Article
Agricultural Engineering
Nathan Innard, James P. J. Chong
Summary: Mixed anaerobic microbial communities play a key role in valorizing waste biomass through anaerobic digestion, and are important in soil and animal microbiomes. Understanding interactions between individual species within these communities is crucial for improving the performance and potential applications of green technology. The challenges associated with assessing the status of anaerobic microbial communities, incorporating measurements into control philosophies, and enhancing their potential to produce higher value products from waste materials are discussed.
BIORESOURCE TECHNOLOGY
(2022)
Article
Microbiology
Laura Sisk-Hackworth, Adrian Ortiz-Velez, Micheal B. Reed, Scott T. Kelley
Summary: Periodontal disease (PD) is a chronic, progressive polymicrobial disease that induces a strong host immune response. Next-generation sequencing (NGS) studies have shown that PD biodiversity increases with pocket depth and PD communities are highly host-specific. By applying compositional data analysis (CoDA) methods, new features associated with PD, including genera Schwartzia and Aerococcus, and the cytokine C-reactive protein, have been identified. Network analysis revealed lower connectivity among taxa in deeper periodontal pockets, indicating a more random microbiome.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Plant Sciences
Izabela Podgorska-Kryszczuk
Summary: Aspergillus flavus is a pathogenic fungus that contaminates many crops with aflatoxins. Researchers have found that two yeast strains, Aureobasidium pullulans PP4 and A. pullulans ZD1, have high potential for biological control of A. flavus. These strains inhibit mycelial growth and spore germination, produce lytic enzymes, and exhibit tolerance to various environmental conditions and fungicides. They also effectively reduce lesion diameter on tomato fruit caused by A. flavus.
Article
Environmental Sciences
Sanni L. Aalto, Suvi Suurnakki, Mathis von Ahnen, Marja Tiirola, Per Bovbjerg Pedersen
Summary: Woodchip bioreactors are effective in removing nitrate from aquaculture effluents, with microbial communities including sulfate reducing bacteria (SRB) and sulfate oxidizing bacteria (SOB) playing crucial roles. The conditions within the bioreactors shape the microbial communities, with similar design and operational settings leading to similar functions. Autotrophic denitrifiers can significantly contribute to H2S consumption and nitrate removal in woodchip bioreactors, improving their overall environmental benefit.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2022)
Review
Plant Sciences
Olga Marin, Bernardo Gonzalez, Maria Josefina Poupin
Summary: Synthetic microbial communities (SynComs) are a valuable tool for understanding the outcomes of various biotic interactions, incorporating microbes, plants, and the environment. A systematic review of the literature identified the diverse composition of SynComs and highlighted the need for more standardized studies to fully harness their potential.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Microbiology
Jianing Wang, Zhuo Pan, Jianshui Yu, Zheng Zhang, Yue-zhong Li
Summary: This study comprehensively investigated the global assembly mechanisms of microbial communities and effects of community-internal influencing factors using the Earth Microbiome Project (EMP) data set. It was found that deterministic and stochastic processes contribute approximately equally to global microbial community assembly, with deterministic processes generally playing a major role in free-living and plant-associated environments, and stochastic processes being the major contributor in animal-associated environments. The assembly of functional genes is mainly attributed to deterministic processes in all microbial communities.
Article
Medicine, General & Internal
Elena M. Turek, Michael J. Cox, Michael Hunter, Jennie Hui, Phillip James, Saffron A. G. Willis-Owen, Leah Cuthbertson, Alan James, A. William Musk, Miriam F. Moffatt, William O. C. M. Cookson
Summary: This study investigated airway bacterial communities in Australian adults, revealing smoking-associated diversity loss and significant abnormalities in microbiota structure, while asthmatic microbiota were selectively affected. The study demonstrated that healthy airway microbiota form a highly structured ecosystem.
Review
Microbiology
Yili Qian, Freeman Lan, Ophelia S. Venturelli
Summary: Microbial communities and their functions are influenced by complex networks of interactions among microbes and with their environment. Dynamic models provide a promising tool to address the limited understanding of these interactions and to predict community responses to perturbations. Utilizing multiple types of models and data can help facilitate the understanding and engineering of microbial communities.
CURRENT OPINION IN MICROBIOLOGY
(2021)
Article
Microbiology
Izabela Podgorska-Kryszczuk, Ewa Solarska, Monika Kordowska-Wiater
Summary: Yeasts isolated from organic cereals showed strong inhibitory activity against Fusarium pathogens, with mechanisms including nutrient competition and inhibition of spore germination.
Article
Biochemistry & Molecular Biology
Chunyu Zhao, Zhou Jason Shi, Katherine S. Pollard
Summary: Detecting genetic variants in metagenomic data is crucial for understanding microbial communities. However, the performance of metagenotyping tools has been degraded due to the increasing diversity and close relation of species databases, which challenges current alignment algorithms. Our study identifies multi-mapping reads as a common source of errors and presents a trade-off between retaining correct alignments and limiting incorrect alignments. We also evaluate mitigation strategies and emerging methods to improve metagenotyping in response to the rapid growth in genome collections.
