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Microorganisms
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Microorganisms in Silage—2nd Edition
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Microorganisms in Silage—2nd Edition

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Food Microbiology".

Deadline for manuscript submissions: 31 October 2026 | Viewed by 3736

Editors

Dr. Musen Wang

E-Mail Website
Guest Editor
School of Tropical Agriculture and Forestry, Hainan University, Danzhou 571737, China
Interests: fermentation; forage silage; ruminant nutrition; feed; microbial community
Special Issues, Collections and Topics in MDPI journals
Dr. Marcia De Oliveira Franco

E-Mail Website
Guest Editor
Production Systems, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland
Interests: biowaste; animal nutrition and feeding; milk production; ruminant nutrition; silage making; feed preservation; ruminant metabolism
Special Issues, Collections and Topics in MDPI journals
Dr. Qing Zhang

E-Mail Website
Guest Editor
College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
Interests: silage fermentation; woody forage; microbial community; metabonomics; silage additives; lactic acid bacteria; plant extracts; bioactive substances; rumen fermentation
Special Issues, Collections and Topics in MDPI journals
Dr. Siran Wang

E-Mail Website
Guest Editor
Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing, China
Interests: silage; fermentation; lactic acid bacteria; ensiling; microbial community; fermented feed
Special Issues, Collections and Topics in MDPI journals
Dr. Chunsheng Bai

E-Mail Website
Guest Editor
College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
Interests: forage processing; storage and utilization
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our previous Special Issue, “Microorganisms in Silage”.

Microbial activity plays a crucial role in the ensiling process, which is widely used to preserve forage crops for animal feed. Silage production involves the fermentation of plant material by lactic acid bacteria and other microbial species under anaerobic conditions. This fermentation process results in a decrease in pH, thus inhibiting the growth of spoilage microorganisms and preserving the nutritional quality of silage. Additionally, microbial interactions within the silage ecosystem influence fermentation efficiency and their extent, hygienic quality, and animal performance upon feed consumption. Understanding the dynamics of microbial populations and communities in silage is essential to optimize silage production, improve hygienic quality, and mitigate the potential risks associated with microbial contamination.

This Special Issue aims to explore various aspects of microbial ecology, physiology, and biotechnology in the silage ecosystem. Original research articles, short communications, and reviews are welcome, and areas of interest may include, but are not limited to, the following:

  • The diversity and dynamics of microbial populations and communities in silage.
  • Functional roles of lactic acid bacteria and other microorganisms in silage fermentation.
  • The influence of environmental factors on microbial activity and silage quality.
  • Biotechnological approaches to improve silage fermentation and feed preservation.
  • The impact of microbial interactions on silage stability, their nutritious value, and animal health.
  • Strategies for monitoring and controlling microbial contamination in silage production.

Dr. Musen Wang
Dr. Marcia De Oliveira Franco
Dr. Qing Zhang
Dr. Siran Wang
Dr. Chunsheng Bai
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-anonymized peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • ensiling
  • microbial community
  • microbial contamination
  • functional lactic acid bacteria
  • fermented feed

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Related Special Issue

Published Papers (5 papers)

