Skip to Content

193 Results Found

  • Review
  • Open Access
81 Citations
12,125 Views
22 Pages

Plant Microbiome Engineering: Hopes or Hypes

  • Muhammad Siddique Afridi,
  • Sher Ali,
  • Abdul Salam,
  • Willian César Terra,
  • Aqsa Hafeez,
  • Sumaira,
  • Baber Ali,
  • Mona S. AlTami,
  • Fuad Ameen and
  • Rohini Karunakaran
  • + 3 authors

7 December 2022

Rhizosphere microbiome is a dynamic and complex zone of microbial communities. This complex plant-associated microbial community, usually regarded as the plant’s second genome, plays a crucial role in plant health. It is unquestioned that plant...

  • Review
  • Open Access
27 Citations
9,320 Views
40 Pages

Microbiome Engineering for Sustainable Rice Production: Strategies for Biofertilization, Stress Tolerance, and Climate Resilience

  • Israt Jahan Misu,
  • Md. Omar Kayess,
  • Md. Nurealam Siddiqui,
  • Dipali Rani Gupta,
  • M. Nazrul Islam and
  • Tofazzal Islam

The plant microbiome, found in the rhizosphere, phyllosphere, and endosphere, is essential for nutrient acquisition, stress tolerance, and the overall health of plants. This review aims to update our knowledge of and critically discuss the diversity...

  • Review
  • Open Access
135 Citations
7,701 Views
25 Pages

Engineered Nanomaterials in Soil: Their Impact on Soil Microbiome and Plant Health

  • Shams Tabrez Khan,
  • Syed Farooq Adil,
  • Mohammed Rafi Shaik,
  • Hamad Z. Alkhathlan,
  • Merajuddin Khan and
  • Mujeeb Khan

30 December 2021

A staggering number of nanomaterials-based products are being engineered and produced commercially. Many of these engineered nanomaterials (ENMs) are finally disposed into the soil through various routes in enormous quantities. Nanomaterials are also...

  • Article
  • Open Access
1 Citations
748 Views
18 Pages

16 December 2025

The effectiveness of microbial inoculants in agriculture is often limited by their unstable colonization in dynamic soil environments. We investigated the impact of application timing and continuity of a four-member synthetic microbial community (Syn...

  • Article
  • Open Access
4 Citations
2,270 Views
23 Pages

19 June 2025

The gut microbiota has emerged as a critical modulator in metabolic diseases, with substantial evidence supporting its role in attenuating diabetes-related nephropathy. Recent investigations demonstrate that strategic manipulation of intestinal micro...

  • Review
  • Open Access
4 Citations
3,850 Views
13 Pages

Innovative Approaches for Engineering the Seed Microbiome to Enhance Crop Performance

  • Piao Yang,
  • Ling Lu,
  • Abraham Condrich,
  • Gavin A. Muni,
  • Sean Scranton,
  • Shixiang Xu,
  • Ye Xia and
  • Shuai Huang

14 May 2025

Seed science is the comprehensive study of seeds. It encompasses their biology, production, technology, genetics, physiology, ecology, and applications in agriculture and conservation. Seed science has undergone transformative advancements through th...

  • Communication
  • Open Access
2 Citations
1,708 Views
11 Pages

Engineering Oilseed Microbiome Synergy for Saline Alkaline Soil Restoration

  • Shijie Ma,
  • Tong Tang,
  • Chang Du,
  • Zheng Yang and
  • Binjie Gan

16 July 2025

Soil salinization poses a critical threat to global agriculture, necessitating innovative strategies for sustainable remediation. This review synthesizes advances in leveraging plant–microbe interactions to remediate saline–alkali soils,...

  • Review
  • Open Access
21 Citations
10,958 Views
16 Pages

Gut luminal dysbiosis and pathobiosis result in compositional and biodiversified alterations in the microbial and host co-metabolites. The primary mechanism of bacterial evolution is horizontal gene transfer (HGT), and the acquisition of new traits c...

  • Review
  • Open Access
28 Citations
13,258 Views
26 Pages

25 June 2025

Microbial interactions within the rhizosphere are fundamental to plant health, influencing nutrient availability, stress tolerance, and pathogen resistance. Beneficial microbes, such as plant growth-promoting microbes (PGPMs), including bacteria and...