Article
Microbiology
Jinlan Wang, Jianqing Feng, Yongbao Zhu, Dandan Li, Jianing Wang, Weiwei Chi
Summary: The oral microbiome plays an important role in human health. This study analyzed human oral saliva samples and found that the diversity of the saliva microbiome is low. Human oral habitats have a common core bacterial community that has the greatest impact on saliva habitats. The populations of the saliva microbiome differ significantly in different regions and may be influenced by living environment and lifestyle/dietary habits. The saliva microbiome shows high similarity with the microbiomes of Aerosol and Surface, suggesting that contact and shared environment are driving factors of microbial transmission.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Jason A. Rothman, Jenna L. Riis, Katrina R. Hamilton, Clancy Blair, Douglas A. Granger, Katrine L. Whiteson
Summary: Human oral microbial communities have significant implications for oral and systemic health due to their diversity. Understanding the differences between healthy and dysbiotic oral microbiomes is important, especially within and between families. This study investigates the changes in oral microbiome composition within individuals and the impact of factors such as environmental tobacco smoke exposure, metabolic regulation, inflammation, and antioxidant potential. The findings reveal differences in oral microbiomes between children and caregivers, with shared diversity but distinct differences, and highlight the associations between the oral microbiome and various salivary markers.
Article
Ecology
Akshat Mall, Sravanti Kasarlawar, Supreet Saini
Summary: The central goal of ecology is to understand the coexistence of species, and microbial communities provide a model system to study community structure. Previous theories and experiments have suggested that communities are stabilized by antagonistic interactions, but recent research shows that synergistic interactions between species play a critical role in maintaining biodiversity and community stability.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Oncology
Angelina De Martin, Mechthild Lutge, Yves Stanossek, Celine Engetschwiler, Jovana Cupovic, Kirsty Brown, Izadora Demmer, Martina A. Broglie, Markus B. Geuking, Wolfram Jochum, Kathy D. McCoy, Sandro J. Stoeckli, Burkhard Ludewig
Summary: Squamous cell carcinoma of the tonsil, associated with high risk-human papilloma virus (HR-HPV) infections, has been found to have a distinct microbiome composition in the tonsillar crypts compared to sleep apnea patients. Specific bacterial species abundance such as Filifactor alocis and Prevotella melaninogenica are identified as traits of tonsil cancer.
Review
Biotechnology & Applied Microbiology
C. G. Conacher, N. A. Luyt, R. K. Naidoo-Blassoples, D. Rossouw, M. E. Setati, F. F. Bauer
Summary: The general interest in microbial ecology has surged in the past decade, driven by technological advances and the recognition of the fundamental services provided by these ecosystems. In biotechnology, ecosystems offer more functionalities than single species, but their complexity and interactions limit their applications. Research shows that next generation sequencing can accurately map microbiomes, but functional microbiomics is needed to bridge the gap between mapping and understanding.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Lihan Huang, Nurul Hawa Ahmad, Vijay Juneja, Erika Stapp-Kamotani, Jose Gabiola, Udit Minocha, Robert Phillips, Marie Hooker, Isabel Walls, Kim Cook, James Lindsay
Summary: This study investigated the growth kinetics of foodborne pathogen B. cereus during the commercial production of liquid egg yolk using PLA(2) treatment. The results showed that B. cytotoxicus NVH391-98 can grow prolifically at 50 degrees C, with estimated minimum, optimum, and maximum temperatures of 16.7-18.5, 47.8-48.1, and 52.1-52.4 degrees C, respectively. The dynamic model was validated with isothermal curves and it was found that holding the temperature below 15 degrees C or above 55 degrees C can effectively prevent the growth of B. cytotoxicus in egg yolk.
Article
Biotechnology & Applied Microbiology
Giacomo Mantegazza, Robin Duncan, Nicolo Telesca, Giorgio Gargari, Susanna Perotti, Patrizia Riso, Simone Guglielmetti
Summary: This study investigates whether salad-associated LAB can survive the gastrointestinal transit (GIT) and contribute to the gut microbiota. The results suggest that salad-associated LAB can survive in the gastrointestinal tract, but their quantity does not significantly alter the composition of the gut microbiota.
Article
Biotechnology & Applied Microbiology
Itsaso Baztarrika, Adrian Salazar-Sanchez, Lorena Laorden, Ilargi Martinez-Ballesteros, Rodrigo Alonso, Irati Martinez-Malaxetxebarria
Summary: The infection mechanisms of Arcobacter are still uncertain. This study found that Arcobacter isolates from food and water sources were able to adhere and invade Caco-2 cells, and carried at least two virulence markers. A. butzleri showed higher virulent activity compared to A. cryaerophilus, while A. lanthieri, A. skirrowii, and A. vitoriensis exhibited even higher adhesion and invasion values. Sewage isolates were more adherent and invasive, and had a higher gene content. The association between cadF and hecA with high adhesion capability was identified for the first time.