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Research

29 pages, 4274 KB  
Article
ESM2-Guided Context-Aware Annotation Completion Supplements Carbohydrate Metabolism Coverage in Silage Microbial Metagenomes
by Jiewei Zhang, Xinyu Du, Jinbiao Tang, Xiaoning Dong, Xusheng Guo, Mingxue Li and Dongmei Xu
Microorganisms 2026, 14(8), 1848; https://doi.org/10.3390/microorganisms14081848 - 20 Aug 2026
Abstract
Functional annotation gaps limit the interpretation of carbohydrate metabolism in silage microbiomes. We developed Context-Aware Annotation Completion (CAAC), a framework integrating ESM2 embeddings, genomic-neighborhood features, three-class classification, confidence-tiered neighbor voting, and Enzyme Commission (EC)-to-KEGG Orthology (KO) mapping. CAAC was applied to 21 metagenomes [...] Read more.
Functional annotation gaps limit the interpretation of carbohydrate metabolism in silage microbiomes. We developed Context-Aware Annotation Completion (CAAC), a framework integrating ESM2 embeddings, genomic-neighborhood features, three-class classification, confidence-tiered neighbor voting, and Enzyme Commission (EC)-to-KEGG Orthology (KO) mapping. CAAC was applied to 21 metagenomes from uninoculated and Lacticaseibacillus paracasei-inoculated silages sampled before ensiling and at 7 and 90 days. Five-fold cross-validation yielded an F1-macro of 84.64% for negative, positive, and hard-sequence classification. Among 800,000 selected annotation-poor sequences, 545,671 Tier 1 or Tier 2 predictions passed the annotation-validity and EC-to-KO mapping criteria, of which 524,814 were eligible for sample-level annotation supplementation. After silage-focused filtering and KO–EC summarization, these predictions yielded 102 KO–EC features repeatedly detected across the silage metagenomes and increased coverage in 25 of 47 carbohydrate-metabolism pathways, mainly by recovering enzyme-level components related to starch and sucrose, cellulose and cellobiose, xylan and hemicellulose, and pectin and glucuronate metabolism. Taxon-linked analyses further revealed treatment- and stage-associated patterns in the taxonomic sources of the supplemented annotations. A database-derived temporal benchmark using the July 2025 CAZy release showed 94.94% Tier 1 family-level annotation-transfer consistency. CAAC extends the enzyme-level interpretation of under-annotated silage metagenomes, while the inferred assignments remain computational predictions requiring experimental validation. Full article
(This article belongs to the Special Issue Microorganisms in Silage—2nd Edition)
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24 pages, 4071 KB  
Article
Effects of Lactic Acid Bacteria from Pickles on the Silage Fermentation and Bacterial Community and Anerobic Stability of Maize, Soybean and Their Mixture in Karst Regions
by Yujia Wang, Xiaokang Huang, Chaosheng Liao, Xiaolong Tang, Tu Hong, Yubo Zhang, Pan Wang, Chao Chen and Ping Li
Microorganisms 2026, 14(3), 528; https://doi.org/10.3390/microorganisms14030528 - 25 Feb 2026
Cited by 1 | Viewed by 1056
Abstract
This study aims to investigate the effects of three lactic acid bacteria (LAB) strains, Lactiplantibacillus plantarum, Lactiplantibacillus pentosus and Limosilactobacillus fermentum, isolated from traditional pickles in Guizhou, on the fermentation process and microbial community dynamics of ensiled whole-plant maize, soybean, and [...] Read more.
This study aims to investigate the effects of three lactic acid bacteria (LAB) strains, Lactiplantibacillus plantarum, Lactiplantibacillus pentosus and Limosilactobacillus fermentum, isolated from traditional pickles in Guizhou, on the fermentation process and microbial community dynamics of ensiled whole-plant maize, soybean, and their mixtures. The results revealed that compared to the CK group, the lactic acid levels of Lactiplantibacillus plantarum and Lactiplantibacillus pentosus were significantly increased in the treatment groups (p < 0.05), resulting in a faster pH reduction, along with decreases in ammonia nitrogen (AN) and butyric acid (BA) content. In contrast, the Limosilactobacillus fermentum treatment (p < 0.05) promoted acetic acid (AA) production and inhibited the growth of harmful microbiota in soybean silage. Notably, inoculation with all LAB strains enhanced the aerobic stability of maize silage by promoting the proliferation of Lactiplantibacillus during the later stages of fermentation, thereby sustaining a low pH and mitigating the depletion of water-soluble carbohydrates (WSC). Furthermore, all treatments accelerated silage fermentation by enhancing the LAB population and competing with yeast and Escherichia coli for available nutrients in mixed silage. These findings indicate that three LAB strains, when used as microbial additives, demonstrated potential to improve silage quality in the Karst region. Full article
(This article belongs to the Special Issue Microorganisms in Silage—2nd Edition)
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20 pages, 2843 KB  
Article
Integrated Bacterial Community and Differential Metabolites Reveal the Impact of Growth Stage on the Quality of Oat Silage
by Jiahui Ren, Lei Han, Xiaoyun Ma, Xiaoming Liu, Yinglu Hao, Jirui Yuan, Ziyao Ding, Xiaoting Li, Jingyu Wang and Juanjuan Sun
Microorganisms 2026, 14(3), 516; https://doi.org/10.3390/microorganisms14030516 - 24 Feb 2026
Cited by 3 | Viewed by 681
Abstract
Growth stage alters substrate availability and moisture in oats, potentially driving microbial succession and metabolite formation during ensiling. Oats were harvested at flowering (FS), milk ripening (MS) and wax ripening (DS) stages and vacuum-bag ensiled for 120 d (n = 4 per [...] Read more.