  • Review
  • Open Access
72 Citations
15,622 Views
25 Pages

The Microbial Connection to Sustainable Agriculture

  • Kalaivani Nadarajah and
  • Nur Sabrina Natasha Abdul Rahman

14 June 2023

Microorganisms are an important element in modeling sustainable agriculture. Their role in soil fertility and health is crucial in maintaining plants’ growth, development, and yield. Further, microorganisms impact agriculture negatively through...

  • Article
  • Open Access
1 Citations
4,738 Views
32 Pages

Modulating Gene Expression within a Microbiome Based on Computational Models

  • Liyam Chitayat Levi,
  • Ido Rippin,
  • Moran Ben Tulila,
  • Rotem Galron and
  • Tamir Tuller

31 August 2022

Recent research in the field of bioinformatics and molecular biology has revealed the immense complexity and uniqueness of microbiomes, while also showcasing the impact of the symbiosis between a microbiome and its host or environment. A core propert...

  • Review
  • Open Access
11 Citations
5,952 Views
20 Pages

Improving Plant Performance Through Microbiome Manipulation: The Potential Role of Current Bioengineering Approaches

  • Diksha Joshi,
  • Amit Kaushik,
  • Reetesh Kumar,
  • Aditi Arya,
  • Gustavo Santoyo,
  • Vipin Kumar Singh,
  • Nikhil Kashyap,
  • Manoj Kumar Solanki,
  • Madhuree Kumari and
  • Ajay Kumar
  • + 1 author

In the recent past, microbiome manipulation has emerged as a promising approach to improve plant growth performance by exploring the deep insight of plant–microbe interactions. The exploration of a plant microbiome either present on an ectosphe...

  • Review
  • Open Access
36 Citations
9,684 Views
29 Pages

Climate-Resilient Microbial Biotechnology: A Perspective on Sustainable Agriculture

  • Chengjia Tan,
  • Mohammad Talib Kalhoro,
  • Yahya Faqir,
  • Jiahua Ma,
  • Matthew Duah Osei and
  • Ghulam Khaliq

We designed this review to describe a compilation of studies to enlighten the concepts of plant–microbe interactions, adopted protocols in smart crop farming, and biodiversity to reaffirm sustainable agriculture. The ever-increasing use of agro...

  • Review
  • Open Access
17 Citations
5,789 Views
21 Pages

Given the novelty of the industrial production of the edible insects sector, research has primarily focused on the zootechnical performances of black soldier fly larvae (BSFL) in response to different substrates and rearing conditions as a basis to o...

  • Article
  • Open Access
14 Citations
4,253 Views
14 Pages

15 February 2021

Technological advances in next-generation sequencing (NGS) have made it possible to uncover extensive and dynamic alterations in diverse molecular components and biological pathways across healthy and diseased conditions. Large amounts of multi-omics...

  • Review
  • Open Access
7 Citations
6,772 Views
22 Pages

Using Gut Microbiota Modulation as a Precision Strategy Against Obesity

  • Kwang-Rim Baek,
  • Saloni Singh,
  • Hye-Seon Hwang and
  • Seung-Oh Seo

Obesity is a complex metabolic disorder with high global prevalence. Recent studies have highlighted the crucial role of gut microbiota in obesity’s onset and progression. This review explores the relationship between gut microbiota composition...

  • Review
  • Open Access
1,015 Views
35 Pages

Programmable Plant Immunity: Synthetic Biology for Climate-Resilient Agriculture

  • Sopan Ganpatrao Wagh,
  • Akshay Milind Patil,
  • Ghanshyam Bhaurao Patil,
  • Sachin Ashok Bhor,
  • Kiran Ramesh Pawar and
  • Harshraj Shinde

4 January 2026

Agricultural systems face mounting pressures from climate change, as rising temperatures, elevated CO2, and shifting precipitation patterns intensify plant disease outbreaks worldwide. Conventional strategies, such as breeding for resistance, pestici...

