Increased hygiene during the pandemic reduced microbial diversity in daycare settings - and this may have affected development of immunity against non-communicable diseases in children by limiting exposure to diverse microbes.

A study by scientists at Northumbria University found that an increased level of hygiene during the COVID-19 pandemic influenced microbial diversity in the daycare environments compared to homes.


The study, ‘Environmental microbiome in the home and daycare settings during the COVID-19 pandemic, and potential risk of non-communicable disease in children’, recently appeared in Environmental Microbiology Reports, an Applied Microbiology International publication.

Exposure to microbes

“An exposure to diverse microbes early in life is important for the development of the immune system which likely helps reduce the risk of various non-communicable diseases such as asthma, childhood leukaemia and other childhood cancers,” said lead author Dr Vartul Sangal.

“Daycare attendance allows social mixing of children, increasing the exposure to diverse microorganisms that are often asymptomatic but can cause minor infections that often go unreported or recalled.

“Our knowledge of microbes that may be involved in conferring protection from non-communicable diseases and impact of robust hygiene and cleaning practices on microbial exposure during the COVID-19 pandemic is currently limited.

Prophylactic intervention

“In this study, we attempted to identify microorganisms in daycare and home settings that may improve immunity against various non-communicable diseases and can help develop effective microbial prophylactic intervention strategies for children.”

The team investigated the environmental microbiome in dust samples collected from various homes and daycare providers using metagenomic approaches.

“We found that microbial communities in the dust samples from homes were more diverse than those of the samples from the daycare providers. Robust hygiene and frequent cleaning practices in the daycare settings have likely resulted in lower microbial diversity,” said Dr Jill McKay who is the co-lead of this study.

Bacterial taxa

“Several bacterial taxa including Acinetobacter and Prevotella were common between the two environments; however, human-associated bacterial taxa such as Corynebacterium, Staphylococcus and Lactobacillus were significantly more abundant in the home samples whereas environment-associated bacterial taxa including Nakamurella and Nocardioides in the daycare samples.

“We believe that outdoor activities may have resulted in higher prevalence of environment-associated taxa in the daycare settings.”

Many of the identified bacteria have previously been reported to induce immune responses that may protect children from various non-communicable and infectious diseases,” she said.

Immune responses

“For example, Acinetobacter species can induce anti-inflammatory responses to environmental allergens, commensal staphylococci can raise skin immunity against opportunistic pathogen Staphylococcus aureus and Prevotella species induce Th17 immune responses and production of various cytokines that are important predictive biomarker for acute lymphoblastic leukaemia.”

One surprising finding was the observation of lower microbial diversity and relatively low prevalence of human-associated taxa in the daycare dust samples despite the numbers of occupants being much higher than the home settings.

Robust hygiene and cleaning practices during the COVID-19 pandemic and more emphasis on outdoor activities have likely altered the composition of microbial communities in the daycare settings, Dr Sangal said.

Personal development

“Daycare attendance is well known for supporting personal development of children such as language and social skills. It is particularly encouraging that daycare attendance may also be contributing to the development of their immune system,” he said.

“This study is a step forward towards understanding the environmental microbiome and identification of bacterial taxa with potential to induce immunity against various non-communicable and infectious diseases. Moving forward, it will be important to explore post-pandemic microbial diversity in daycare environments. This knowledge will be important for developing potential behavioural or probiotic/microbial prophylactic interventions to reduce the risks of non-communicable disease among children in the future.”

In-depth studies

The next step needed will be to carry out more in-depth temporal studies across different geographical regions to understand differential environmental microbiomes.

“While some of the identified bacterial taxa are known to induce immune response among children, the potential role of majority of microbial diversity is not yet characterised. Therefore, further studies will also be important to understanding the role of uncharacterised bacterial taxa in development of immunity that may lower the risk of some non-communicable diseases,” Dr Sangal said.

The lead author on this study was Dr Vartul Sangal with Dr Jill A. McKay as co-lead. This study was supported by Northumbria University.

‘Environmental microbiome in the home and daycare settings during the COVID-19 pandemic, and potential risk of non-communicable disease in children’ appears in Environmental Microbiology Reports, an Applied Microbiology International publication.