Growth stage alters substrate availability and moisture in oats, potentially driving microbial succession and metabolite formation during ensiling. Oats were harvested at flowering (FS), milk ripening (MS) and wax ripening (DS) stages and vacuum-bag ensiled for 120 d (n = 4 per stage). We measured chemical composition and fermentation products, enumerated key microbes, profiled bacterial communities by 16S rRNA gene amplicon sequencing, and characterised metabolites by untargeted LC–MS. With advancing growth stage, dry matter (DM), neutral detergent fibre (NDF) and acid detergent fibre (ADF) increased, whereas crude protein (CP) decreased. MS silage had the lowest pH (4.63) and the highest CP, whereas FS showed higher lactic acid, but the butyric acid (BA) and NH3-N/TN were also significantly higher than those at MS and DS (p < 0.001). Community composition shifted from Enterobacter (FS) toward Lactobacillus enrichment (DS), accompanied by stage-specific metabolite signatures (biogenic amines and indoleacetic acid at FS; betaine and purine metabolites at MS; reduced amines and more amino-acid derivatives at DS). Overall, under the conditions of this study, considering fermentation stability, nutrient preservation, microbial diversity, and metabolic pathways, the best balance was achieved during MS. Full article
(This article belongs to the Special Issue Microorganisms in Silage—2nd Edition)
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17 pages, 3175 KB  
Article
Flavonoid-Rich Cyperus esculentus Extracts Disrupt Cellular and Metabolic Functions in Staphylococcus aureus
by Yaning Zhang, Zhengdong Ma, Xuzhe Wang, Qilong Jiang, Xue Kang and Hongmei Gao
Microorganisms 2026, 14(1), 260; https://doi.org/10.3390/microorganisms14010260 - 22 Jan 2026
Cited by 2 | Viewed by 746
Abstract
The escalating threat of antibiotic resistance, particularly from Staphylococcus aureus (S. aureus), has become a critical challenge in both public health and animal husbandry. The extensive use of conventional antibiotics in livestock production accelerates the emergence of resistant strains, heightening risks [...] Read more.
The escalating threat of antibiotic resistance, particularly from Staphylococcus aureus (S. aureus), has become a critical challenge in both public health and animal husbandry. The extensive use of conventional antibiotics in livestock production accelerates the emergence of resistant strains, heightening risks to food safety and human health. Although plant-derived bioactive compounds are increasingly recognized as promising alternatives to synthetic antimicrobials, the mechanisms underlying their efficacy—and the potential for synergistic action among different plant parts—remain poorly understood. In particular, the antibacterial interactions among extracts from different tissues of Cyperus esculentus L. (C. esculentus), a plant rich in flavonoids and phenolics, have yet to be systematically evaluated. Here, we investigated the antibacterial properties and mechanisms of ethanol extracts from the tubers, stems–leaves and their mixture of C. esculentus against S. aureus. Using Oxford cup diffusion assays, scanning electron microscopy (SEM), bacterial growth kinetics, and untargeted metabolomics, we assessed both phenotypic inhibition and metabolic disruption. The mixed extract exhibited the strongest antibacterial effect, producing a 26.15 mm inhibition zone—approximately 7% greater than that of single-part extracts—and induced cell wall rupture and disintegration as observed by SEM. Growth curve analyses revealed time-dependent bacterial suppression, while metabolomic profiling identified 845 differential metabolites, indicating disturbances in amino acid, lipid, and nucleotide metabolism. Flavonoids such as acacetin, diosmetin, naringenin, and silybin A were identified as principal active compounds contributing to these effects. Full article
(This article belongs to the Special Issue Microorganisms in Silage—2nd Edition)
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12 pages, 3259 KB  
Article
Insights into Nutrient Contents, Fermentation Profiles, Bacterial Communities and Co-Occurrence Network of Small-Bale Oat Silage Prepared with/Without Lentilactobacillus buchneri or Lacticaseibacillus rhamnosus
by Baiyila Wu, Xue Cao, Shuo Liu, Tong Ren, Yuxin Bao, Hua Mei, Shiba Liu, Chelegeri Zhao, Longli Cong, Shiyang Jiao, Huaxin Niu, Shubo Wen, Haifeng Wang and Yang Song
Microorganisms 2026, 14(1), 101; https://doi.org/10.3390/microorganisms14010101 - 2 Jan 2026
Viewed by 620
Abstract
Oat is a forage with high protein value (10–14% DM) and good palatability, and is considered one of the main feed sources for ruminants. In this experiment, Lacticaseibacillus rhamnosus and Lentilactobacillus buchneri were selected as silage additives to investigate the fermentation quality, nutrient [...] Read more.
Oat is a forage with high protein value (10–14% DM) and good palatability, and is considered one of the main feed sources for ruminants. In this experiment, Lacticaseibacillus rhamnosus and Lentilactobacillus buchneri were selected as silage additives to investigate the fermentation quality, nutrient composition, microbial community and relationship between fermentation products and bacterial community of small-bale oat silage after ensiling. The experiment was set up with three treatment groups and three replications in each group, which were the control (C) group, L. rhamnosus (LR) group and L. buchneri (LB) group, and oat silages were subjected to 10-day and 30-day storage periods. The results show that both LR and LB additions significantly increased water-soluble carbohydrate, crude protein, lactic acid, propionic acid and acetic acid contents, and decreased pH, butyric acid, acid detergent fiber, neutral detergent fiber, and ammonia nitrogen contents and yeast and enterobacteria numbers in small-bale oat silage, compared with the C group. The highest content of acetic acid and the lowest numbers of enterobacteria and yeast were found in the LB group after 30 days of fermentation. Lentilactobacillus and Lacticaseibacillus were the dominant genera in the LB and LR groups, regardless of fermentation time. Lentilactobacillus and Lacticaseibacillus were positively correlated with a correlation value of 0.9, but both were negatively correlated with Bacillus. Lentilactobacillus and Lacticaseibacillus were positively correlated with acetic and lactic acids, while pH and butyric acid were positively correlated with Bacillus. This experiment revealed that the addition of homofermentative and heterofermentative lactic acid bacteria enhanced the relative abundance of Lentilactobacillus and Lacticaseibacillus, reduced harmful microbes, and improved fermentation quality of small-bale oat silage. Full article
(This article belongs to the Special Issue Microorganisms in Silage—2nd Edition)
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