  • Review
  • Open Access
1 Citations
4,173 Views
24 Pages

CRISPR-Cas Systems: Bridging Bacterial Immunity and Host Interactions

  • Chinedu Eucharia Joseph,
  • Aashika Jain,
  • Muneer Oladipupo Yaqub and
  • Lekshmi K. Edison

CRISPR-Cas systems are best known as adaptive immune defenses in prokaryotes, but they also function as versatile regulators bridging bacterial immunity with host-related processes. Beyond neutralizing invasive phages and plasmids, these systems infl...

  • Review
  • Open Access
19 Citations
6,403 Views
27 Pages

Rhizosphere Microbiomes Mediating Abiotic Stress Mitigation for Improved Plant Nutrition

  • Bartholomew Saanu Adeleke,
  • Parul Chaudhary,
  • Modupe Stella Ayilara,
  • Funmilola Mabel Ojo,
  • Sakiru Morenikeji Erinoso,
  • Viabhav Kumar Upadhayay,
  • Adeyemi Isaiah Adeyemo and
  • Saheed Adekunle Akinola

27 July 2024

The extreme conditions linked with abiotic stresses have greatly affected soil and plant health. The diverse biochemical activities occurring in the soil environment have been attributed to shaping the dynamics of plant–soil microbiomes by cont...

  • Review
  • Open Access
102 Citations
12,574 Views
24 Pages

Plant–Microbiome Crosstalk: Dawning from Composition and Assembly of Microbial Community to Improvement of Disease Resilience in Plants

  • Muhammad Noman,
  • Temoor Ahmed,
  • Usman Ijaz,
  • Muhammad Shahid,
  • Azizullah,
  • Dayong Li,
  • Irfan Manzoor and
  • Fengming Song

Plants host diverse but taxonomically structured communities of microorganisms, called microbiome, which colonize various parts of host plants. Plant-associated microbial communities have been shown to confer multiple beneficial advantages to their h...

  • Review
  • Open Access
15 Citations
6,950 Views
40 Pages

18 January 2025

This review delves into innovative technologies to improve the control of vascular fungal plant pathogens. It also briefly summarizes traditional biocontrol approaches to manage them, addressing their limitations and emphasizing the need to develop m...

  • Review
  • Open Access
67 Citations
9,416 Views
12 Pages

2 April 2021

Plant growth-promoting bacteria (PGPB) have great potential to provide economical and sustainable solutions to current agricultural challenges. The Methylobacteria which are frequently present in the phyllosphere can promote plant growth and developm...

  • Feature Paper
  • Concept Paper
  • Open Access
97 Citations
13,152 Views
18 Pages

The accelerating marks of climate change on coral-reef ecosystems, combined with the recognition that traditional management measures are not efficient enough to cope with climate change tempo and human footprints, have raised a need for new approach...

  • Review
  • Open Access
37 Citations
9,136 Views
21 Pages

20 February 2025

Plants host a complex but taxonomically assembled set of microbes in their natural environment which confer several benefits to the host plant including stress resilience, nutrient acquisition and increased productivity. To understand and simplify th...

  • Article
  • Open Access
13 Citations
4,560 Views
18 Pages

Engineering the Rhizosphere Microbiome with Plant Growth Promoting Bacteria for Modulation of the Plant Metabolome

  • Maria J. Ferreira,
  • Ana C. S. Veríssimo,
  • Diana C. G. A. Pinto,
  • Isabel N. Sierra-Garcia,
  • Camille E. Granada,
  • Javier Cremades,
  • Helena Silva and
  • Ângela Cunha

20 August 2024

Plant-growth-promoting bacteria (PGPB) have beneficial effects on plants. They can promote growth and enhance plant defense against abiotic stress and disease, and these effects are associated with changes in the plant metabolite profile. The researc...

  • Article
  • Open Access
11 Citations
4,549 Views
22 Pages

Stimulation of Nicotiana tabacum L. In Vitro Shoot Growth by Endophytic Bacillus cereus Group Bacteria

  • Elena Andriūnaitė,
  • Inga Tamošiūnė,
  • Monika Aleksandravičiūtė,
  • Dalia Gelvonauskienė,
  • Jurgita Vinskienė,
  • Rytis Rugienius and
  • Danas Baniulis

In vitro plant tissue cultures face various unfavorable conditions, such as mechanical damage, osmotic shock, and phytohormone imbalance, which can be detrimental to culture viability, growth efficiency, and genetic stability. Recent studies have rev...

