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Male worker in bottling factory checking water ottles before shipment. Inspection quality control.

Bacteria Removal in Water and Juice Filtration

Explore how to safeguard quality and hygiene with the right filtration methods

October 27, 2025

For water and juice applications, contamination with bacteria can be a significant problem, affecting safety, quality as well and shelf stability. For those who run a bottling line or a processing plant, choosing a suitable process filtration technology can be a deciding factor. This blog outlines proven techniques for aseptic elimination of microbial contaminants as well as actionable steps for maintaining product quality at each stage.

Understanding the importance of filtration

If not filtered out effectively, harmful bacteria like E. coli, Salmonella, Pseudomonas, Cryptosporidium, and Giardia Oocyst in water can create numerous health risks.

In juices, spoilage organisms such as Alicyclobacillus acidoterrestris are tougher to eliminate and can survive standard pasteurization, producing off-flavors or cloudiness. Introducing filtration in your process offers a clean, reliable way to prevent these issues, without altering the final product or relying heavily on chemical treatments.

For product owners, it’s also a matter of compliance. Filters used in drinking water systems must meet a variety of legislation depending on geographic location, such as NSF/ANSI, UK/DWI Regulation 10, EU-10/2020/2184, and ACS standards, while juice processing must follow hygiene principles such as HACCP.  Installing long-lasting, easy-to-maintain filtration systems, and integrating them into your process ensures compliance, safety, and product integrity across various production conditions.

Filtration mechanisms for bacterial control

At its core, filtration works by physically removing bacteria through a barrier, usually through a membrane. These membranes are designed with microscopic pores that trap unwanted microorganisms as liquid passes through. The level of removal depends on the pore size, the type of filter material, and the system’s configuration. Different filtration technologies are better suited to different needs. Let's take a look at some examples: 

Microfiltration membranes
Microfiltration membranes
Microfiltration membranes, which range from 0.1 to 1 µm in pore size, are often used to remove visible particles and bacteria from both juice and water.
 
Microfiltration membranes, which range from 0.1 to 1 µm in pore size, are often used to remove visible particles and bacteria from both juice and water.
Ultrafiltration
Ultrafiltration
With pores as small as 0.01 µm, ultrafiltration offers a strong barrier against bacteria and even some viruses. It’s a popular choice for cold sterilization in juice processing.
 
With pores as small as 0.01 µm, ultrafiltration offers a strong barrier against bacteria and even some viruses. It’s a popular choice for cold sterilization in juice processing.
Reverse Osmosis (RO)
Reverse Osmosis (RO)
Reverse osmosis removes nearly everything, including dissolved solids, and delivers high-level filtration but can also strip minerals and alter taste, particularly in juices.
 
Reverse osmosis removes nearly everything, including dissolved solids, and delivers high-level filtration but can also strip minerals and alter taste, particularly in juices.
UV disinfection
UV disinfection
UV disinfection is often added to kill bacteria that make it past other filters. It doesn’t remove anything physically, but acts as a strong backup when used correctly.
 
UV disinfection is often added to kill bacteria that make it past other filters. It doesn’t remove anything physically, but acts as a strong backup when used correctly.

Water filtration applications

Close up view of bottles of water in bottling factory being transported by conveyor belt

Reverse osmosis or ultrafiltration are commonly used in industrial water filtration systems to manage microbiological hazards. Chlorine and other chemicals are not necessary with these efficient systems.

Ceramic filters are also widely used, particularly in gravity-fed or countertop systems. Membrane filtration and UV therapy are frequently used in bigger water treatment systems. UV typically comes after a particle removal process like microfiltration because it only works well on clear fluids. This combination guarantees complete bacterial protection, particularly in applications with strict safety requirements.

Deciding which solution works best depends on how the filtered water will be used: drinking, rinsing, or as part of food or beverage processing. Each scenario comes with its own hygiene benchmarks to meet. 

Juice filtration and microbial control

Beverage factory interior. Conveyor with bottles for juice or water.

Juice products are especially sensitive to spoilage from bacteria and yeasts that can grow in acidic environments. Alicyclobacillus, for example, is known for surviving mild heat treatment and causing odd smells.

Cold filtration is frequently used in production facilities to deal with this without compromising flavor or scent. Because they are made for sterile-grade performance and eliminate heat-resistant germs and spores without compromising juice quality, pleated PES membranes like our SME⁺ are perfect for this. These membranes have been approved as last filters prior to bottling and are typically graded at 0.2 µm.

In addition to the filter itself, cleanliness needs to be preserved at every stage. Compressed air, transfer lines, and tanks must all be clean. Inline steam sterilization and sterile air filters can help with it. 

Atlas Copco filtration solutions for juice and water bottling

Atlas Copco offers sterile air filters, high-performance membrane cartridges, and validated filtration systems designed for bottled water and juice processing. These solutions support microbial safety while maintaining reliable flow and system performance.

  • SMT-G for tank venting and ensuring sterility
  • PFP-A⁺ for pre filtration and membrane protection
  • PFP-C⁺ specifically for the challenge of removing Cryptosporidium and Giardia Oocyst
  • SME⁺ for cold filtration and final bottling applications for a safe, microorganism-free product

Maintenance and validation tips

Taking care of your system is just as important as choosing the right filter in the first place. Follow these steps for protecting your system: 
  • Change filters on schedule: Don’t wait for signs of failure. Follow the change intervals set by the manufacturer to keep performance consistent.
  • Use proper cleaning agents: Clean-in-place (CIP) with sodium hypochlorite or peroxyacetic acid, as they can prevent biofilm and bacterial buildup.
  • Run integrity tests: Especially in juice applications, it is important to confirm that the sterile filters are functioning as expected.
  • Watch for pressure shifts: A steady rise in differential pressure usually signals fouling, which can compromise efficiency.

Filtering out bacteria in water and juice isn’t just about safety, it’s also about preserving flavor, meeting compliance goals, and building consumer confidence. At Atlas Copco, we offer filtration solutions that are engineered for microbial safety, beverage-grade compliance, and system reliability. Our process filtration solutions help beverage producers and water bottlers maintain the high hygiene standards without compromising efficiency. Contact our filtration expert to know more.

 

Frequently asked questions

Can all bacteria in juice and water be eliminated by ultrafiltration?

Indeed. Bacteria and many viruses can be effectively eliminated from both liquids using ultrafiltration membranes rated at 0.01 µm or smaller.

Is reverse osmosis always the better choice?

Not always. While it removes more contaminants overall, RO also eliminates minerals and can change flavor, especially in juice. It’s also more complex to maintain.

How can I remove Alicyclobacillus from juice?

Use a sterile membrane rated at 0.2 µm and validate it for spore removal like the SME⁺. Make sure to run regular integrity checks.

Do I still need UV if I already have ultrafiltration?

That depends on the application. UV can provide an extra safety layer, but it’s not always necessary if the membrane system is properly maintained.