discuss the complex association between the maternal microbiome and the risk of PTB and also focus on recent aspects of the prevention of PTB. Full article

(This article belongs to the Topic Novel Concepts and Approaches in Neglected, Emerging and Re-Emerging Pathogens: From Environment to Patient)

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Microbiol. Res., Volume 13, Issue 1 (March 2022) – 12 articles

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