  • Review
  • Open Access
42 Citations
9,028 Views
41 Pages

Harnessing Beneficial Microbes for Drought Tolerance: A Review of Ecological and Agricultural Innovations

  • Grzegorz Mikiciuk,
  • Tymoteusz Miller,
  • Anna Kisiel,
  • Danuta Cembrowska-Lech,
  • Małgorzata Mikiciuk,
  • Adrianna Łobodzińska and
  • Kamila Bokszczanin

5 December 2024

Drought is an increasingly critical global challenge, significantly impacting agricultural productivity, food security, and ecosystem stability. As climate change intensifies the frequency and severity of drought events, innovative strategies are ess...

  • Review
  • Open Access
4 Citations
4,139 Views
35 Pages

Microbiome Engineering for Biotherapeutic in Alzheimer’s Disease Through the Gut–Brain Axis: Potentials and Limitations

  • Editha Renesteen,
  • Jacqueline L. Boyajian,
  • Paromita Islam,
  • Amal Kassab,
  • Ahmed Abosalha,
  • Stephanie Makhlouf,
  • Madison Santos,
  • Hongmei Chen,
  • Cedrique Shum-Tim and
  • Satya Prakash

Alzheimer’s disease (AD) is a neurodegenerative condition characterized by considerable cognitive decline and functional impairment, primarily due to the progressive alteration of neurons, microglia, and astrocytes. Pathological manifestations...

  • Review
  • Open Access
3 Citations
2,664 Views
18 Pages

Hidden Partner of Immunity: Microbiome as an Innovative Companion in Immunotherapy

  • Pyoseung Kim,
  • Sunggeun Joe,
  • Heeyoung Kim,
  • Hyejeong Jeong,
  • Sunghwan Park,
  • Jihwan Song,
  • Wondong Kim and
  • Yong Gu Lee

Recent studies have highlighted that the microbiome is the essential factor that can modulate the clinical activity of immunotherapy. However, the role of the microbiome varies significantly across different immunotherapies, suggesting that it is cri...

  • Review
  • Open Access
1 Citations
1,202 Views
21 Pages

Cultivated pasture grasses contribute forage to more than 40% of cattle produced in 11 southern states in the USA. In recent years the increasing intoxication of cattle feeding on pasture grasses raised serious concerns about their palatability. Whil...

  • Article
  • Open Access
1 Citations
1,447 Views
32 Pages

Synthetic Bacterial Consortium Induces Dynamic Shifts in Fungal Community and Alters Microbial Network Topology in Barley Soil Under Field Conditions

  • Roderic Gilles Claret Diabankana,
  • Ernest Nailevich Komissarov,
  • Daniel Mawuena Afordoanyi,
  • Bakhtiyar Islamov,
  • Artemiy Yurievich Sukhanov,
  • Elena Shulga,
  • Maria Nikolaevna Filimonova,
  • Keremli Saparmyradov,
  • Natalia V. Trachtmann and
  • Shamil Z. Validov

Microorganisms are fundamental drivers of soil productivity, mediating nutrient cycling and pathogen suppression. In this study, we evaluated changes in the fungal community in the soil of barley (Hordeum vulgare L.) in a field experiment involving t...

  • Review
  • Open Access
3 Citations
4,724 Views
67 Pages

Oral Treatment of Obesity by GLP-1 and Its Analogs

  • Natasa Holler,
  • Ivana Ruseska,
  • Anna-Laurence Schachner-Nedherer,
  • Andreas Zimmer and
  • Christina Petschacher

Obesity is a multifaceted disease that significantly increases the risk of various chronic conditions. GLP-1R (co)-agonists first emerged as therapeutics for treatment of type 2 diabetes mellitus and have since become an established drug class for im...

  • Review
  • Open Access
14 Citations
5,362 Views
21 Pages

Engineering Multigenerational Host-Modulated Microbiota against Soilborne Pathogens in Response to Global Climate Change

  • Paola Durán,
  • Gonzalo Tortella,
  • Michael J. Sadowsky,
  • Sharon Viscardi,
  • Patricio Javier Barra and
  • Maria de la Luz Mora

3 September 2021

Crop migration caused by climatic events has favored the emergence of new soilborne diseases, resulting in the colonization of new niches (emerging infectious diseases, EIDs). Soilborne pathogens are extremely persistent in the environment. This is i...

