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Due to their numerous well-established applications in the food industry, there have been many studies regarding the adaptation and evolution of lactic acid bacteria (LAB) in a wide variety of hosts and environments. Progress in sequencing technology and continual decreases in its costs have led to the availability of LAB genome sequence data. Bioinformatics has been central to the extraction of valuable information from these raw genome sequence data. This paper presents the roles of bioinformatics tools and databases in understanding the adaptation and evolution of LAB, as well as the bioinformatics methods used in the initial screening of LAB for probiotic potential. Moreover, the advantages, challenges, and limitations of employing bioinformatics for these purposes are discussed.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9992694 | PMC |
http://dx.doi.org/10.1007/s10068-022-01142-8 | DOI Listing |
Int J Biol Macromol
September 2025
Academy of Advanced Carbon Conversion Technology, Huaqiao University, Xiamen, 361021, China; Fujian Provincial Key Laboratory of Biomass Low-Carbon Conversion, Huaqiao University, Xiamen, 361021, China; College of Chemical Engineering, Huaqiao University, Xiamen, 361021, China. Electronic address: l
Over recent decades, the indiscriminate use of antibiotics in animal production to enhance product quality and maximize economic returns has raised critical concerns. However, antibiotic misuse has led to the development of antimicrobial resistance in livestock and poses substantial health risks to humans through drug residue accumulation. In response, nations globally have progressively implemented bans on antibiotic inclusion in animal nutrition, redirecting scientific attention toward antibiotic-free feed additives that maintain or enhance animal health performance.
View Article and Find Full Text PDFJ Nutr
September 2025
University Paris-Saclay, INRAE, MetaGenoPolis, 78350 Jouy-en-Josas, France; University Paris-Saclay, INRAE, MICALIS, 78350 Jouy-en-Josas, France. Electronic address:
This review explores the century-long trajectory of gut microbiome research and its contribution to shaping our modern diet. It further highlights the transformative potential of current discoveries to revolutionize future dietary habits and nutritional practices. From the pioneering work of E.
View Article and Find Full Text PDFJ Control Release
September 2025
Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, Department of Pharmaceutics, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, PR China. Electronic address:
The tumor microenvironment (TME) is a complex and dynamic ecosystem that significantly influences tumor progression, immune modulation, and therapeutic response. A key component of the TME is the tumor-associated microbiota, which has emerged as an important player in cancer biology, affecting tumor metastasis, immune evasion, and resistance to treatments. The recent advent of high-throughput sequencing technologies has revolutionized our understanding of the microbiome, revealing distinct microbial communities across various tumor types.
View Article and Find Full Text PDFArch Med Res
September 2025
Department of Gastroenterology, General Hospital of Northern Theater Command, Teaching Hospital of Shenyang Pharmaceutical University, Shenyang, China; Department of Clinical Pharmacy, Shenyang Pharmaceutical University, Shenyang, China. Electronic address:
Cirrhosis is the terminal stage of various chronic liver diseases, and its decompensated stage is mainly characterized by serious complications, such as hepatic encephalopathy, ascites, spontaneous bacterial peritonitis, and gastrointestinal bleeding. Gut microbial dysbiosis is prevalent in patients with cirrhosis. Considering the bidirectional regulation of the gut-liver axis, dysbiosis is closely related to the development and progression of liver cirrhosis.
View Article and Find Full Text PDFMed Oncol
September 2025
Department of Basic Medical Sciences, College of Medicine, Majmaah University, 11952, Al-Majmaah, Saudi Arabia.
The global incidence of early-onset cancer has surged by nearly 80% over the past three decades, yet the underlying causes remain poorly understood. While genetics and lifestyle are among the traditional risk factors, emerging evidence implicates the human microbiome as a potent and overlooked contributor to early tumorigenesis. Increases in the studies that are exploring the tissue-specific microbiome signatures such as the enrichment of Actinomyces and Bacteroidia in early-onset colorectal cancer, or Enterobacter and Neisseria in pancreatic tumors offer compelling evidence for age-stratified microbial contributions.
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