Review
Microbiology
Sven Kleine Bardenhorst, Tom Berger, Frank Klawonn, Marius Vital, Andre Karch, Nicole Ruebsamen
Summary: Reproducibility in microbiome studies is hindered by a lack of consensus on data analysis strategies. The complex nature of microbiome data, combined with increasingly sophisticated research questions, requires more advanced analytical methods. Current analysis strategies in microbiome studies show significant heterogeneity, particularly in differential abundance testing, indicating a need for better guidance in analyzing increasingly complex research questions.
Review
Gastroenterology & Hepatology
Yinglin Xia
Summary: Mounting evidence has shown a link between gut microbiome and various cancers, but analyzing microbiome data poses challenges and requires proper statistical methods and normalization. This review provides an overview of the unique characteristics of microbiome data and the available normalization methods in microbiome cancer research using examples. The evaluation of these normalization methods is also comprehensively investigated.
Article
Gastroenterology & Hepatology
Anthony Mannion, Alexander Sheh, Zeli Shen, JoAnn Dzink-Fox, M. Blanca Piazuelo, Keith T. Wilson, Richard Peek, James G. G. Fox
Summary: In this study, whole metagenomic shotgun sequencing (WMS) was used to survey the microbiome in gastric biopsy samples from high-risk and low-risk gastric cancer towns in Colombia. WMS demonstrated its capability to identify and characterize bacterial taxa and functional profiles of the gastric microbiome, with advantages over traditional culture and 16S rRNA sequencing. WMS detected more bacterial taxa and risk factors for H. pylori-associated gastric disease compared to other sequencing approaches.
Review
Dermatology
Samuel C. Williams, John W. Frew, James G. Krueger
Summary: Hidradenitis suppurativa is a chronic inflammatory skin disease with unknown pathogenesis. Recent studies using gene sequencing and culture have shed light on the microbial world of HS. Specific bacteria have been identified in HS lesions, but methodologies and analyses vary in current studies.
EXPERIMENTAL DERMATOLOGY
(2021)
Article
Food Science & Technology
Jiwon Park, Dongryeoul Bae, Sun Ae Kim
Summary: Since poultry is highly susceptible to contamination by pathogens and is frequently associated with foodborne outbreaks, it is crucial to ensure microbiological safety in the chicken production chain. This study used amplicon sequencing to investigate bacterial communities in chickens and their associated environments across different stages of production. The results revealed distinct microbiota at each step, with certain bacteria dominating the final products. The study also identified the importance of hygiene management in preventing bacterial transmission and highlighted the significant contribution of processing plants to microbial contamination in the poultry industry.
FOOD RESEARCH INTERNATIONAL
(2023)
Review
Biochemistry & Molecular Biology
Yu Shi, Guoping Wang, Harry Cheuk-Hay Lau, Jun Yu
Summary: Whole genome metagenomic sequencing is a powerful technology that allows the identification of all genes from different organisms in a complex sample. However, the presence of excessive host DNA poses a challenge in metagenomic studies, and various methods have been developed to remove host DNA and improve microbial detection sensitivity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Immunology
Madiha Fida, Matthew J. Wolf, Ahmed Hamdi, Prakhar Vijayvargiya, Zerelda Esquer Garrigos, Sarwat Khalil, Kerryl E. Greenwood-Quaintance, Matthew J. Thoendel, Robin Patel
Summary: In this study, conventional blood cultures were compared to plasma cell-free DNA-based 16S rRNA gene NGS for detecting potential pathogens in septic patients. The results showed that 16S rRNA gene NGS could be useful for detecting bacteria in plasma, and in some cases, pinpointing the source of sepsis based on the profile of bacteria detected in plasma.
CLINICAL INFECTIOUS DISEASES
(2021)
Article
Microbiology
Alexander S. F. Berry, Meghann K. Pierdon, Ana M. Misic, Megan C. Sullivan, Kevin O'Brien, Ying Chen, Samuel J. Murray, Lydia A. Ramharack, Robert N. Baldassano, Thomas D. Parsons, Daniel P. Beiting
Summary: The study reveals that parity is an important factor modulating the gut microbiome during pregnancy, impacting the community of bacteria that colonize the offspring gut early in life, potentially influencing host metabolism. The results underscore the importance of considering parity in human microbiome studies during pregnancy and in infants.
Article
Endocrinology & Metabolism
Shili Zhang, Shuxian Li, Jiali Huang, Xinyi Ding, Yan Qiu, Xiangrong Luo, Jianfu Meng, YanJun Hu, Hao Zhou, Hongying Fan, Ying Cao, Fang Gao, Yaoming Xue, Mengchen Zou
Summary: The imbalance of the skin microbial community could impair skin immune homeostasis, leading to skin lesions. This study aimed to investigate the composition and function of the foot skin microbiome in relation to the risk of diabetic foot and determine if dysbiosis of the skin microbiome induces diabetic skin lesions.
JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM
(2023)
Article
Biochemistry & Molecular Biology
Klaudia Tutka, Magdalena Zychowska, Anna Zaczek, Karolina Maternia-Dudzik, Jakub Pawelczyk, Dominik Strapagiel, Jakub Lach, Adam Reich
Summary: This study evaluated the diversity and composition of the bacterial microbiome in PN lesions and found that the abundance of Staphylococcus was significantly higher in samples from PN and AD patients compared to controls. The microbiome composition in PN was highly similar to that of AD. These findings suggest a potential role of the microbiome in the pathogenesis of PN.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Endocrinology & Metabolism
Qing Wang, Qi Wang, Lanbo Zhao, Yadi Bin, Li Wang, Lei Wang, Kailu Zhang, Qiling Li
Summary: The blood microbiome of PCOS patients showed significantly lower alpha diversity, different beta diversity, and significant taxonomic variations compared to healthy controls.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Veterinary Sciences
Sofie Rutjens, Nick Vereecke, Jannes Sauer, Siska Croubels, Mathias Devreese
Summary: Cephalosporins have great concern on their effect on the fecal microbiome and potential spread of resistance-associated genes. This study investigates the impact of ceftiofur and cefquinome on the porcine microbiome and resistome using sequencing methods. Ceftiofur treatment results in an increase in Proteobacteria members at the microbiome level, while cefquinome treatment affects more genera on the genus level. Both treatments temporarily affect the resistome, but it returns to control levels after 21 days. These findings contribute to better understanding and tailoring of treatment strategies for bacterial infections.
VETERINARY RESEARCH
(2023)
Article
Microbiology
Chian Teng Ong, Gry Boe-Hansen, Elizabeth M. Ross, Patrick J. Blackall, Conny Turni, Ben J. Hayes, Ala E. Tabor
Summary: This study compared the effectiveness of different host depletion and DNA extraction methods for bovine vaginal metagenomic samples. The findings indicated that Soft-spin and QIAamp were the most effective methods in reducing host DNA contamination and increasing sequencing depth for microbial reads. Thus, a combination of these methods provided the most robust representation of the vaginal microbial community in cattle.
MICROBIOLOGY SPECTRUM
(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
Environmental Sciences
Ahmed Salah-Tantawy, Ching-Sung Gavin Chang, Min-Yun Liu, Shuh-Sen Young
Summary: The study collected 44 sediment samples from the Siangshan wetland in Taiwan to investigate the effects of heavy metals on sediment-associated microbiota. Results revealed that polluted sites exhibited higher richness and diversity compared to unpolluted sites, with beta diversity analysis showing significantly different microbial community compositions between surface and sub-surface groups. Redundancy analysis indicated that Mn, Cu, Al, Co, Ni, Sand, and Cr had a significant effect on the structure of microbiota communities at the class level.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Public, Environmental & Occupational Health
Anaclara Ferreira Veiga Tipple, Dayane de Melo Costa, Lillian Kelly de Oliveira Lopes, Thais Rodrigues Veloso, Luiz Antonio Pereira, Honghua Hu, Dulcelene de Sousa Melo, Junnia Pires de Amorim Trindade, Karen Vickery
Summary: This study evaluates the practices of management and reprocessing of loaned surgical instruments and non-sterile implants in Australia and Brazil. The study found that the quality indicators for management and reprocessing were higher in Australia compared to Brazil, but both countries had challenges such as delivery delays and improper cleaning practices.
INFECTION DISEASE & HEALTH
(2022)
Article
Surgery
P. Patiniott, A. Jacombs, L. Kaul, H. Hu, M. Warner, B. Klosterhalfen, A. Karatassas, G. Maddern, K. Richter
Summary: This study investigated the link between bacterial biofilms and negative outcomes of hernia repair surgery. The results suggest that staphylococci biofilms may contribute to hernia repair failure, chronic pain, and exacerbation of disease.
Article
Public, Environmental & Occupational Health
D. de Melo Costa, R. Castillo, K. Vickery, A. Ferreira Veiga Tipple, L. K. de Oliveira Lopes, H. Hu
Summary: This study compared the efficacy of double manual cleaning with enzymatic detergent followed by alkaline detergent on biofilm removal on hinged surgical instruments to automated cleaning. The results showed that both double manual cleaning with hinge brushing and automated cleaning effectively removed biofilm and residual protein. Additionally, there was no significant difference in efficacy between double manual cleaning with hinge brushing and automated cleaning.