  • Article
  • Open Access
31 Citations
5,503 Views
21 Pages

An E.coli-specific phage was encapsulated in three different pH responsive polymer formulations using the process of membrane emulsification. Small 100 µm capsules were fabricated and shown to afford phages suitable acid protection upon exposure to p...

  • Review
  • Open Access
37 Citations
5,394 Views
21 Pages

20 October 2022

Periodontal disease, a major cause of tooth loss, is an infectious disease caused by bacteria with the additional aspect of being a noncommunicable disease closely related to lifestyle. Tissue destruction based on chronic inflammation is influenced b...

  • Article
  • Open Access
1,708 Views
18 Pages

Moderate Phosphorus Addition to Field-Grown Bananas Enhanced Soil Microbial Enzyme Activities but Had Negligible Impacts on Bacterial, Fungal, and Nematode Diversity

  • Anna-Belle C. Clarke,
  • Hazel R. Lapis-Gaza,
  • Stuart Irvine-Brown,
  • Rebecca Lyons,
  • Jiarui Sun,
  • Anthony B. Pattison and
  • Paul G. Dennis

29 November 2024

On commercial banana (Musa spp.) plantations, soils are often supplemented with phosphorus (P) fertiliser to optimise production. Such additions may influence the diversity and function of soil microbial communities, which play important roles in P c...

  • Review
  • Open Access
37 Citations
7,201 Views
18 Pages

Recent Advances of Microbiome-Associated Metabolomics Profiling in Liver Disease: Principles, Mechanisms, and Applications

  • Ganesan Raja,
  • Haripriya Gupta,
  • Yoseph Asmelash Gebru,
  • Gi Soo Youn,
  • Ye Rin Choi,
  • Hyeong Seop Kim,
  • Sang Jun Yoon,
  • Dong Joon Kim,
  • Tae-Jin Kim and
  • Ki Tae Suk

25 January 2021

Advances in high-throughput screening of metabolic stability in liver and gut microbiota are able to identify and quantify small-molecule metabolites (metabolome) in different cellular microenvironments that are closest to their phenotypes. Metagenom...

  • Review
  • Open Access
36 Citations
6,376 Views
25 Pages

Plant-Microbe Interactions under the Extreme Habitats and Their Potential Applications

  • Pragya Tiwari,
  • Subir Kumar Bose,
  • Kyeung-Il Park,
  • Laurent Dufossé and
  • Mireille Fouillaud

Plant-microbe associations define a key interaction and have significant ecological and biotechnological perspectives. In recent times, plant-associated microbes from extreme environments have been extensively explored for their multifaceted benefits...

  • Article
  • Open Access
20 Citations
5,244 Views
25 Pages

11 June 2021

Increasing antibiotic resistance in bacteria that cause zoonotic infections is a major problem for farmers rearing animals for food as well as for consumers who eat the contaminated meat resulting in food-borne infections. Bacteriophages incorporated...

  • Conference Report
  • Open Access
1 Citations
2,687 Views
8 Pages

Characterizing and Exploiting Tumor Microenvironments to Optimize Treatment Outcomes

  • Emma H. Allott,
  • Kellie Dean,
  • Tracy Robson and
  • Claire Meaney

17 November 2021

Our understanding of cancer initiation, progression, and treatment is continually progressing through dedicated research achieved through laboratory investigation, clinical trials, and patient engagement. The importance and complexity of the microenv...

  • Article
  • Open Access
20 Citations
5,332 Views
22 Pages

A Novel In Planta Enrichment Method Employing Fusarium graminearum-Infected Wheat Spikes to Select for Competitive Biocontrol Bacteria

  • Waldo Deroo,
  • Larissa De Troyer,
  • Fréderic Dumoulin,
  • Sarah De Saeger,
  • Marthe De Boevre,
  • Steven Vandenabeele,
  • Leen De Gelder and
  • Kris Audenaert

17 March 2022

This work introduces an alternative workflow for the discovery of novel bacterial biocontrol agents in wheat against Fusarium head blight (FHB). Unlike the mass testing of isolate collections, we started from a diverse inoculum by extracting microbio...

