This is a two goal post. First, to see if literature indicating that healthy partners of microbiome dysfunction reflect their partner’s microbiome. Second, just a look at his microbiome and any possible concerns.
There is a very significant difference between the two in terms of diet:
- Patient has been eating gluten free for years, supplements. etc
- Husband eats gluten and dairy and some junk food. Minimal supplements. High lipids, possibly genetic.
Similarity between CFS and Spouse
End Products Outlier – CFS 11 x Husband 0
KEGG Enzymes Outliers: Wife 639 – Husband: 30 Common: 1 (but opposite extremes)
Items that are common
- (class) Anaerolineae Both High
- (family) Dysgonamonadaceae Both High
- (genus) Adlercreutzia Both Low
- (species) Adlercreutzia equolifaciens Both Low
Items with stark differences:
- (species) Blautia producta W:99%ile H:5.5%ile
- (species) Faecalibacterium prausnitzii W: 4%ile H:82%ile
- (species) Haemophilus parainfluenzae W: 1%ile H:91%ile
- (family) Acetobacteraceae W:0 H:97%ile
- (family) Bacteroidaceae W:93%ile H:9%ile
Goal #1 Bottom Line
Contrary to some studies, there appear to be little similarity between these people microbiomes. The reason is likely that the shifts due to diet are so very significant. It does raise the issue of using uncorrected ranges for diet types (junk food, organic, gluten free, vegetarian, pork eater, chicken eater [Yes, studies have shown difference between people that eat pork mainly instead of chicken!], etc.). Similarly age is a factor How the microbiome ages 
Goal #2 Husband Health
As I know first hand, a wife usually cares more about a husband eating habits than he does himself. The risk of a kiss on the spouse cascading microbiome changes is a technical possibility.
First I went to Expert consensus
On the resulting screen, I checked all of the genus and species that were out of range and create a hand-picked selection and then got suggestions for them, shown below. Given that they are in the sixties, I note with interest that the first suggestion is the type of sugars found in mother’s milk, it almost seems to be a collection of restoring a younger microbiome suggestions.
Next I checked the Nat.Library of Medicine Explorer. To my delight, there were only two items above 50.
The items are:
- hypertension (High Blood Pressure) — at 60%ile — still fine and not unexpected since hypertension is age related (likely connected to aging of the microbiome) see Hypertension – What we know 
- NonCeliac Gluten Sensitivity – This may be a false positive. Let me explained, since the wife is Gluten free, the husband will likely eat more gluten free food than most people. It you starve the gluten consuming bacteria… the shift may look like gluten sensitivity.
Going over to citizen science, there were no matches for symptoms. Again, compared to most people that have uploaded samples — no concerns.
Standard Kaltoft-Moldrup Suggestions
The suggestions are similar to those above. Many of the items are not unexpected for someone in the 60’s — Vitamin D. There is one significant change from above — resistant starch is a to Add, above, a common source of resistant starch (broad beans, black beans, etc) were on the to avoid list. Personally, I would go for eating the beans and other sources of resistant starch (see Resistant Starch Content in Foods Commonly Consumed in the United States: A Narrative Review ).
High lipids – any known microbiome component?
I do not have lipids in the database yet, so the reader should review the following studies.
- The Gut Microbiome Contributes to a Substantial Proportion of the Variation in Blood Lipids 
- Contribution of Gut Bacteria to Lipid Levels: Another Metabolic Role for Microbes? 
- Genetic and microbiome influence on lipid metabolism and dyslipidemia 
- Dietary lipids, gut microbiota and lipid metabolism 
- Genetic and environmental determinants of variation in the plasma lipidome of older Australian twins 
The husband seems fine and has no apparent health issues associated with the microbiome. There are suggestions above which may help prevent microbiome issues developing.