Article
Biotechnology & Applied Microbiology
Balaji Sundararaman, Karen Shapiro, Andrea Packham, Lauren E. Camp, Rachel S. Meyer, Beth Shapiro, Richard E. Green
Summary: Pathogenic bacteria, viruses, fungi, and protozoa can cause food and waterborne diseases, and surveillance methods are needed. In this study, CNER method was used to prepare enrichment baits for difficult-to-grow pathogens. This method allows direct sequencing of pathogens from samples.
Article
Biotechnology & Applied Microbiology
Guanghui Zhou, Pengcheng Dong, Xin Luo, Lixian Zhu, Yanwei Mao, Yunge Liu, Yimin Zhang
Summary: Interactions between bacterial species in the formation of dual-species biofilms in the food industry are affected by environmental stresses, such as temperature and pH. This study found that the combination of cold and acid stresses significantly increased biofilm formation, and different temperatures resulted in variations in the presence of specific bacterial species and the secretion of extracellular substances. The findings provide valuable insights for addressing mixed biofilms in food processing under diverse stressful conditions.
Article
Biotechnology & Applied Microbiology
Carmen Sanchez, Sonia Garde, Jose Maria Landete, Javier Calzada, Dave J. Baker, Rhiannon Evans, Arjan Narbad, Melinda J. Mayer, Marta Avila
Summary: This study sequenced and compared the genomes of bacteriophages active against C. tyrobutyricum, identifying novel species and phage proteins. A phage showed high lytic activity against C. tyrobutyricum cells and remained stable under different environmental conditions. Additionally, engineered strains successfully delivered endolysin and fluorescent protein to dairy products without affecting their technological properties.
Article
Biotechnology & Applied Microbiology
Danai Etter, Michael Biggel, Mariella Greutmann, Nicole Cernela, Sophia Johler
Summary: Bacillus cytotoxicus is a thermotolerant bacterium that is linked to rare but sometimes fatal cases of diarrheal disease. It is mostly found in dehydrated foods containing potato starch or insects and may be missed in routine screening.
Article
Biotechnology & Applied Microbiology
Tong Jin, Xiangjun Zhan, Liuxin Pang, Bo Peng, Xinpeng Zhang, Wenxiu Zhu, Baowei Yang, Xiaodong Xia
Summary: The study found that CpxAR TCS is an important regulatory mechanism for the virulence of C. sakazakii. Mutants showed weakened adhesion, invasion, and survival ability, and exhibited attenuated virulence in animal models. In addition, CpxAR TCS is involved in regulating the expression of genes associated with bacterial virulence and cellular invasion.
Article
Biotechnology & Applied Microbiology
Soo-Hwan Kim, Sang-Hyun Park, Jun-Bae Ahn, Dong-Hyun Kang
Summary: In this study, a semi continuous SHS system was developed to inactivate foodborne pathogens on radish seed surfaces and enhance the seeds' salinity tolerance. The results showed that higher temperature and more treatments led to a significant reduction in microbial count on the seed surface.
Article
Biotechnology & Applied Microbiology
Yujun Zhai, Weina Tian, Kewei Chen, Linshu Lan, Jianquan Kan, Hui Shi
Summary: This research investigates the role of flagella-related genes in the adhesion of E. coli O157:H7 and the effects of certain cations on bacterial adhesion and motility. The results demonstrate that flagellar-mediated motility is critical in the early stage of adhesion, and the presence of Fe2+, Ca2+, and Mn2+ affects the adhesion and motility of wildtype strains but not flagellar function-impaired strains. These findings provide new insights into the mechanisms of bacterial adhesion and have implications for the development of anti-adhesion agents.
Article
Biotechnology & Applied Microbiology
Mariana Marggraf, Andrea Barac, Jens Andre Hammerl, Stefan Hertwig
Summary: Isolating Yersinia enterocolitica from food is challenging due to overgrowth by other microflora and the lack of a selective medium. The authors improved the standard isolation procedure, resulting in a more sensitive method, reduced background bacteria, and time savings.
Article
Biotechnology & Applied Microbiology
Rafael D. Chaves, Samuel H. Kumazawa, Amin Mousavi Khaneghah, Veronica O. Alvarenga, Humberto M. Hungaro, Anderson S. Sant'Ana
Summary: This study investigated the susceptibility to sanitizers and biofilm-forming ability of 43 Salmonella enterica and Listeria monocytogenes strains on stainless steel surfaces. The results showed variations in susceptibility to sanitizers and biofilm resistance among different strains of the pathogens, with chlorine compounds being more effective in inactivating planktonic cells and biofilms.
Article
Biotechnology & Applied Microbiology
So Yeong Mun, Wooje Lee, Soo-Young Lee, Ji Yoon Chang, Hae Choon Chang
Summary: This study reveals that lactobacilli with a strong defense system dominate the final stage of kimchi fermentation and proposes a model for the succession mechanism of kimchi lactobacilli.