  • Review
  • Open Access
200 Citations
20,975 Views
17 Pages

Biofertilizers and Biocontrol Agents for Agriculture: How to Identify and Develop New Potent Microbial Strains and Traits

  • Anna Maria Pirttilä,
  • Habibollah Mohammad Parast Tabas,
  • Namrata Baruah and
  • Janne J. Koskimäki

Microbiological tools, biofertilizers, and biocontrol agents, which are bacteria and fungi capable of providing beneficial outcomes in crop plant growth and health, have been developed for several decades. Currently we have a selection of strains ava...

  • Review
  • Open Access
14 Citations
9,558 Views
63 Pages

Hacking the Immune Response to Solid Tumors: Harnessing the Anti-Cancer Capacities of Oncolytic Bacteria

  • Jason M. Roe,
  • Kevin Seely,
  • Caleb J. Bussard,
  • Emily Eischen Martin,
  • Elizabeth G. Mouw,
  • Kenneth W. Bayles,
  • Michael A. Hollingsworth,
  • Amanda E. Brooks and
  • Kaitlin M. Dailey

Oncolytic bacteria are a classification of bacteria with a natural ability to specifically target solid tumors and, in the process, stimulate a potent immune response. Currently, these include species of Klebsiella, Listeria, Mycobacteria, Streptococ...

  • Review
  • Open Access
22 Citations
5,663 Views
20 Pages

Every land plant exists in a close relationship with microbial communities of several niches: rhizosphere, endosphere, phyllosphere, etc. The growth and yield of potato—a critical food crop worldwide—highly depend on the diversity and str...

  • Review
  • Open Access
14 Citations
6,078 Views
25 Pages

Optimizing Cancer Treatment Through Gut Microbiome Modulation

  • Kyuri Kim,
  • Mingyu Lee,
  • Yoojin Shin,
  • Yoonji Lee and
  • Tae-Jung Kim

7 April 2025

The gut microbiome plays a pivotal role in modulating cancer therapies, including immunotherapy and chemotherapy. Emerging evidence demonstrates its influence on treatment efficacy, immune response, and resistance mechanisms. Specific microbial taxa...

  • Review
  • Open Access
47 Citations
10,681 Views
12 Pages

Targeted Approaches for In Situ Gut Microbiome Manipulation

  • Hui Ling Lee,
  • Haosheng Shen,
  • In Young Hwang,
  • Hua Ling,
  • Wen Shan Yew,
  • Yung Seng Lee and
  • Matthew Wook Chang

12 July 2018

Microbial communities and their collective genomes form the gut microbiome, of which bacteria are the major contributor. Through their secreted metabolites, bacteria interact with the host, influencing human health and physiology. Perturbation of the...

  • Review
  • Open Access
14 Citations
6,768 Views
22 Pages

27 October 2023

While emerging evidence highlights the significance of gut microbiome in gastrointestinal infectious diseases, treatments like Fecal Microbiota Transplantation (FMT) and probiotics are gaining popularity, especially for diarrhea patients. However, th...

  • Review
  • Open Access
20 Citations
5,309 Views
14 Pages

Drought Tolerance of Legumes: Physiology and the Role of the Microbiome

  • Ivan S. Petrushin,
  • Ilia A. Vasilev and
  • Yulia A. Markova

Water scarcity and global warming make drought-tolerant plant species more in-demand than ever. The most drastic damage exerted by drought occurs during the critical growth stages of seed development and reproduction. In the course of their evolution...

  • Review
  • Open Access
51 Citations
14,839 Views
17 Pages

26 February 2019

Microbial cooperation pervades ecological scales, from single-species populations to host-associated microbiomes. Understanding the mechanisms promoting the stability of cooperation against potential threats by cheaters is a major question that only...

  • Review
  • Open Access
58 Citations
8,266 Views
26 Pages

Colorectal cancer (CRC) is a fatal disease caused by the uncontrolled propagation and endurance of atypical colon cells. A person’s lifestyle and eating pattern have significant impacts on the CRC in a positive and/or negative way. Diet-derived...

of 4