JOURNAL OF HOSPITAL INFECTION
(2022)
Review
Nutrition & Dietetics
Fatemah Sadeghpour Heravi, Honghua Hu
Summary: The development and health of infants are closely linked to the gut microbiota, which acts as a protective and regulatory system. Imbalances in the gut microbiota in preterm infants can increase the risk of various diseases. This review examines the role of the probiotic Bifidobacterium in the development of gut microbiota and prevention of diseases in preterm infants, as well as its mechanisms of action.
Editorial Material
Microbiology
Honghua Hu, Leyi Wang, Qi Zhao
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Farhana Parvin, Md. Arifur Rahman, Anand K. Deva, Karen Vickery, Honghua Hu
Summary: Staphylococcus aureus biofilms exhibit resistance to antibiotics and disinfectants, which is attributed to changes in the bacterial cell wall. Proteins involved in cell wall synthesis are upregulated in biofilms compared to planktonic organisms. Furthermore, the width of the cell wall and peptidoglycan production increase with biofilm culture duration and dehydration. Disinfectant tolerance is highest in dry surface biofilms, followed by hydrated biofilms, and lowest in planktonic bacteria, indicating that changes in the cell wall may contribute to the biocide resistance of S. aureus biofilms.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Gastroenterology & Hepatology
Simone Vieira Toledo Guadagnin, Dayane de Melo Costa, Mariusa Gomes Borges Primo, Adriana Azevedo Silva, Lara Stefania Netto de Oliveira Leao-Vasconcelos, Karen Vickery, Anaclara Ferreira Veiga Tipple
Summary: This study aimed to determine bacterial contamination in flexible gastroscopes channels after storage in a cabinet without forced-air drying. The results showed that bacterial contamination increased with longer storage time.
JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY
(2023)
Letter
Hematology
Honghua Hu, Elena Shklovskaya, Anand Deva, Haiying Xu, Kelly Fan, Kristen Brosamer, Richard Willson, Imran Khan, Mithun Sinha, Marshall E. Kadin
AMERICAN JOURNAL OF HEMATOLOGY
(2023)
Review
Nutrition & Dietetics
Fatemah Sadeghpour Heravi, Kaveh Naseri, Honghua Hu
Summary: This systematic review provides a comprehensive understanding of the gut microbiota composition in patients with Parkinson's disease and Alzheimer's disease compared to healthy controls. The study found significant differences in gut microbiota composition between patients and healthy controls, as well as specific changes in abundance of certain bacterial taxa. The microbial diversity evaluations also revealed differences between the case and control groups. These findings offer promising prospects for the management and treatment of Parkinson's disease and Alzheimer's disease.
Article
Multidisciplinary Sciences
Rajdeep Chakraborty, Charbel Darido, Arthur Chien, Aidan Tay, Karen Vickery, Honghua Hu, Fei Liu, Shoba Ranganathan
Summary: The role of Gipie in adenoid cystic carcinoma (ACC) and mucoepidermoid carcinoma (A-253) was evaluated in this study. Results showed that silencing Gipie led to morphological changes in the cells, increased apoptosis, decreased T regulatory cells, and increased activated NK cells.
SCIENTIFIC REPORTS
(2023)
Article
Oncology
Victoria G. Zeyl, Haiying Xu, Imran Khan, Jason T. Machan, Mark W. Clemens, Honghua Hu, Anand Deva, Caroline Glicksman, Patricia McGuire, William P. Adams Jr, David Sieber, Mithun Sinha, Marshall E. Kadin
Summary: A rare complication of breast implants is the development of lymphoma, which usually requires time-consuming and costly laboratory testing for diagnosis. This research presents a method for quickly detecting lymphoma using a smaller amount of fluid, potentially enabling point-of-care diagnosis in the future.
Article
Public, Environmental & Occupational Health
Dayane de Melo Costa, Luiz Antonio Pereira, Karen Vickery, Honghua Hu, Roel Castillo, Anaclara Ferreira Veiga Tipple
Summary: The management practices of loaner surgical instruments (SI) were evaluated in Australia and Brazil, revealing failures to meet recommended practices in both countries. These failures included lack of standard operating procedures, minimum delivery time, transport container, and decontamination. Standardization and improvement of reprocessing and management processes are needed.
INFECTION DISEASE & HEALTH
(2022)
Article
Biotechnology & Applied Microbiology
Shamaila Tahir, Sarah Emanuel, David W. Inglis, Karen Vickery, Anand K. Deva, Honghua Hu
Summary: Current protocols using liquid disinfectants often fail due to biofilm formation. Researchers hypothesize that mild positive pressure can disrupt biofilm structure and improve disinfectant penetration for better killing.
BIOENGINEERING-BASEL
(2022)